Chromosome-scale genome assembly and annotation of the white star apple (Gambeya albida)

Chromosome-scale genome assembly and annotation of the white star apple (Gambeya albida) | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF data-descriptor Chromosome-scale genome assembly and annotation of the white star apple (Gambeya albida) Michael Landi, Sadik Muzemil, Adedapo Adediji, Laurah Ondari, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9271727/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract White star apple ( Gambeya albida ) is native to the lowland rainforests of Central, East, and West Africa. This species is highly valued for its nutritious fruits and offers medicinal, socio-cultural, and economic benefits. In West Africa, it contributes to food security for rural and urban communities alike. However, no genomic resources are available to untap the agronomic and medicinal traits of the white star apple. Here, we present its first chromosome-scale genome, generated using PacBio HiFi and Omni-C sequencing. The star apple genome is highly homozygous (0.317%), and we assembled 98.9% of the estimated haploid genome size (822 Mb) into 13 pseudochromosomes. It has a base-level accuracy (QV) of 58.14, an N50 of 57 Mbp, and 97.5% BUSCO completeness, representing a reference-quality assembly. About 58.5% of the genome constitutes repetitive sequences, and homology-based prediction identified 75,057 gene models. This reference-quality genome of the white star apple will serve as a valuable resource to enhance our understanding of its underlying nutritional and pharmacological traits and facilitate improvement research. Figures Figure 1 Figure 2 Figure 3 Background & Summary White star apple ( Gambeya albida (G. Don) Aubrév. & Pellegr., syn. Chrysophyllum albidum G. Don) is a woody plant species belonging to the family Sapotaceae, with its native range across the lowland rainforests of Central, East, and West Africa 1 . Commonly called Agbalumo (Yoruba), Udara (Igbo), and Agwaliba (Hausa) in Nigeria and Alasa in Ghana 2 , it can grow up to 45m in height, with mature girth varying from 1.5 to 2m 3 . The fruit is five-celled, enclosing five brown, bean-shaped seeds within a yellowish, pleasantly acidic pulp. These seeds are shiny when ripe and are distinctively arranged in a star pattern inside the fruits, hence the tree’s unique name. The tree is indigenous to West and Central Africa with numerous nutritional, medicinal, socio-cultural, and economic benefits 4 , 5 . It plays a crucial role in food security, particularly in rural and urban areas of West Africa, serving as a vital food source and snack. Its fruit is a significant contributor to the diets of many communities, especially during its peak fruiting season from December to March 2 .The fleshy pulp of the fruit is highly relished by both young and old. Beyond direct consumption, the fruit is also utilized in the production of various food products such as stewed fruit, marmalade, syrup, and soft drinks, highlighting its versatility in food processing. Nutritionally, the white star apple fruit is rich in ascorbic acid, alkaloids, tannins, carbohydrates, crude fibre, lipids, potassium, and calcium 6 – 8 . For example, Amusa et al. 9 found that white star apple fruits have a higher vitamin C content than oranges and 10 times that of guava or cashew. Its proximate analysis has shown the presence of moisture (73.33%), ash (2.64%), fiber (3.61%), protein (16.99%), and vitamins A, B1, and B2 10 . The presence of pectin, polyphenols, and various minerals further enhances its nutritional value, with potential for detoxification and reducing sugar absorption 11 . Studies have also indicated that the nutritional content can vary between sweet and sour fruits, though lipid and crude fiber values remain similar 12 . This rich nutritional profile underscores its importance in combating malnutrition and enhancing dietary diversity in regions where it is consumed 6 . Traditional African medicine widely utilizes different parts of the white star apple for treating a wide range of ailments. Every part of the plant, including its leaf, seed, pulp, peel, bark, and root, is essentially considered valuable because of its anti-nociceptive, anti-inflammatory, and