Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii

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While IUCN currently lists it as a Least Concern species, growing demand and pressures such as overfishing, habitat loss, and degradation may elevate its conservation risk. To support sustainable fisheries management and aquaculture, we sequenced, assembled, and annotated the whole genome of this species. The specimen was part of an expedition to document and preserve the genetic resources of aquatic animals in Kalimantan’s freshwater ecosystems. Using 27 Gb of sequence data, we assembled a 1.1 Gb genome comprising 5,790 scaffolds. This genome assembly has high contiguity and completeness, with N50 of 33.7 Mb and a BUSCO score of 98.8%. Repeat annotation revealed that 48.17% of the genome consisted of repetitive elements, predominantly DNA transposons (18.56%) and retroelements (13.30%). Structural annotation identified 30,099 protein-coding genes and 37,734 transcripts, most of which were multi-exonic and rich in alternative splicing. BUSCO analysis confirmed the high completeness of the genome and annotation, with 97.7% of the conserved orthologs being detected." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/14-787/v1", "name": "Draft genome assembly of the slender walking catfish, Prophagorus..." } } ] } Home Browse Draft genome assembly of the slender walking catfish, Prophagorus... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Imron I, Anggraeni F, Hidayat R et al. Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.12688/f1000research.166849.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Genome Note Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] Imron Imron 1 , Fajar Anggraeni 1 , Rahmat Hidayat https://orcid.org/0000-0003-3076-6288 1 , [...] Jadmiko Darmawan 1 , Otong Zenal Arifin 2 , Daniel Frikli Mokodongan 3 , Rosita Rosita 4 , Luthfi Nurhidayat https://orcid.org/0000-0002-0625-2984 5 Imron Imron 1 , Fajar Anggraeni 1 , [...] Rahmat Hidayat https://orcid.org/0000-0003-3076-6288 1 , Jadmiko Darmawan 1 , Otong Zenal Arifin 2 , Daniel Frikli Mokodongan 3 , Rosita Rosita 4 , Luthfi Nurhidayat https://orcid.org/0000-0002-0625-2984 5 PUBLISHED 14 Aug 2025 Author details Author details 1 Research Center for Fishery, National Research and Innovation Agency Republic of Indonesia, Cibinong, West Java, 16915, Indonesia 2 Research Center for Applied Zoology, National Research and Innovation Agency Republic of Indonesia, Cibinong, West Java, 16915, Indonesia 3 Research Center for Biosystematics and Evolution, National Research and Innovation Agency Republic of Indonesia, Cibinong, West Java, 16915, Indonesia 4 Department of Fisheries, Faculty of Agriculture, Palangka Raya University, Palangka Raya, Central Kalimantan, Indonesia 5 Faculty of Biology, Universitas Gadjah Mada, Sleman, DI Yogyakarta, 55281, Indonesia Imron Imron Roles: Conceptualization, Funding Acquisition, Investigation, Supervision, Writing – Original Draft Preparation Fajar Anggraeni Roles: Investigation, Project Administration, Resources, Writing – Review & Editing Rahmat Hidayat Roles: Investigation, Resources, Writing – Review & Editing Jadmiko Darmawan Roles: Investigation, Project Administration, Resources, Writing – Review & Editing Otong Zenal Arifin Roles: Investigation, Resources, Writing – Review & Editing Daniel Frikli Mokodongan Roles: Investigation, Resources, Writing – Review & Editing Rosita Rosita Roles: Investigation, Resources, Writing – Review & Editing Luthfi Nurhidayat Roles: Data Curation, Formal Analysis, Writing – Original Draft Preparation, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Genomics and Genetics gateway. Abstract The slender walking catfish, Prophagorus nieuhofii , plays an important role in small-scale fisheries across Southeast Asia, supporting food security. While IUCN currently lists it as a Least Concern species, growing demand and pressures such as overfishing, habitat loss, and degradation may elevate its conservation risk. To support sustainable fisheries management and aquaculture, we sequenced, assembled, and annotated the whole genome of this species. The specimen was part of an expedition to document and preserve the genetic resources of aquatic animals in Kalimantan’s freshwater ecosystems. Using 27 Gb of sequence data, we assembled a 1.1 Gb genome comprising 5,790 scaffolds. This genome assembly has high contiguity and completeness, with N50 of 33.7 Mb and a BUSCO score of 98.8%. Repeat annotation revealed that 48.17% of the genome consisted of repetitive elements, predominantly DNA transposons (18.56%) and retroelements (13.30%). Structural annotation identified 30,099 protein-coding genes and 37,734 transcripts, most of which were multi-exonic and rich in alternative splicing. BUSCO analysis confirmed the high completeness of the genome and annotation, with 97.7% of the conserved orthologs being detected. READ ALL READ LESS Keywords Whole genome sequencing, genome assembly, genome annotation, slender walking catfish, Prophagorus nieuhofii. Corresponding Author(s) Luthfi Nurhidayat ( [email protected] ) Close Corresponding author: Luthfi Nurhidayat Competing interests: No competing interests were disclosed. Grant information: The author(s) declared that no grants were involved in supporting this work. Copyright: © 2025 Imron I et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Imron I, Anggraeni F, Hidayat R et al. Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.12688/f1000research.166849.1 ) First published: 14 Aug 2025, 14 :787 ( https://doi.org/10.12688/f1000research.166849.1 ) Latest published: 10 Nov 2025, 14 :787 ( https://doi.org/10.12688/f1000research.166849.2 )  There is a newer version of this article available. Suppress this message for one day. Introduction The slender walking catfish, Prophagorus nieuhofii (previously known as Clarias nieuhofii ), is widespread in Southeast Asia, including Indonesia –specifically Java, Sumatra, and Kalimantan–, the Malay Peninsula, Singapore, Thailand, and the Philippines. 1 It is a popular food fish due to its good taste and nutritional benefits and is an important species for food security by supporting artisanal fisheries. While the IUCN Red List of threatened species classifies it as Least Concern in the global assessment of species conservation, habitat loss and degradation and fishing pressure have resulted in a decline in many natural populations. 2 – 4 In Thailand, it has been classified as a vulnerable species, 5 and a genetic assessment has been carried out to manage its natural populations. 4 In addition to maintaining the sustainability of this fish population in its natural environment, several studies have been conducted to develop it into a farmed species. This species, owing to its air-breathing capability, resilience, and adaptability, shows significant potential for domestication and aquaculture. Preliminary studies on domestication and aquaculture have been conducted. These included the study of growth and survival during the early stages of domestication, 6 breeding and reproduction 7 and exploration as a probiotic source. 8 Although further research is necessary to optimize its cultivation, its inherent characteristics are conducive to successful aquaculture. Generation of the whole genome sequence of this species will provide a good resource for both fisheries management and aquaculture development. In the former case, the large discovery of single nucleotide polymorphisms (SNPs) that cover genome wide (neutral) and allele-specific (adaptive) diversity patterns will provide a good resource for genomic stock identification, traceability, fisheries-induced evolution and climate change. 9 In the latter case, the whole genome sequence, combined with other technologies, such as quantitative trait loci (QTL) analysis, genome-wide association studies (GWAS), and expression profiling, allowing for the prediction of genotypic variants associated with phenotypic traits, can be used to improve traits in breeding programs. 10 , 11 Methods Sample collection, DNA extraction, and genome sequencing Fish samples were collected during a 2024 expedition aimed at characterizing genetic resources of aquatic animals from a natural population in South Kalimantan, Indonesia (3°21′43.0″S, 114°42′08.3″E). Specimen were captured using bubu traps and held in a pond with 60 cm water depth at 27-28°C for three days to reduce stress. Prior to DNA tissue sampling, fish were anesthetized following 12 : they were placed in a 35-liter bucket with 7 cm of water at 28°C, cooled with liquid ice to 21°C, and then clove oil was added at 160 mg/L. Tissue samples were collected when the fish showed minimal movement after anesthesia. A 10 mg tissue sample was collected from an individual measuring of 32.5 cm in length and weighing 277 g, preserved in DNA shield solution and transported to the laboratory for sequencing. High-quality DNA was extracted using the Quick-DNA high molecular weight (HMW) MagBead kit (Zymo Research) with overnight proteinase K digestion incubation. The DNA extract was quantified using a Qubit fluorometer with an Equalbit 1x ds-DNA HS assay kit for sequencing. Whole genome sequencing was performed using Oxford Nanopore Technology (ONT) – PromethION. Genomic DNA (1500 ng DNA in 48uL nuclease free water was incubated at 20°C for 30 min, followed by incubation at 65°C for 5 min. Sequencing by ligation was performed using the Ligation Sequencing DNA V14 workflow kit (SQK-LSK114). The basecaller tool was Dorado v0.9.1, using [email protected] basecalling model, with a minimum Q score of 10 and trimming of adapters and barcodes. The quality of the sequencing data was checked using NanoPlot. 13 Genome assembly and annotation Genome assembly estimation was done using Flye 2.9.5, 14 while genome scaffolding was conducted with RagTag 2.1.0 15 guided by the reference genome of Clarias gariepinus (GCF_024256425.1). Genome size was estimated using Jellyfish software version 2.3.1 16 and further processed with GenomeScope 2.0 v2.0.1. The assembly statistics were calculated using assembly-stat version 1.0.1. The completeness of the assembly was estimated using Benchmarking Universal Single-Copy Orthologous (BUSCO) version 5.8.2, utilizing miniport. 