antioxidant properties 13 , 14 . Extracts from these various parts have demonstrated good antimicrobial and antifungal activities. For example, Eleagnine, an alkaloid isolated from white star apple seed cotyledon, has been found to exhibit these properties 15 . The fruit's rich sources of natural antioxidants have been established to promote health by acting against oxidative stress-related diseases such as diabetes, cancer, and coronary heart diseases 16 . The plant's therapeutic value is attributed to its rich phytochemical composition, including alkaloids, tannins, flavonoids, phenols, anthocyanins, and proanthocyanidins. In addition, the socio-economic usefulness of the white star apple has been reported in several studies 17 – 19 , highlighting its high value as a tree of support, financial profitability, and monetary returns, especially for African rural dwellers. The fruit also contains anacardic acid, industrially used for wood protection and as a resin source, while the seeds are a source of oil used for diverse purposes and for local games 20 . The numerous uses of star apple in tropical Africa have led to its unsustainable exploitation, which is the greatest threat to this species, combined with other factors such as habitat loss, deforestation, urbanisation, and climate change 21 . This has led to its classification as a ‘Near Threatened’ species by the International Union for Conservation of Nature 1 . Thus, conservation efforts aimed at reviving the declining populations of the white star apple are necessary 22 . Here, we present a high-quality chromosome-level genome of the white star apple. In addition, we report one of the first plant genome sequenced and assembled 100% locally in Africa, utilising highly accurate PacBio HiFi and Omni-C chromatin conformation data. As at 2022, of the 798 plant species sequenced globally, only 20 are endemic to Africa, and none of these were sequenced locally in Africa 23 . Previous plant species sequenced in Africa either utilised Oxford Nanopore Technologies (ONT) and chromosome conformation capture (Hi-C) sequencing lablab ( Lablab purpureus ) and African yam bean ( Sphenostylis stenocarpa ) 24 , 25 . This white star apple genome will facilitate breeding and conservation efforts, enhance our understanding of important metabolic pathways and underlying genes for nutritional and pharmacological applications and showcase the possibility of genomic studies fully implemented in Africa. Methods Ethics statement Sample collection procedure, including processing and handling of the plant used in this study followed and Collection Policy for tree propagation at the International Institute of Tropical Agriculture (IITA), was approved by the Manager of the IITA Forest Center. Approval for the collection, handling, and international transfer of plant genetic material was granted via a legally binding Material Transfer Agreement (MTA) executed between the Federal Ministry of Environment of the Federal Republic of Nigeria, and Inqaba Biotec West Africa Ltd. These were guided by the African BioGenome Project (AfricaBP) Ethical Legal, and Social Issues Subcommittee practical guide on accessing and sharing biological materials and data 26 , enabling the later-stage processes that were carried out in accordance with local biodiversity, biosafety, and access‑and‑benefit‑sharing regulations of the Federal Republic of Nigeria, including adherence to the Nagoya Protocol. The transfer of DNA samples for sequencing was conducted strictly under this MTA, and no materials were used outside of the agreed scope. Sampling and botanical information In 2012, white star apple seeds were collected from an elite mother tree, recognized for producing the sweetest fruits of the species, on the IITA campus in Ibadan, Nigeria (Fig. 1 c). These seeds were sown and nurtured in the IITA Botanical Nursery in Ibadan before being planted out in the area in 2013. Among the 10 seedlings planted, this tree produced its first fruit in 2019, ahead of all others which fruited for the first time in 2020. Leaf samples were collected from the lower branches of this tree located at N7°30.183' E3°53.582' (147 m above sea level). The tree measured 8.9 m in height and 15.92 cm in diameter at breast height on 27 June 2025. DNA Extraction and Sequencing DNA Extraction Healthy young leaves of white star apple were collected from mature trees at the IITA Botanical Nursery. Immediately after collection as described above, the leaves were placed on ice and stored at -20°C. All the samples were processed within 24 hours of collection to ensure DNA integrity. Approximately 2.5 g of the leaves were thoroughly cleaned and finely ground into a homogeneous powder using a porcelain mortar and pestle. During grinding, liquid nitrogen was added continuously for 20 minutes to keep the sample frozen and enhance the cell lysis efficiency. After grinding, 1.5 g of the leaf powder was transferred into a pre-cooled 50 mL centrifuge tube. The homogenized sample was processed for ultra-pure, high molecular weight DNA isolation using the NucleoBond HMW DNA Kit (Macherey-Nagel, Germany), following the manufacturer’s instructions for chemical lysis, incubation, RNA digestion, column equilibration, binding, flushing and washing, elution, precipitation, and resuspension. The purity and concentration of the DNA were assessed using a NanoDrop spectrophotometer. DNA quality was further verified by electrophoresis on a 1% agarose gel. HiFi SMRTbell Library Construction and Sequencing The initial evaluation of the quantity and size distribution of the purified gDNA was performed using the Agilent 2200 TapeStation Nucleic Acid System (G2965AA), operated with Agilent 2200 TapeStation Software A.01.05. Analysis was conducted using the Agilent Genomic DNA ScreenTape (5067–5365) and Agilent Genomic DNA Reagents (5067–5366), with samples drawn from a 96-well plate. The isolated high molecular weight (HMW) gDNA yielded a concentration of 96 ng/µl in a total volume of 150 µl. High molecular weight genomic DNA was sheared into 15–25 kb fragments using the Megaruptor® 3 system (Diagenode, Cat# B06010003) according to the manufacturer’s specifications. An input of 66 ng/µl gDNA in a 30 µl volume was used for library preparation. HiFi SMRTbell libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences). Sequencing was performed on two SMRT cells, with the first SMRT cell producing 1,916,709 reads, while the second generated 1,775,843 reads. The raw sequence reads were assessed for quality using the default settings of FastQC version 0.11.5 ( https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) to determine the parameters for the subsequent filtering step. Filtering of the raw reads was performed using Fastp version 0.23.1 27 (parameters: --length_required 10000,--length_limit 30000, -f 15). The read length was set at an acceptable read length between 10 Kbp and 30 Kbp to enhance genome assembly performance. The filtered reads were merged, resulting in a total of 3,668,683 reads (99.36%). Omni-C Library Construction and Sequencing Frozen plant leaves (300 mg) were crushed into fine powder with a mortar and pestle in liquid nitrogen and transferred into a 50 mL Falcon tube. Formaldehyde (37% solution), PBS, and DSG were added to the ground tissue to facilitate chromatin crosslinking. After a series of washes, the enzyme mix was added to the sample for enzymatic digestion, followed by lysate QC assessment using the Tapestation D5000 kit (Agilent). The ideal fragment distribution is 100 to 2,500 bp for successful crosslinking and digestion. The next step involved performing proximity ligation by capturing the chromatin with chromatin capture beads, followed by end polishing and bridge ligation. Reverse crosslinking and DNA fragment purification were then performed. Post-DNA fragment purification and Illumina library prep (part of Dovetail Omni-C kits) were performed according to the manufacturer's protocol. For sequencing on the PacBio Onso system, the library was converted by adding PacBio A and P1 adapter sequences in a limited PCR cycle. Sequencing was performed on the PacBio Onso system using a 300-cycle kit (2×150 bp), generating a total of 107,723,424 paired-end Omni-C reads. Quality control was conducted with FastQC (v0.11.3), and reads were filtered using fastp (v0.23.4) (parameters: - -length_required 50 -f 14 -F 14). After filtering, 91,493,006 (98.5%) high-quality Omni-C reads were retained and used for genome