17 – 19 Repetitive elements within the genome assembly were identified using RepeatModeler v2.0.6 in conjunction with RepeatMasker v4.1.7 ( http://www.repeatmasker.org ). Prior to annotation, these repetitive regions were soft masked to minimize interference. Structural genome annotation encompassing gene prediction was conducted using the GALBA pipeline, 20 which employs miniprot 17 and AUGUSTUS, 21 integrating protein data from closely related species as extrinsic evidence. Specifically, protein data from Clarias gariepinus (GCF_024256425.1), Ictalurus furcatus (GCF_023375685.1), Ictalurus punctatus (GCF_001660625.3), and Tachysurus fulvidraco (GCF_022655615.1) were utilized. Functional annotation of the resulting gene predictions was then performed using the ‘funannotate annotate’ command from the Funannotate pipeline ( https://funannotate.readthedocs.io/en/latest/install.html ), incorporating tools such as InterProScan5, 22 Eggnog-Mapper, 23 and SignalP 5.0 24 to assign gene names and predict protein functions. Finally, the completeness of the genome annotation was evaluated using BUSCO v5.8.2. 19 Ethical approval This research was approved by the Ethics Commission for Animal Husbandry and Use, National Research and Innovation Agency (Approval No. 174/KE.02/SK/07/2024). All animal-related procedures were conducted in accordance with institutional guidelines and complied with the ARRIVE 2.0 reporting standards, the checklists for which are available at https://doi.org/10.6084/m9.figshare.29612615.v1 . 25 Results Sequence output and genome assembly Sequencing produced a total of 27,388,841,658 bases from 4,440,560 reads, with 99.8% of bases meeting the designated quality standards. The highest observed mean basecall quality score was 46.4 with a read length of 133, while the longest read reached 6,129,425 with a mean basecall quality score of 14.5 ( Table 1 ). The draft of genome assembly, as illustrated in the snail graph ( Figure 1 ), comprises approximately 5,790 scaffolds, totaling 1.1 gigabases, with the longest scaffold of 54 spanning megabases. Table 1. Summary statistics of sequences of slender walking catfish ( Prophagorus nieuhofii ). Total bases (bases) 27,388,841,658.0 Mean read length 6,167.9 Mean read quality 20.2 Median read length 4,772.0 Median read quality 23.6 Number of reads 4,440,560 Read length (N50) 8,687.0 STDEV read length 5,796.8 Figure 1. A snail graph showing the main features of Prophagorus nieuhofii genome assembly. The N50 and N90 values, measuring assembly continuity, are 33.7Mb and 20.6Mb, respectively. The base composition showed 39.5% GC content and 60.5% AT content, whereas the N content (gaps) remained minimal at 0.04%, indicating a highly contiguous and well-assembled genome. Using the Actinopterygii ortholog database, which is based on 3640 universal genes, the assembly demonstrated 98.8% completeness with a low percentage of missing BUSCO (1.15%), suggesting that most expected genes are present. The genome size of this species is similar to that of a related species, Clarias gariepinus , which has a genome size of 969.62 Mb and contig N50 of 33.71 Mb. 26 Genome composition based on a 21-mer based characterization shows a heterozygosity rate of 0.78%, while the homozygosity rate was 99.12%. Genome annotation Repeats annotation Repeat annotation analysis revealed that approximately 48.17% of the genome (529,073,132 bp) consisted of repetitive elements ( Table 2 ). Among these, retroelements accounted for 13.30% of the genome, spanning over 146 million base pairs across 492,154 elements. This category includes SINEs, which comprise 1.93% of the genome, and LINEs, the largest subgroup of retroelements, which occupy 5.33%. The LINEs were mainly composed of L2/CR1/Rex elements (4.01%), followed by the R1/LOA/Jockey, RTE/Bov-B, and L1/CIN4 subfamilies. LTR elements were also prominent, comprising 6.04% of the genome, largely represented by Gypsy/DIRS1 (2.55%) and retroviral elements (1.05%), along with smaller contributions from BEL/Pao and Ty1/Copia. Notably, some retroelement families such as CRE/SLACS were not detected. Table 2. Classification of repeat elements of the slender walking catfish ( Prophagorus nieuhofii ) genome assembly. Repeat category Count Occupied bp % of Genome Retroelements 492,154 146,089,956 13.30% SINEs 104,157 21,222,223 1.93% Penelope 3,786 390,741 0.04% LINEs 170,940 58,512,142 5.33% CRE/SLACS 0 0 0.00% L2/CR1/Rex 115,148 43,988,622 4.01% R1/LOA/Jockey 15,957 3,985,162 0.36% R2/R4/NeSL 343 218,349 0.02% RTE/Bov-B 11,503 2,944,056 0.27% L1/CIN4 8,590 3,281,609 0.30% LTR elements 217,057 66,355,591 6.04% BEL/Pao 4,144 3,425,287 0.31% Ty1/Copia 93 112,540 0.01% Gypsy/DIRS1 51,836 27,984,797 2.55% Retroviral 43,638 11,543,937 1.05% DNA Transposons 924,291 203,850,283 18.56% hobo-Activator 163,993 37,319,984 3.40% TC1-IS630-Pogo 581,362 124,970,541 11.38% En-Spm 0 0 0.00% MULE-MuDR 1,323 99,951 0.01% PiggyBac 13,967 4,552,618 0.41% Tourist/Harbinger 25,580 7,005,418 0.64% Other (e.g. Mirage, P- element, Transib) 4,950 5,389 0.04% **Rolling-circles** 30,262 6,192,298 0.56% **Unclassified** 986,211 133,225,464 12.13% **Total Interspersed** 483,556,444 44.03% **Small RNA** 57,989 13,482,676 1.23% **Satellites** 1,781 570,181 0.05% **Simple repeats** 773,672 34,790,247 3.17% **Low complexity** 59,081 3,378,970 0.31% **Total Masked Bases** 529,073,132 48.17% DNA transposons represented the largest category of repeats, both in number and genomic coverage, with 924,291 elements occupying 18.56% of the genome (203.9 million base pairs). Within this group, the TC1-IS630-Pogo family was predominant, covering 11.38% of the genome. Other notable contributors included hobo-Activator (3.40%), PiggyBac (0.41%), Tourist/Harbinger (0.64%), and MULE-MuDR (0.01%), while some families, such as En-Spm, showed no representation. Additionally, rolling-circle transposons comprising 30,262 elements and 0.56% of the genome were identified. A substantial portion of the genome (12.13%) contained unclassified elements, amounting to 986,211 entries. These may represent novel, divergent, or currently uncategorized repeat families. Other repetitive elements included small RNA-related sequences (1.23%), simple repeats (e.g. microsatellites, 3.17%), low-complexity regions (0.31%), and satellite DNA (0.05%). Overall, interspersed repeats alone account for 44.03% of the genome (483.6 million base pairs), underscoring the genomic complexity and abundance of repetitive sequences, especially DNA transposons and retroelements. Structural and functional annotation The genome annotation process resulted in the identification of 30,099 protein-coding genes, which in turn produced 37,734 predicted transcripts with an average of 1.3 transcripts per gene ( Table 3 ). Alternative splicing was observed in 5,459 of these genes. The majority of genes (87.5%, corresponding to 26,327 genes) were found to be multi-exonic, whereas the remaining 12.5% were composed of a single exon. Each gene spans an average locus length of 15,993.4 base pairs, measured from the first exon to the last exon. On average, genes are composed of 8.9 distinct exons, with a total of 268,395 exons annotated across the genome. The mean exon size was 180.2 bp, and the average transcript size, inclusive of UTRs and coding regions, was 1,812.4 bp. Table 3. Genome annotation summary of the slender walking catfish ( Prophagorus nieuhofii ) genome assembly. Annotation features Values Max number of transcripts per gene 8 Mean exon size 180.2 Mean gene locus size (first to last exon) 15993.4 Mean number of distinct exons per gene 8.9 Mean number of transcripts per gene 1.3 Mean transcript size (UTR, CDS) 1812.4 Number of distinct exons 268,395 Number of genes 30,099 Number of genes with alternative transcript variants 5,459 (18.1%) Number of multi-exon genes 26,327 (87.5%) Number of predicted transcripts 37,734 Number of single-exon genes 3,772 (12.5%) Regarding genome composition, exons constitute 4% of the genome, spanning approximately 48 Mb, with a GC content of 51% ( Table 4 ). Genes collectively occupy 44% of the genome, covering approximately 481 Mb, and have a GC content of 40%. The median length of annotated genes was 6,955 bp. Introns accounted for an additional 40% of the genome, totaling 434 Mb. Their average length was 1,861 bp, a median of 481 bp, and a GC content of 39%. In total, 233,110 introns were identified. Table 4. Genome composition of the slender walking catfish ( Prophagorus nieuhofii ) genome assembly. % GC % of genome Average size (bp) Median size (bp) Number Total length (Mb) Exon 51% 4% 180 126 268,395 48 Mb Gene 40% 44% 15,993 6,955 30,099 481 Mb Intron 39% 40% 1,861 481 233,110 434 Mb To assess the completeness of the annotation, BUSCO analysis was conducted using the actinopterygii_odb10 lineage dataset. The analysis revealed that 97.7% of the 3,640 expected single-copy orthologs were complete, with 79.3% identified as single-copy and 18.5% as duplicated BUSCOs ( Figure 2 ). Only 0.7% were fragmented and 1.6% were missing, indicating a highly complete and well-annotated gene set. The high BUSCO score highlights the robustness of the genome annotation, affirming its appropriateness for subsequent biological and comparative analyses. Figure 2. BUSCO assessment of genome annotation results for the slender walking catfish ( Prophagorus nieuhofii) genome assembly. Data availability The project contains two underlying data: 1. The raw whole genome sequence. 2. The genome assembly. The raw whole genome sequences are available on NCBI’s Short Read Archive (SRA): Whole genome sequence of Prophagorus nieuhofii , accession number: SRR34064805 ( https://www.ncbi.nlm.nih.gov/sra/?term=SRR34064805 ). The raw sequences were also deposited and are accessible on the Zenodo repository: Data set for draft genome assembly of the slender walking catfish, Prophagorus nieuhofii DOI: https://doi.org/10.5281/zenodo.16689652 . 27 The genome assembly data were deposited and made accessible to Dataverse: Replication data for draft genome assembly of the slender walking catfish, Prophagorus nieuhofii. https://hdl.handle.net/20.500.12690/RIN/ULQDHU . 28 All the underlying data of this study are openly available under the terms of Creative Commons Zero v1.0 (CC0 1.0) Universal Public Domain Dedication. Acknowledgements We would like to thank BRIN and LPDP for funding this research through the RIIM funding program. We would also like to thank Indonesia Genome Factory (IGF) Faculty of Biology UGM and Yayasan Satriabudi Dharma Setia (YSDS) for providing the sequencing service and the computing facility access. References 1. Kottelat M, Whitten AJ, Kartikasari SN, et al. : Freshwater fishes of Western Indonesia and Sulawesi.1993; 221. 