scaffolding. Genome size and heterozygosity estimation To estimate the genome size, heterozygosity, and ploidy of the white star apple genome, k-mer analysis was performed using high-quality filtered PacBio HiFi reads. The k-mer frequency distribution was generated using Jellyfish (v2.2.8) 28 (parameters: count -C -m 21 -s 1000000; histo). The resulting histogram was visualised with the default parameters of GenomeScope (v2.0) 29 (Fig. 2 ). The analysis estimated the haploid genome size to be approximately 822 Mbp. The k-mer distribution displays a strong unimodal peak centered around a k-mer coverage of ~ 60×, representing the homozygous portion of the genome. A minor peak near ~ 30× coverage corresponds to a very small proportion of heterozygous k-mers. The ploidy level of the genome was estimated as diploid. The low heterozygosity rate of 0.317%, combined with a higher homozygosity, indicates that the white star apple genome is highly homozygous. Genome assembly Filtered HiFi sequence reads of approximately 75X genome coverage with an average read length of 16,951 bp were assembled de novo using three assembly tools. Hifiasm v0.16.1-r375 (parameter: --primary), HiCanu v2.3 (parameters: -pacbio-hifi genomeSize=800m -useGrid=false -merylThreads = 4 -merylMemory = 8 corOverlapper = ovl), and Flye v2.9.6-b1802 (parameters: --pacbio-hifi --genome-size 800 m) 30–32 . The genome statistics from the three assemblies were compared using the default settings of QUAST 33 (v5.1.0rc1) (Table 1 ). Table 1 Genome assembly quality metrics Total length HiFiasm assembly HiCanu assembly Flye assembly HiFiasm assembly purged HiFiasm assembly purged (second round) Hi-C scaffolded assembly Final assembly 2,407,389,064 2,832,626,671 1,532,658,079 901,469,050 821,339,754 821,384,454 813,971,461 #Contig/scaffold 7111 28200 26505 1114 1023 596 586 N50 1,359,676 236,513 106,680 3,005,615 3,111,027 57,681,698 57,681,045 L50 454 1707 3420 95 84 6 6 N90 147,003 35,005 27,602 683,202 778,075 30,446,293 46,682,311 L90 2353 16719 14831 322 280 13 12 Gaps 0 0 0 0 0 1153 146 On the basis of the N50 value and the number of contigs, we selected the hifiasm primary assembly. This assembly had an N50 of 1.3 Mbp and the fewest number of contigs (7,111), making it the most contiguous draft genome among the outputs of the three assemblers. However, its total size of the draft genome was larger than the estimated genome size, likely due to a high level of duplication (87.6%) (Table 3 ). We implemented a two-round purging strategy using the purge_dups pipeline 34 . First, PacBio clean HiFi reads were aligned to the draft primary assembly using Minimap2 (v2.24-r1122) 35 , and coverage statistics along with cutoff thresholds were computed to inform the purging process. The assembly was then split and self-aligned with Minimap2 to identify and remove redundant haplotigs. The final purged genome (draft genome) had an N50 of 3.1 Mbp and a total size of 821 Mbp and was subsequently used for scaffolding. Omni-C scaffolding, manual curation and gap filling A chromosome-scale assembly comprising thirteen chromosomes was constructed by integrating Omni-C data with the contig-level draft assembly, followed by manual curation and gap filling (Fig. 1 a). Filtered high-quality paired-end Omni-C reads were aligned to the draft genome using bwa (v0.7.19-r1273) 36 (parameters: mem -SP -T0). The resulting alignments were processed using the pairtools (v1.1.2) 37 , which performed parsing, sorting, duplicate marking, and splitting of read pairs to generate a contact map. The final alignment file was sorted and indexed using samtools (v1.15.1) 38 and was used for scaffolding with YaHS (v1.2.2) 39 with default parameters, which incorporated the proximity ligation data to reorder and orient contigs into scaffolds. YaHS’s alignment matrix was subsequently converted into a contact map in pairs format using PretextMap ( https://github.com/sanger-tol/PretextMap ) (parameters: --sortby length --sortorder descend --mapq 0), which was then visualized in PretextView ( https://github.com/sanger-tol/PretextView ) for manual curation. The PretextView enabled inspection of Omni-C read contact patterns against the scaffolds, allowing correction of mis-assemblies and refinement of scaffold anchoring and orientation into chromosome-scale pseudomolecules, guided by the genomic proximity signal of the Omni-C data. To reduce assembly fragmentation, gaps introduced during scaffolding and manual curation were filled using LR_GapCloser 40 . LR_Gapcloser employs a tiling path-based approach by fragmenting long reads into short tags and aligning them using bwa (v0.7.19-r1273) to the assembly to identify and fill gaps. Before gap filling, the curated genome contained 1,153 gaps. Using default parameters, LR_Gapcloser reduced the number of gaps to 146. The final chromosome-scaled genome had an improved contiguity of N50 value of 57 Mbp and an L90 value of 12 (Table 1 ). Genome annotation Transposable Elements (TE) annotation The repeat landscape of G. albida was characterized and annotated using Extensive de novo TE Annotator (EDTA) v2.2.2 41 (parameters: –genome –overwrite 1 –sensitive 1 –anno 1 –evaluate 1). This pipeline integrates structure-based and homology-based approaches to detect primary TEs within the assembled genome. It employs a combination of specialized tools, including HelitronScanner, LTR_FINDER, LTRHarvest, LTR_retriever, TIR-Learner, RepeatModeler2, and RepeatMasker, to classify and annotate novel TE sequences 42 – 47 . The repeats accounted for 58.62% of the genome. EDTA was able to categorise the repeats into major categories such as LTR transposons (38.97%), LINE transposons (4.22%), TIR (6.93%), nonTIR (4,71%), nonLTR (0.41%) and other repeats (Fig. 3 a). LTR transposons were the most abundant repeats identified across the genome (Fig. 3 b). After repeat identification and annotation, the genome was soft-masked using the make_masked.pl utility from the EDTA pipeline, and the masked genome was subsequently used for gene prediction. Gene Prediction and Functional Annotation Gene prediction was performed using BRAKER (v2.0) 48 , which integrates ab initio predictions from AUGUSTUS 49 with evidence of external homologous proteins. The protein evidence was sourced from the Viridiplantae dataset in OrthoDB version 11 50 . The protein dataset was processed for compatibility with the BRAKER2 pipeline. BRAKER2 predicted 75,057 gene models (Table 2 ). The functional information was then transferred onto the protein coding models, interrogating the eggNOG database (v5.0.2) using eggNOG-mapper (v2.1.12) and the InterPro member databases using InterProScan 51 – 54 (v5.66-98.0). As a final step, the annotated clusters of orthologous groups (COGs) from eggNOG, the resulting InterProScan outputs and the original gene models from BRAKER2 were parsed to funannotate annotate 55 (v1.8.1) (parameters: --eggnog, --iprscan and –gff) for final functional annotation in the form of a gff3 file. Table 2 Annotation counts and gene models supported with functional annotation Feature Count Genes 75,057 CDS complete 81,156 Total exons 292,568 Total introns 211,405 Total protein 81,163 Number of genes with GO terms 33,767 Number of genes with InterProScan annotations 48,771 Number of genes with eggnog annotations 61,085 Number of genes with Pfam annotations 38,601 Number of genes with Cazyme annotations 1,504 Data Records The raw PacBio HiFi reads and Omni-C reads used for the assembly are available from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under the BioProject PRJNA1255872 with accession numbers SRR33323859 56 and SRR33422445 57 , respectively. The genome has been submitted under the same BioProject with the accession number JBNXVW000000000 58 . The genome annotation files are uploaded to Zenodo 59 . Technical Validation To assess the accuracy and completeness of the white star apple genome assembly, we conducted a Benchmarking Universal Single-Copy Orthologs (BUSCO) 60 analysis using the eudicots lineage dataset. This analysis identified 2,267 complete BUSCO genes out of 2,326, indicating a genome completeness of 97.5% (Table 3 ). We aligned clean PacBio HiFi reads to the final assembly using Minimap2 to evaluate assembly accuracy, yielding a mapping rate of 99.29%. Additionally, a k-mer- based quality assessment using merqury 61 (v1.3) ( k-mer = 21) produced a quality value (QV) score of 58.14 and a k-mer completeness of 88.10% (Table 4 ). These assessments confirmed the high quality