2. Manullang HM, Khairul K: Growth Pattern Study of Slender Walking Catfish (Clarias nieuhofii) as Environmental Biology Indicator. J. Mangifera Edu. 2020; 5 (1): 1–7. Publisher Full Text 3. Ng HH: Clarias nieuhofii. The IUCN Red List of Threatened Species e.T181236A89799198.2019 [updated 06/6/2025. Reference Source 4. Pechsiri J, Vanichanon A: Genetic diversity in slender walking catfish ( Clarias nieuhofii ) populations: Implications for population management. Walailak J. Sci. Tech. 2016; 13 (7): 511–519. 5. Vidthayanon C: Thailand red data: fishes. Vol. 16 . . Bangkok, Thailand: Office of Natural Resources and Environmental Policy and Planning, Bangkok, Thailand; 2005. 6. Syarifa AF, Gustomib A, Ajia ASP: Growth and survival performance of local catfish ( Clarias nieuhofii ) from Bangka Island raised in different water sources in the early stages of domestication. J. Fish. Mar. Res. 2020; 4 (1): 66–70. 7. Restu R, Nataleo P: Crossbreeding between male Keli ( Clarias nieuhofii ) and female local catfish ( Clarias batrachus ) with different parent weight ratios. J. Trop. Anim. Sci. 2016; 5 (2): 101–104. 8. Adibrata S, Lingga R, Roanisca O: Exploration of the potential of local fish resources, Kelik Catfish ( Clarias nieuhofii ) as a Source of Probiotics. Saintek Perikanan: Indonesian. J. Fish. Sci. Technol. 2023; 19 (2). 9. Valenzuela-Quiñonez F: How fisheries management can benefit from genomics? Brief. Funct. Genomics. 2016; 15 (5): 352–357. Publisher Full Text 10. Ahmad SF, Jehangir M, Srikulnath K, et al. : Fish genomics and its impact on fundamental and applied research of vertebrate biology. Rev. Fish Biol. Fish. 2022; 32 (2): 357–385. Publisher Full Text 11. Abdelrahman H, ElHady M, Alcivar-Warren A, et al. : Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics. 2017; 18 (1): 191. PubMed Abstract | Publisher Full Text | Free Full Text 12. Hur JW, Gil HW, Choi SH, et al. : Anesthetic efficacy of clove oil and the associated physiological responses in olive flounder ( Paralichthys olivaceus ). Aquac. Rep. 2019; 15 : 100227. Publisher Full Text 13. De Coster W, Rademakers R: NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics. 2023; 39 (5): btad311. PubMed Abstract | Publisher Full Text | Free Full Text 14. Kolmogorov M, Yuan J, Lin Y, et al. : Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 2019; 37 (5): 540–546. PubMed Abstract | Publisher Full Text 15. Alonge M, Lebeigle L, Kirsche M, et al. : Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 2022; 23 (1): 258. PubMed Abstract | Publisher Full Text | Free Full Text 16. Marçais G, Kingsford C: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011; 27 (6): 764–770. PubMed Abstract | Publisher Full Text | Free Full Text 17. Li H: Protein-to-genome alignment with miniprot. Bioinformatics. 2023; 39 : 1. Publisher Full Text 18. Simão F, Waterhouse R, Ioannidis P, et al. : Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31 : 3210–3212. Publisher Full Text 19. Manni M, Berkeley MR, Seppey M, et al. : BUSCO: Assessing Genomic Data Quality and Beyond. Curr. Protoc. 2021; 1 (12): e323. PubMed Abstract | Publisher Full Text 20. Brůna T, Li H, Guhlin J, et al. : Galba: genome annotation with miniprot and AUGUSTUS. BMC Bioinformatics. 2023; 24 (1): 327. PubMed Abstract | Publisher Full Text | Free Full Text 21. Hoff KJ, Stanke M: Predicting genes in single genomes with AUGUSTUS. Curr. Protoc. Bioinformatics. 2019; 65 (1): e57. PubMed Abstract | Publisher Full Text 22. Jones P, Binns D, Chang H-Y, et al. : InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014; 30 (9): 1236–1240. PubMed Abstract | Publisher Full Text | Free Full Text 23. Cantalapiedra CP, Hernández-Plaza A, Letunic I, et al. : eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol. Biol. Evol. 2021; 38 (12): 5825–5829. PubMed Abstract | Publisher Full Text | Free Full Text 24. Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, et al. : SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 2019; 37 (4): 420–423. PubMed Abstract | Publisher Full Text 25. Imron I, Anggraeni F, Hidayat R, et al. : The ARRIVE guidelines 2.0: author checklist. FIgshare. 2025. Publisher Full Text 26. Nguinkal JA, Zoclanclounon YA, Brunner RM, et al. : Haplotype-resolved and near-T2T genome assembly of the African catfish ( Clarias gariepinus ). Sci. Data. 2024; 11 (1): 1095. PubMed Abstract | Publisher Full Text | Free Full Text 27. Imron I, Anggraeni F, Darmawan J, et al. : Data set for draft genome assembly of the slender walking catfish, Prophagorus nieuhofii. Zenodo. 2025. V1 ed. Publisher Full Text 28. Imron I, Anggraeni F, Hidayat R, et al. : Replication Data for: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii. RIN Dataverse. 2025. V1 ed. Reference Source Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 14 Aug 2025 ADD YOUR COMMENT Comment Author details Author details 1 Research Center for Fishery, National Research and Innovation Agency Republic of Indonesia, Cibinong, West Java, 16915, Indonesia 2 Research Center for Applied Zoology, National Research and Innovation Agency Republic of Indonesia, Cibinong, West Java, 16915, Indonesia 3 Research Center for Biosystematics and Evolution, National Research and Innovation Agency Republic of Indonesia, Cibinong, West Java, 16915, Indonesia 4 Department of Fisheries, Faculty of Agriculture, Palangka Raya University, Palangka Raya, Central Kalimantan, Indonesia 5 Faculty of Biology, Universitas Gadjah Mada, Sleman, DI Yogyakarta, 55281, Indonesia Imron Imron Roles: Conceptualization, Funding Acquisition, Investigation, Supervision, Writing – Original Draft Preparation Fajar Anggraeni Roles: Investigation, Project Administration, Resources, Writing – Review & Editing Rahmat Hidayat Roles: Investigation, Resources, Writing – Review & Editing Jadmiko Darmawan Roles: Investigation, Project Administration, Resources, Writing – Review & Editing Otong Zenal Arifin Roles: Investigation, Resources, Writing – Review & Editing Daniel Frikli Mokodongan Roles: Investigation, Resources, Writing – Review & Editing Rosita Rosita Roles: Investigation, Resources, Writing – Review & Editing Luthfi Nurhidayat Roles: Data Curation, Formal Analysis, Writing – Original Draft Preparation, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information The author(s) declared that no grants were involved in supporting this work. Article Versions (2) version 2 Revised Published: 10 Nov 2025, 14:787 https://doi.org/10.12688/f1000research.166849.2 version 1 Published: 14 Aug 2025, 14:787 https://doi.org/10.12688/f1000research.166849.1 Copyright © 2025 Imron I et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Imron I, Anggraeni F, Hidayat R et al. Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.12688/f1000research.166849.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 1 VERSION 1 PUBLISHED 14 Aug 2025 Views 0 Cite How to cite this report: Liu H. Reviewer Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r411495 ) The direct URL for this report is: https://f1000research.com/articles/14-787/v1#referee-response-411495 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 27 Sep 2025 Haiyang Liu , Pearl River Fisheries Research Institute, Guangzhou, China Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.183897.r411495 This manuscript reports the first draft genome assembly and annotation of the slender walking catfish ( Prophagorus nieuhofii ). Given the ecological and economic importance of this species, generating genomic resources is valuable for fisheries management, germplasm utilization, and molecular breeding. The ... Continue reading READ ALL This manuscript reports the first draft genome assembly and annotation of the slender walking catfish ( Prophagorus nieuhofii ). Given the ecological and economic importance of this species, generating genomic resources is valuable for fisheries management, germplasm utilization, and molecular breeding. The study provides initial genomic data and methodological details, but there are notable shortcomings in sequencing depth, assembly strategy, biological interpretation, and data usability. These limitations reduce its utility as a long-term genomic reference resource. 1. The reported dataset (~27 Gb) represents 50×—coverage is generally recommended. The relatively low coverage increases risks of collapsed repeats, gaps, and structural errors, which compromise annotation accuracy. 2. Scaffolding was performed using Clarias gariepinus as the reference. Reference-guided assembly may introduce biases and misassemblies, especially if structural rearrangements exist between species. Independent scaffolding methods (e.g., Hi-C, optical mapping, or ultra-long ONT reads) are needed to improve reliability. The manuscript title should explicitly indicate that this is a reference-guided assembly . 3. Gene annotation results are presented mainly as averages (gene length, exon number, etc.), which lack biological interpretation. Comparisons with other catfish genomes would strengthen the significance of these findings. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: genomics, genetics, breeding, I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Liu H. Reviewer Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r411495 ) The direct URL for this report is: https://f1000research.com/articles/14-787/v1#referee-response-411495 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Waldbieser GC. Reviewer Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r405799 ) The direct URL for this report is: https://f1000research.com/articles/14-787/v1#referee-response-405799 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 16 Sep 2025 Geoffrey C. Waldbieser , USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, USA Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.183897.r405799 This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is well presented. The Nanopore sequencing, assembly, and repeat annotation are described ... Continue reading READ ALL This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is well presented. The Nanopore sequencing, assembly, and repeat annotation are described sufficiently to be replicated. The fasta sequence of the genome is available but there is no available annotation of the scaffolds. The contigs were scaffolded based on the Claris gariepinus reference genome. This does not mean the assembly is correct. The authors point to two other Ictalurus catfish genomes, and the first genome assembly of Ictalurus furcatus was a reference based assembly based on Ictalurus punctatus. However, an independent assembly of I. furcatus revealed three major chromosomal inversions between the two species that did not show up on the reference-guided assembly. The title should reflect this is a reference-based assembly. The assembly will still be useful for some molecular marker approaches - but they should be cautious about QTL and GWAS experiments. Page 4: What is the minimum length of sequence put into the assembler? Figures 1 and 2 add no value to the data already presented in the text and tables. Both figures should be removed. Average values are used for gene length, etc, but those are just mathematical calculations and may not mean anything biological. How do these numbers compare with the annotation of other catfish genomes? Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly Competing Interests: No competing interests were disclosed. Reviewer Expertise: Molecular biology, genomics, genome assembly I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Waldbieser GC. Reviewer Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r405799 ) The direct URL for this report is: https://f1000research.com/articles/14-787/v1#referee-response-405799 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 10 Nov 2025 Imron Imron , Research Center for Fishery, National Research and Innovation Agency, Bogor, Indonesia 10 Nov 2025 Author Response This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is ... Continue reading This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is well presented. The Nanopore sequencing, assembly, and repeat annotation are described sufficiently to be replicated. The .fasta sequence of the genome is available but there is no available annotation of the scaffolds. Response: Thank you for the comments. We are sorry that we missed the annotation file within the manuscript. We have now provided link to the annotation results within the manuscript in Data availability section: “....The genome annotation data were deposited and made accessible in the Zenodo repository: Genome annotation of the previously assembled genome of the slender walking catfish, Prophagorus nieuhofii (DOI https://doi.org/10.5281/zenodo.17422526 )” The contigs were scaffolded based on the Claris gariepinus reference genome. This does not mean the assembly is correct. The authors point to two other Ictalurus catfish genomes, and the first genome assembly of Ictalurus furcatus was a reference-based assembly based on Ictalurus punctatus. However, an independent assembly of I. furcatus revealed three major chromosomal inversions between the two species that did not show up on the reference-guided assembly. The title should reflect this is a reference-based assembly. The assembly will still be useful for some molecular marker approaches - but they should be cautious about QTL and GWAS experiments. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. We also agree that the genome assembly will remain valuable for other research involving coding regions. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii. ” Page 4: What is the minimum length of sequence put into the assembler? Response: We used 3286 bp as a minimum length for the sequence put into assembler. This number was determined based on the N90 value of our raw sequences. Figures 1 and 2 add no value to the data already presented in the text and tables. Both figures should be removed. Response: We have removed the figure 1 and 2 from the main text and moved them into the Zoenodo repository as extended data Average values are used for gene length, etc, but those are just mathematical calculations and may not mean anything biological. How do these numbers compare with the annotation of other catfish genomes? Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae) . As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is well presented. The Nanopore sequencing, assembly, and repeat annotation are described sufficiently to be replicated. The .fasta sequence of the genome is available but there is no available annotation of the scaffolds. Response: Thank you for the comments. We are sorry that we missed the annotation file within the manuscript. We have now provided link to the annotation results within the manuscript in Data availability section: “....The genome annotation data were deposited and made accessible in the Zenodo repository: Genome annotation of the previously assembled genome of the slender walking catfish, Prophagorus nieuhofii (DOI https://doi.org/10.5281/zenodo.17422526 )” The contigs were scaffolded based on the Claris gariepinus reference genome. This does not mean the assembly is correct. The authors point to two other Ictalurus catfish genomes, and the first genome assembly of Ictalurus furcatus was a reference-based assembly based on Ictalurus punctatus. However, an independent assembly of I. furcatus revealed three major chromosomal inversions between the two species that did not show up on the reference-guided assembly. The title should reflect this is a reference-based assembly. The assembly will still be useful for some molecular marker approaches - but they should be cautious about QTL and GWAS experiments. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. We also agree that the genome assembly will remain valuable for other research involving coding regions. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii. ” Page 4: What is the minimum length of sequence put into the assembler? Response: We used 3286 bp as a minimum length for the sequence put into assembler. This number was determined based on the N90 value of our raw sequences. Figures 1 and 2 add no value to the data already presented in the text and tables. Both figures should be removed. Response: We have removed the figure 1 and 2 from the main text and moved them into the Zoenodo repository as extended data Average values are used for gene length, etc, but those are just mathematical calculations and may not mean anything biological. How do these numbers compare with the annotation of other catfish genomes? Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae) . As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 10 Nov 2025 Imron Imron , Research Center for Fishery, National Research and Innovation Agency, Bogor, Indonesia 10 Nov 2025 Author Response This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is ... Continue reading This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is well presented. The Nanopore sequencing, assembly, and repeat annotation are described sufficiently to be replicated. The .fasta sequence of the genome is available but there is no available annotation of the scaffolds. Response: Thank you for the comments. We are sorry that we missed the annotation file within the manuscript. We have now provided link to the annotation results within the manuscript in Data availability section: “....The genome annotation data were deposited and made accessible in the Zenodo repository: Genome annotation of the previously assembled genome of the slender walking catfish, Prophagorus nieuhofii (DOI https://doi.org/10.5281/zenodo.17422526 )” The contigs were scaffolded based on the Claris gariepinus reference genome. This does not mean the assembly is correct. The authors point to two other Ictalurus catfish genomes, and the first genome assembly of Ictalurus furcatus was a reference-based assembly based on Ictalurus punctatus. However, an independent assembly of I. furcatus revealed three major chromosomal inversions between the two species that did not show up on the reference-guided assembly. The title should reflect this is a reference-based assembly. The assembly will still be useful for some molecular marker approaches - but they should be cautious about QTL and GWAS experiments. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. We also agree that the genome assembly will remain valuable for other research involving coding regions. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii. ” Page 4: What is the minimum length of sequence put into the assembler? Response: We used 3286 bp as a minimum length for the sequence put into assembler. This number was determined based on the N90 value of our raw sequences. Figures 1 and 2 add no value to the data already presented in the text and tables. Both figures should be removed. Response: We have removed the figure 1 and 2 from the main text and moved them into the Zoenodo repository as extended data Average values are used for gene length, etc, but those are just mathematical calculations and may not mean anything biological. How do these numbers compare with the annotation of other catfish genomes? Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae) . As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is well presented. The Nanopore sequencing, assembly, and repeat annotation are described sufficiently to be replicated. The .fasta sequence of the genome is available but there is no available annotation of the scaffolds. Response: Thank you for the comments. We are sorry that we missed the annotation file within the manuscript. We have now provided link to the annotation results within the manuscript in Data availability section: “....The genome annotation data were deposited and made accessible in the Zenodo repository: Genome annotation of the previously assembled genome of the slender walking catfish, Prophagorus nieuhofii (DOI https://doi.org/10.5281/zenodo.17422526 )” The contigs were scaffolded based on the Claris gariepinus reference genome. This does not mean the assembly is correct. The authors point to two other Ictalurus catfish genomes, and the first genome assembly of Ictalurus furcatus was a reference-based assembly based on Ictalurus punctatus. However, an independent assembly of I. furcatus revealed three major chromosomal inversions between the two species that did not show up on the reference-guided assembly. The title should reflect this is a reference-based assembly. The assembly will still be useful for some molecular marker approaches - but they should be cautious about QTL and GWAS experiments. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. We also agree that the genome assembly will remain valuable for other research involving coding regions. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii. ” Page 4: What is the minimum length of sequence put into the assembler? Response: We used 3286 bp as a minimum length for the sequence put into assembler. This number was determined based on the N90 value of our raw sequences. Figures 1 and 2 add no value to the data already presented in the text and tables. Both figures should be removed. Response: We have removed the figure 1 and 2 from the main text and moved them into the Zoenodo repository as extended data Average values are used for gene length, etc, but those are just mathematical calculations and may not mean anything biological. How do these numbers compare with the annotation of other catfish genomes? Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae) . As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Khedkar GD. Reviewer Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r413914 ) The direct URL for this report is: https://f1000research.com/articles/14-787/v1#referee-response-413914 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 16 Sep 2025 Gulab D. Khedkar , Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, India Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.183897.r413914 Review report Overall Assessment The manuscript presents the first draft genome assembly of Prophagorus nieuhofii (slender walking catfish), an ecologically and economically important species in Southeast Asia. The study addresses an ecologically and economically relevant species, and I appreciate the ... Continue reading READ ALL Review report Overall Assessment The manuscript presents the first draft genome assembly of Prophagorus nieuhofii (slender walking catfish), an ecologically and economically important species in Southeast Asia. The study addresses an ecologically and economically relevant species, and I appreciate the effort to make genomic resources available for a taxon of regional importance. However, after a careful evaluation, I have major concerns that prevent me from recommending acceptance in its current form. Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed repeats, gaps, and structural errors, which in turn reduce the reliability of annotations and downstream analyses. b. Assembly completeness is limited The assembly is fragmented and scaffolded with reliance on a reference genome ( Clarias gariepinus ). This strategy risks introducing misassemblies and biases. Independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads are required to approach chromosome-level quality, which is expected for a lasting genomic reference. Although the BUSCO score is high, it does not fully compensate for the lack of structural completeness. c. Limited utility of the current resource A genome note should provide a robust foundation for comparative genomics, conservation, and applied research. In its present form, the assembly’s limitations significantly restrict its long-term usefulness. The manuscript would be strengthened by deeper sequencing, improved scaffolding, and expanded biological interpretation (e.g., comparative analysis with related catfish species). d. Minor points Please consider providing a clear summary table that links raw sequencing datasets to analytical steps (assembly, polishing, annotation). Functional annotation could be expanded to highlight gene families of ecological or aquacultural interest. e. Decision While the study has potential, I regret to say that the present version does not meet the standards required for indexing as a genome note. I therefore recommend rejection in its current form. I encourage the authors to consider resequencing at higher depth and applying independent scaffolding approaches. With these improvements, the dataset could provide a far more valuable and reliable genomic resource. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? No Competing Interests: No competing interests were disclosed. Reviewer Expertise: Evolutionary biology, genomics, population genetics I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Khedkar GD. Reviewer Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r413914 ) The direct URL for this report is: https://f1000research.com/articles/14-787/v1#referee-response-413914 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 10 Nov 2025 Imron Imron , Research Center for Fishery, National Research and Innovation Agency, Bogor, Indonesia 10 Nov 2025 Author Response Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed ... Continue reading Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed repeats, gaps, and structural errors, which in turn reduce the reliability of annotations and downstream analyses. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. b. Assembly completeness is limited The assembly is fragmented and scaffolded with reliance on a reference genome ( Clarias gariepinus ). This strategy risks introducing misassemblies and biases. Independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads are required to approach chromosome-level quality, which is expected for a lasting genomic reference. Although the BUSCO score is high, it does not fully compensate for the lack of structural completeness. Response: We thank the reviewer for this valuable comment and fully agree that independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads would improve the structural completeness of the assembly. The primary goal of this work, however, was to generate a high-quality draft genome for Prophagorus nieuhofii as a foundational resource, rather than a chromosome-level reference assembly. We have revised the manuscript title to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii ” in order to be transparent about using a reference-guided approach based on the closely related Clarias gariepinus genome. This strategy was chosen because Hi-C and ultra-long read sequencing technologies are currently limited in availability within our country, and reference-based scaffolding remains a practical and widely accepted alternative for non-model species under such constraints. While we acknowledge that reference-guided scaffolding can introduce some degree of structural bias, the assembly’s high contiguity (N50 = 33.7 Mb), completeness (BUSCO = 98.8%), and minimal gap content (0.04%) demonstrate its robustness and reliability for downstream genomic and comparative analyses. c. Limited utility of the current resource A genome note should provide a robust foundation for comparative genomics, conservation, and applied research. In its present form, the assembly’s limitations significantly restrict its long-term usefulness. The manuscript would be strengthened by deeper sequencing, improved scaffolding, and expanded biological interpretation (e.g., comparative analysis with related catfish species). Response: We thank the reviewer for this thoughtful comment and agree that deeper sequencing, improved scaffolding, and comparative analyses with related catfish species would further strengthen this genomic resource. Our study focused on generating a high-quality draft genome as an initial reference for Prophagorus nieuhofii . We acknowledge that additional long-range scaffolding and deeper sequencing would enhance structural resolution, and we plan to pursue these improvements as such technologies become more accessible in our country. While we appreciate the suggestion for broader comparative analyses, the genome note format emphasizes concise presentation of sequencing and assembly results. Nonetheless, we have included annotation statistics and genome composition comparisons with four related catfish species (Clarias gariepinus, Ictalurus furcatus, Ictalurus punctatus, and Tachysurus fulvidraco) , consistent with the scope of this article type. 1. The reported dataset (~27 Gb) represents 50×—coverage is generally recommended. The relatively low coverage increases risks of collapsed repeats, gaps, and structural errors, which compromise annotation accuracy. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. 2. Scaffolding was performed using Clarias gariepinus as the reference. Reference-guided assembly may introduce biases and misassemblies, especially if structural rearrangements exist between species. Independent scaffolding methods (e.g., Hi-C, optical mapping, or ultra-long ONT reads) are needed to improve reliability. The manuscript title should explicitly indicate that this is a reference-guided assembly. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii.” 3. Gene annotation results are presented mainly as averages (gene length, exon number, etc.), which lack biological interpretation. Comparisons with other catfish genomes would strengthen the significance of these findings. Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae). As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed repeats, gaps, and structural errors, which in turn reduce the reliability of annotations and downstream analyses. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. b. Assembly completeness is limited The assembly is fragmented and scaffolded with reliance on a reference genome ( Clarias gariepinus ). This strategy risks introducing misassemblies and biases. Independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads are required to approach chromosome-level quality, which is expected for a lasting genomic reference. Although the BUSCO score is high, it does not fully compensate for the lack of structural completeness. Response: We thank the reviewer for this valuable comment and fully agree that independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads would improve the structural completeness of the assembly. The primary goal of this work, however, was to generate a high-quality draft genome for Prophagorus nieuhofii as a foundational resource, rather than a chromosome-level reference assembly. We have revised the manuscript title to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii ” in order to be transparent about using a reference-guided approach based on the closely related Clarias gariepinus genome. This strategy was chosen because Hi-C and ultra-long read sequencing technologies are currently limited in availability within our country, and reference-based scaffolding remains a practical and widely accepted alternative for non-model species under such constraints. While we acknowledge that reference-guided scaffolding can introduce some degree of structural bias, the assembly’s high contiguity (N50 = 33.7 Mb), completeness (BUSCO = 98.8%), and minimal gap content (0.04%) demonstrate its robustness and reliability for downstream genomic and comparative analyses. c. Limited utility of the current resource A genome note should provide a robust foundation for comparative genomics, conservation, and applied research. In its present form, the assembly’s limitations significantly restrict its long-term usefulness. The manuscript would be strengthened by deeper sequencing, improved scaffolding, and expanded biological interpretation (e.g., comparative analysis with related catfish species). Response: We thank the reviewer for this thoughtful comment and agree that deeper sequencing, improved scaffolding, and comparative analyses with related catfish species would further strengthen this genomic resource. Our study focused on generating a high-quality draft genome as an initial reference for Prophagorus nieuhofii . We acknowledge that additional long-range scaffolding and deeper sequencing would enhance structural resolution, and we plan to pursue these improvements as such technologies become more accessible in our country. While we appreciate the suggestion for broader comparative analyses, the genome note format emphasizes concise presentation of sequencing and assembly results. Nonetheless, we have included annotation statistics and genome composition comparisons with four related catfish species (Clarias gariepinus, Ictalurus furcatus, Ictalurus punctatus, and Tachysurus fulvidraco) , consistent with the scope of this article type. 1. The reported dataset (~27 Gb) represents 50×—coverage is generally recommended. The relatively low coverage increases risks of collapsed repeats, gaps, and structural errors, which compromise annotation accuracy. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. 2. Scaffolding was performed using Clarias gariepinus as the reference. Reference-guided assembly may introduce biases and misassemblies, especially if structural rearrangements exist between species. Independent scaffolding methods (e.g., Hi-C, optical mapping, or ultra-long ONT reads) are needed to improve reliability. The manuscript title should explicitly indicate that this is a reference-guided assembly. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii.” 3. Gene annotation results are presented mainly as averages (gene length, exon number, etc.), which lack biological interpretation. Comparisons with other catfish genomes would strengthen the significance of these findings. Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae). As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 10 Nov 2025 Imron Imron , Research Center for Fishery, National Research and Innovation Agency, Bogor, Indonesia 10 Nov 2025 Author Response Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed ... Continue reading Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed repeats, gaps, and structural errors, which in turn reduce the reliability of annotations and downstream analyses. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. b. Assembly completeness is limited The assembly is fragmented and scaffolded with reliance on a reference genome ( Clarias gariepinus ). This strategy risks introducing misassemblies and biases. Independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads are required to approach chromosome-level quality, which is expected for a lasting genomic reference. Although the BUSCO score is high, it does not fully compensate for the lack of structural completeness. Response: We thank the reviewer for this valuable comment and fully agree that independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads would improve the structural completeness of the assembly. The primary goal of this work, however, was to generate a high-quality draft genome for Prophagorus nieuhofii as a foundational resource, rather than a chromosome-level reference assembly. We have revised the manuscript title to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii ” in order to be transparent about using a reference-guided approach based on the closely related Clarias gariepinus genome. This strategy was chosen because Hi-C and ultra-long read sequencing technologies are currently limited in availability within our country, and reference-based scaffolding remains a practical and widely accepted alternative for non-model species under such constraints. While we acknowledge that reference-guided scaffolding can introduce some degree of structural bias, the assembly’s high contiguity (N50 = 33.7 Mb), completeness (BUSCO = 98.8%), and minimal gap content (0.04%) demonstrate its robustness and reliability for downstream genomic and comparative analyses. c. Limited utility of the current resource A genome note should provide a robust foundation for comparative genomics, conservation, and applied research. In its present form, the assembly’s limitations significantly restrict its long-term usefulness. The manuscript would be strengthened by deeper sequencing, improved scaffolding, and expanded biological interpretation (e.g., comparative analysis with related catfish species). Response: We thank the reviewer for this thoughtful comment and agree that deeper sequencing, improved scaffolding, and comparative analyses with related catfish species would further strengthen this genomic resource. Our study focused on generating a high-quality draft genome as an initial reference for Prophagorus nieuhofii . We acknowledge that additional long-range scaffolding and deeper sequencing would enhance structural resolution, and we plan to pursue these improvements as such technologies become more accessible in our country. While we appreciate the suggestion for broader comparative analyses, the genome note format emphasizes concise presentation of sequencing and assembly results. Nonetheless, we have included annotation statistics and genome composition comparisons with four related catfish species (Clarias gariepinus, Ictalurus furcatus, Ictalurus punctatus, and Tachysurus fulvidraco) , consistent with the scope of this article type. 1. The reported dataset (~27 Gb) represents 50×—coverage is generally recommended. The relatively low coverage increases risks of collapsed repeats, gaps, and structural errors, which compromise annotation accuracy. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. 2. Scaffolding was performed using Clarias gariepinus as the reference. Reference-guided assembly may introduce biases and misassemblies, especially if structural rearrangements exist between species. Independent scaffolding methods (e.g., Hi-C, optical mapping, or ultra-long ONT reads) are needed to improve reliability. The manuscript title should explicitly indicate that this is a reference-guided assembly. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii.” 3. Gene annotation results are presented mainly as averages (gene length, exon number, etc.), which lack biological interpretation. Comparisons with other catfish genomes would strengthen the significance of these findings. Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae). As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed repeats, gaps, and structural errors, which in turn reduce the reliability of annotations and downstream analyses. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. b. Assembly completeness is limited The assembly is fragmented and scaffolded with reliance on a reference genome ( Clarias gariepinus ). This strategy risks introducing misassemblies and biases. Independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads are required to approach chromosome-level quality, which is expected for a lasting genomic reference. Although the BUSCO score is high, it does not fully compensate for the lack of structural completeness. Response: We thank the reviewer for this valuable comment and fully agree that independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads would improve the structural completeness of the assembly. The primary goal of this work, however, was to generate a high-quality draft genome for Prophagorus nieuhofii as a foundational resource, rather than a chromosome-level reference assembly. We have revised the manuscript title to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii ” in order to be transparent about using a reference-guided approach based on the closely related Clarias gariepinus genome. This strategy was chosen because Hi-C and ultra-long read sequencing technologies are currently limited in availability within our country, and reference-based scaffolding remains a practical and widely accepted alternative for non-model species under such constraints. While we acknowledge that reference-guided scaffolding can introduce some degree of structural bias, the assembly’s high contiguity (N50 = 33.7 Mb), completeness (BUSCO = 98.8%), and minimal gap content (0.04%) demonstrate its robustness and reliability for downstream genomic and comparative analyses. c. Limited utility of the current resource A genome note should provide a robust foundation for comparative genomics, conservation, and applied research. In its present form, the assembly’s limitations significantly restrict its long-term usefulness. The manuscript would be strengthened by deeper sequencing, improved scaffolding, and expanded biological interpretation (e.g., comparative analysis with related catfish species). Response: We thank the reviewer for this thoughtful comment and agree that deeper sequencing, improved scaffolding, and comparative analyses with related catfish species would further strengthen this genomic resource. Our study focused on generating a high-quality draft genome as an initial reference for Prophagorus nieuhofii . We acknowledge that additional long-range scaffolding and deeper sequencing would enhance structural resolution, and we plan to pursue these improvements as such technologies become more accessible in our country. While we appreciate the suggestion for broader comparative analyses, the genome note format emphasizes concise presentation of sequencing and assembly results. Nonetheless, we have included annotation statistics and genome composition comparisons with four related catfish species (Clarias gariepinus, Ictalurus furcatus, Ictalurus punctatus, and Tachysurus fulvidraco) , consistent with the scope of this article type. 1. The reported dataset (~27 Gb) represents 50×—coverage is generally recommended. The relatively low coverage increases risks of collapsed repeats, gaps, and structural errors, which compromise annotation accuracy. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. 2. Scaffolding was performed using Clarias gariepinus as the reference. Reference-guided assembly may introduce biases and misassemblies, especially if structural rearrangements exist between species. Independent scaffolding methods (e.g., Hi-C, optical mapping, or ultra-long ONT reads) are needed to improve reliability. The manuscript title should explicitly indicate that this is a reference-guided assembly. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii.” 3. Gene annotation results are presented mainly as averages (gene length, exon number, etc.), which lack biological interpretation. Comparisons with other catfish genomes would strengthen the significance of these findings. Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae). As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 14 Aug 2025 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 2 3 4 Version 2 (revision) 10 Nov 25 read Version 1 14 Aug 25 read read read Gulab D. Khedkar , Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India Geoffrey C. Waldbieser , USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, USA Haiyang Liu , Pearl River Fisheries Research Institute, Guangzhou, China Adauto Cardoso , Universidade Estadual Paulista, Botucatu, Brazil Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Cardoso A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 26 Dec 2025 | for Version 2 Adauto Cardoso , Universidade Estadual Paulista, Botucatu, Brazil 0 Views copyright © 2025 Cardoso A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions This study describes the sequencing, assembly, and annotation of a first version of the genome of the species Prophagorus nieuhofii , a species of economic and food health relevance. The methods employed are well described, and the results are clearly presented. Although the work presents some limitations related to coverage and completeness of the assembly, the data presented are relevant and may have diverse biological, evolutionary and biotechnological applications. Efforts to present genomic data for species still unknown in this respect should be considered, although improvements should be sought in the future. My only major concern is the lack of more detailed characterization of satellite DNAs, even though computational tools are available to detect them in long-reads. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Cytogenomics, Genomics I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (0) Cardoso A. Peer Review Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.190588.r436285) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/14-787/v2#referee-response-436285 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Liu H. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 27 Sep 2025 | for Version 1 Haiyang Liu , Pearl River Fisheries Research Institute, Guangzhou, China 0 Views copyright © 2025 Liu H. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved With Reservations info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions This manuscript reports the first draft genome assembly and annotation of the slender walking catfish ( Prophagorus nieuhofii ). Given the ecological and economic importance of this species, generating genomic resources is valuable for fisheries management, germplasm utilization, and molecular breeding. The study provides initial genomic data and methodological details, but there are notable shortcomings in sequencing depth, assembly strategy, biological interpretation, and data usability. These limitations reduce its utility as a long-term genomic reference resource. 1. The reported dataset (~27 Gb) represents 50×—coverage is generally recommended. The relatively low coverage increases risks of collapsed repeats, gaps, and structural errors, which compromise annotation accuracy. 2. Scaffolding was performed using Clarias gariepinus as the reference. Reference-guided assembly may introduce biases and misassemblies, especially if structural rearrangements exist between species. Independent scaffolding methods (e.g., Hi-C, optical mapping, or ultra-long ONT reads) are needed to improve reliability. The manuscript title should explicitly indicate that this is a reference-guided assembly . 3. Gene annotation results are presented mainly as averages (gene length, exon number, etc.), which lack biological interpretation. Comparisons with other catfish genomes would strengthen the significance of these findings. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise genomics, genetics, breeding, I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. reply Respond to this report Responses (0) Liu H. Peer Review Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r411495) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/14-787/v1#referee-response-411495 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Waldbieser G. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 16 Sep 2025 | for Version 1 Geoffrey C. Waldbieser , USDA-ARS Warmwater Aquaculture Research Unit, Stoneville, USA 0 Views copyright © 2025 Waldbieser G. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Approved With Reservations info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is well presented. The Nanopore sequencing, assembly, and repeat annotation are described sufficiently to be replicated. The fasta sequence of the genome is available but there is no available annotation of the scaffolds. The contigs were scaffolded based on the Claris gariepinus reference genome. This does not mean the assembly is correct. The authors point to two other Ictalurus catfish genomes, and the first genome assembly of Ictalurus furcatus was a reference based assembly based on Ictalurus punctatus. However, an independent assembly of I. furcatus revealed three major chromosomal inversions between the two species that did not show up on the reference-guided assembly. The title should reflect this is a reference-based assembly. The assembly will still be useful for some molecular marker approaches - but they should be cautious about QTL and GWAS experiments. Page 4: What is the minimum length of sequence put into the assembler? Figures 1 and 2 add no value to the data already presented in the text and tables. Both figures should be removed. Average values are used for gene length, etc, but those are just mathematical calculations and may not mean anything biological. How do these numbers compare with the annotation of other catfish genomes? Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly Competing Interests No competing interests were disclosed. Reviewer Expertise Molecular biology, genomics, genome assembly I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. reply Respond to this report Responses (1) Author Response 10 Nov 2025 Imron Imron, Research Center for Fishery, National Research and Innovation Agency, Bogor, Indonesia This Genome Note describes an assembly of Nanopore sequence from the catfish species Prophagorus nieuhofii. The rationale for sequencing the genome and the significance of this species is well presented. The Nanopore sequencing, assembly, and repeat annotation are described sufficiently to be replicated. The .fasta sequence of the genome is available but there is no available annotation of the scaffolds. Response: Thank you for the comments. We are sorry that we missed the annotation file within the manuscript. We have now provided link to the annotation results within the manuscript in Data availability section: “....The genome annotation data were deposited and made accessible in the Zenodo repository: Genome annotation of the previously assembled genome of the slender walking catfish, Prophagorus nieuhofii (DOI https://doi.org/10.5281/zenodo.17422526 )” The contigs were scaffolded based on the Claris gariepinus reference genome. This does not mean the assembly is correct. The authors point to two other Ictalurus catfish genomes, and the first genome assembly of Ictalurus furcatus was a reference-based assembly based on Ictalurus punctatus. However, an independent assembly of I. furcatus revealed three major chromosomal inversions between the two species that did not show up on the reference-guided assembly. The title should reflect this is a reference-based assembly. The assembly will still be useful for some molecular marker approaches - but they should be cautious about QTL and GWAS experiments. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. We also agree that the genome assembly will remain valuable for other research involving coding regions. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii. ” Page 4: What is the minimum length of sequence put into the assembler? Response: We used 3286 bp as a minimum length for the sequence put into assembler. This number was determined based on the N90 value of our raw sequences. Figures 1 and 2 add no value to the data already presented in the text and tables. Both figures should be removed. Response: We have removed the figure 1 and 2 from the main text and moved them into the Zoenodo repository as extended data Average values are used for gene length, etc, but those are just mathematical calculations and may not mean anything biological. How do these numbers compare with the annotation of other catfish genomes? Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae) . As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Waldbieser GC. Peer Review Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r405799) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/14-787/v1#referee-response-405799 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Khedkar G. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 16 Sep 2025 | for Version 1 Gulab D. Khedkar , Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra, India 0 Views copyright © 2025 Khedkar G. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Not Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Review report Overall Assessment The manuscript presents the first draft genome assembly of Prophagorus nieuhofii (slender walking catfish), an ecologically and economically important species in Southeast Asia. The study addresses an ecologically and economically relevant species, and I appreciate the effort to make genomic resources available for a taxon of regional importance. However, after a careful evaluation, I have major concerns that prevent me from recommending acceptance in its current form. Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed repeats, gaps, and structural errors, which in turn reduce the reliability of annotations and downstream analyses. b. Assembly completeness is limited The assembly is fragmented and scaffolded with reliance on a reference genome ( Clarias gariepinus ). This strategy risks introducing misassemblies and biases. Independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads are required to approach chromosome-level quality, which is expected for a lasting genomic reference. Although the BUSCO score is high, it does not fully compensate for the lack of structural completeness. c. Limited utility of the current resource A genome note should provide a robust foundation for comparative genomics, conservation, and applied research. In its present form, the assembly’s limitations significantly restrict its long-term usefulness. The manuscript would be strengthened by deeper sequencing, improved scaffolding, and expanded biological interpretation (e.g., comparative analysis with related catfish species). d. Minor points Please consider providing a clear summary table that links raw sequencing datasets to analytical steps (assembly, polishing, annotation). Functional annotation could be expanded to highlight gene families of ecological or aquacultural interest. e. Decision While the study has potential, I regret to say that the present version does not meet the standards required for indexing as a genome note. I therefore recommend rejection in its current form. I encourage the authors to consider resequencing at higher depth and applying independent scaffolding approaches. With these improvements, the dataset could provide a far more valuable and reliable genomic resource. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? No Competing Interests No competing interests were disclosed. Reviewer Expertise Evolutionary biology, genomics, population genetics I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (1) Author Response 10 Nov 2025 Imron Imron, Research Center for Fishery, National Research and Innovation Agency, Bogor, Indonesia Detailed Assessment a. Sequencing depth appears insufficient The reported coverage is below the accepted standards for reliable genome assembly (generally ≥30× long-read depth). Low coverage increases the likelihood of collapsed repeats, gaps, and structural errors, which in turn reduce the reliability of annotations and downstream analyses. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. b. Assembly completeness is limited The assembly is fragmented and scaffolded with reliance on a reference genome ( Clarias gariepinus ). This strategy risks introducing misassemblies and biases. Independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads are required to approach chromosome-level quality, which is expected for a lasting genomic reference. Although the BUSCO score is high, it does not fully compensate for the lack of structural completeness. Response: We thank the reviewer for this valuable comment and fully agree that independent scaffolding methods such as Hi-C, optical mapping, or ultra-long ONT reads would improve the structural completeness of the assembly. The primary goal of this work, however, was to generate a high-quality draft genome for Prophagorus nieuhofii as a foundational resource, rather than a chromosome-level reference assembly. We have revised the manuscript title to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii ” in order to be transparent about using a reference-guided approach based on the closely related Clarias gariepinus genome. This strategy was chosen because Hi-C and ultra-long read sequencing technologies are currently limited in availability within our country, and reference-based scaffolding remains a practical and widely accepted alternative for non-model species under such constraints. While we acknowledge that reference-guided scaffolding can introduce some degree of structural bias, the assembly’s high contiguity (N50 = 33.7 Mb), completeness (BUSCO = 98.8%), and minimal gap content (0.04%) demonstrate its robustness and reliability for downstream genomic and comparative analyses. c. Limited utility of the current resource A genome note should provide a robust foundation for comparative genomics, conservation, and applied research. In its present form, the assembly’s limitations significantly restrict its long-term usefulness. The manuscript would be strengthened by deeper sequencing, improved scaffolding, and expanded biological interpretation (e.g., comparative analysis with related catfish species). Response: We thank the reviewer for this thoughtful comment and agree that deeper sequencing, improved scaffolding, and comparative analyses with related catfish species would further strengthen this genomic resource. Our study focused on generating a high-quality draft genome as an initial reference for Prophagorus nieuhofii . We acknowledge that additional long-range scaffolding and deeper sequencing would enhance structural resolution, and we plan to pursue these improvements as such technologies become more accessible in our country. While we appreciate the suggestion for broader comparative analyses, the genome note format emphasizes concise presentation of sequencing and assembly results. Nonetheless, we have included annotation statistics and genome composition comparisons with four related catfish species (Clarias gariepinus, Ictalurus furcatus, Ictalurus punctatus, and Tachysurus fulvidraco) , consistent with the scope of this article type. 1. The reported dataset (~27 Gb) represents 50×—coverage is generally recommended. The relatively low coverage increases risks of collapsed repeats, gaps, and structural errors, which compromise annotation accuracy. Response: Thank you for your comments. We fully acknowledge the necessity of higher coverage for creating a reliable genome assembly. However, due to certain limitations, including funding constraints, we were unable to achieve more than 30x coverage. Nonetheless, if given the opportunity in the future, we would like to enhance the genome assembly. 2. Scaffolding was performed using Clarias gariepinus as the reference. Reference-guided assembly may introduce biases and misassemblies, especially if structural rearrangements exist between species. Independent scaffolding methods (e.g., Hi-C, optical mapping, or ultra-long ONT reads) are needed to improve reliability. The manuscript title should explicitly indicate that this is a reference-guided assembly. Response: Thank you for the comments. We recognize the potential for misassembly when using a reference-guided approach. Consequently, we have revised the title of this manuscript, as suggested by the reviewer, to “Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii.” 3. Gene annotation results are presented mainly as averages (gene length, exon number, etc.), which lack biological interpretation. Comparisons with other catfish genomes would strengthen the significance of these findings. Response: Thank you for the comments. We have consolidated Table 3 and Table 4 into comparative tables, which now include a comparison with the genome assemblies of four other catfish species: Clarias gariepinus (Clariidae), Ictalurus furcatus (Ictaluridae), Ictalurus punctatus (Ictaluridae), and Tachysurus fulvidraco (Bagridae). As a result, we have revised the text in the “Structural and Functional Annotation” subsection to enhance the comparative description. “The genome annotation of Prophagorus nieuhofii resulted in the identification of 30,099 protein-coding genes, a count comparable to that of Ictalurus punctatus (approx 31,040 genes), which produced 37,734 predicted transcripts. Relative to the other four catfish species examined (Table 3), P. nieuhofii exhibits a compact gene architecture and reduced splicing complexity. This is evidenced by the lowest mean number of transcripts per gene at 1.3 (others range from 1.7 to 2.3), and alternative splicing detected in only 18.1% of genes, significantly less than the 32.2% to 48.0% observed in the remaining species. Furthermore, P. nieuhofii has a substantially higher proportion of single-exon genes (12.5%), far exceeding the 3.5% to 4.4% found in the other catfish, which possess a more uniformly multi-exonic architecture. Structural measurements confirm this compactness: P. nieuhofii genes have a smaller average locus length (15,993.4 bp vs. 19,155.7 bp to 22,083.0 bp) and fewer distinct exons per gene (8.9 vs. 11.3 to 12.3). Its mean exon size is also the smallest at 180.2 bp (others range from 269.4 bp to 327.1 bp), resulting in a significantly shorter average transcript size (1,812.4 bp). In terms of genome composition (Table 4), the P. nieuhofii genome has the lowest overall content dedicated to coding and genic regions. Exons constitute only 4% of the genome (48 Mb), which is notably low compared to the 8% to 13% seen elsewhere but exhibit the highest GC content at 51% (compared to 45%─46% in the others). Genes collectively occupy 44% of the genome (481 Mb), marking the smallest genic fraction (others range from 55% to 68%). Introns, totaling 233,110, account for 40% of the genome (434 Mb) with an average length of 1,862 bp, also representing the lowest proportional content in the comparison. The structural and compositional differences collectively indicate that the P. nieuhofii genome exhibits a more compact gene structure and less complexity in transcript diversity compared to the other catfish assemblies studied.” View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Khedkar GD. Peer Review Report For: Draft genome assembly of the slender walking catfish, Prophagorus nieuhofii [version 1; peer review: 2 approved with reservations, 1 not approved] . F1000Research 2025, 14 :787 ( https://doi.org/10.5256/f1000research.183897.r413914) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. 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