and completeness of the white star apple genome assembly. Table 3 BUSCO assessment of the G.albida genome assembly Draft assembly Final assembly Number Percent (%) Number Percent (%) Complete BUSCOs (C) 2296 98.7% 2267 97.5% Complete and single-copy BUSCOs (S) 258 11.1% 2124 91.3% Complete and duplicated BUSCOs (D) 2038 87.6% 143 6.1% Fragmented BUSCOs (F) 9 0.4% 8 0.3% Missing BUSCOs (M) 21 0.9% 51 2.2% Total BUSCO groups searched 2326 2326 Table 4 Quality value scores of the G.albida genome assembly Quality Value (QV) score K-mer completeness White star apple genome 58.1437 88.1048 Declarations Competing interests K.B., A.M., and L.A.A. are employees of Inqaba Biotec (Nigeria and South Africa). The remaining authors declare no competing interests. Funding Declaration This work was supported by no external funding. Author Contribution L.A.A. conceived the overall project idea and led the project. A.O.A. and A.G.A. conducted the literature review and produced the manuscript's first draft. T.R.O, A.D.A and A.G.A. handled sample collections of the plant materials. L.A.A., A.O.M. T.R.O., A.G.A., and T.E.E. carried out ethical compliance functions/consultations. A.M. T.R.O and K.B. carried out library preparation and sequencing involving long and short reads. M.L. and A.G. performed the sequence quality check and assembly. M.L., A.G, S.M. and T.E.E advised ways to improve overall genome quality, assembly, and completion. S.M. performed manual genome curation. L.O. conducted the genome annotation workflow and Y.A.B.Z generated the circos plot diagram. L.A.A., T.E.E., A.G., and S.M. provided overall supervision throughout the analysis. All authors reviewed, edited, and approved the final manuscript. Acknowledgement The sequencing data were generated with funding from the Malimbe Foundation and Inqaba Biotec West Africa. Computational resources for genome assembly and annotation, including storage and processing, were provided by the IITA Bioinformatics Unit. IITA Forest Center granted permission for collecting leaf samples. The African BioGenome Project (AfricaBP) contributed to project coordination, implementation, and ELSI guidance as well as negotiating sponsorship for Omni-C sequencing. We would like to thank Inqaba Biotec West Africa, IITA, and SolveLean for sponsoring capacity-building training as part of the ethical and permit approval process described in the ethics section of this work. The authors thank Zahra Mungloo-Dilmohamud, University of Mauritius, Mauritius, Adetutu E. Olumeh, Inqaba Biotec West Africa, and Uchenna N. Urom, Inqaba Biotec West Africa for their assistance in editing the initial manuscript draft. Thanks to Sally Katee Mueni, International Livestock Research Institute (ILRI), Nairobi, Kenya, and Marietjie Botes, School of Law, University of KwaZulu-Natal, Durban, South Africa and University of Texas at Austin, Austin, United States for reviewing the ethics of this work and providing feedback. We thank Laurent Falquet from the University of Fribourg for his contributions to discussions on the genome assembly. Data Availability The raw PacBio HiFi reads and Omni-C reads used for the assembly are available from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under the BioProject PRJNA1255872 with accession numbers SRR3332385956 and SRR3342244557, respectively. The genome has been submitted under the same BioProject with the accession number JBNXVW00000000058. The genome annotation files are uploaded to Zenodo. Code Availability All data processing pipelines and commands were executed according to the manuals and protocols of the respective bioinformatics tools. References Hills, R. Gambeya albida. The IUCN Red List of Threatened Species 2019: e.T61961750A61961761. Report No. 2307–8235, (2019). Adekanmi, D. G. & Olowofoyeku, A. E. African Star Apple: Potentials and Application of Some Indigenous Species in Nigeria. 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Nat Commun 11, 1432 (2020). https://doi.org:10.1038/s41467-020-14998-3 Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). https://doi.org:10.1038/s41592-020-01056-5 Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37, 540–546 (2019). https://doi.org:10.1038/s41587-019-0072-8 Nurk, S. et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res 30, 1291–1305 (2020). https://doi.org:10.1101/gr.263566.120 Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013). https://doi.org:10.1093/bioinformatics/btt086 Guan, D. et al. Identifying and removing haplotypic duplication in primary genome assemblies. 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Gigascience 8 (2019). https://doi.org:10.1093/gigascience/giy157 Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome biology 20, 1–18 (2019). Xiong, W., He, L., Lai, J., Dooner, H. K. & Du, C. HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes. Proceedings of the National Academy of Sciences 111, 10263–10268 (2014). Ou, S. & Jiang, N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant physiology 176, 1410–1422 (2018). Ou, S. & Jiang, N. LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. Mobile DNA 10, 48 (2019). Chen, N. Using Repeat Masker to identify repetitive elements in genomic sequences. Current protocols in bioinformatics 5, 4.10. 11-14.10. 14 (2004). Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences 117, 9451–9457 (2020). Ellinghaus, D., Kurtz, S. & Willhoeft, U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC bioinformatics 9, 1–14 (2008). Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP + and AUGUSTUS supported by a protein database. NAR genomics and bioinformatics 3, lqaa108 (2021). König, S., Romoth, L. W., Gerischer, L. & Stanke, M. Simultaneous gene finding in multiple genomes. Bioinformatics 32, 3388–3395 (2016). Kuznetsov, D. et al. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic acids research 51, D445-D451 (2023). Burge, S. et al. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database 2012, bar068 (2012). Mitchell, A. L. et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic acids research 47, D351-D360 (2019). Mulder, N. & Apweiler, R. InterPro and InterProScan: tools for protein sequence classification and comparison. Comparative genomics , 59–70 (2007). Huerta-Cepas, J. et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Molecular biology and evolution 34, 2115–2122 (2017). Palmer, J. M. & Stajich, J. (Zenodo, 2020). NCBI Sequence Read Archive (HiFi reads). (2026). https://doi.org:https://www.ncbi.nlm.nih.gov/sra/SRR33323859 NCBI Sequence Read Archive (Omni-C reads). (2026). https://doi.org:https://www.ncbi.nlm.nih.gov/sra/SRR33422445 Chromosome-scale genome assembly of the white star apple (Gambeya albida). GenBank (2026). https://doi.org:https://www.ncbi.nlm.nih.gov/nuccore/JBNXVW000000000 Chromosome-scale genome assembly and annotation of the white star apple ( Gambeya albida ). (2026). https://doi.org: https://doi.org/10.5281/zenodo.19257247 Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). https://doi.org:10.1093/bioinformatics/btv351 Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21, 245 (2020). https://doi.org:10.1186/s13059-020-02134-9 Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9271727","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"data-descriptor","associatedPublications":[],"authors":[{"id":617823232,"identity":"12868a51-8c20-4c64-910e-99e28f426be0","order_by":0,"name":"Michael 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Foundation","correspondingAuthor":false,"prefix":"","firstName":"Lukman","middleName":"","lastName":"Aroworamimo","suffix":""}],"badges":[],"createdAt":"2026-03-30 20:23:15","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9271727/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9271727/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":106387340,"identity":"d6c3980d-22c9-417b-8423-31b05efc0440","added_by":"auto","created_at":"2026-04-08 06:33:07","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":293705,"visible":true,"origin":"","legend":"\u003cp\u003eOverview of white star apple (\u003cem\u003eGambeya albida\u003c/em\u003e) genome. (a) Circos plot displaying the gene and repeat densities of the genome. (b) The white star apple photo taken at the IITA Botanical Nursery - IITA Forest Center\u003c/p\u003e","description":"","filename":"Picture1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-9271727/v1/46ff77956957138c0752e042.jpg"},{"id":106404871,"identity":"fe4a7451-1c57-473a-a055-e62e56ea4d0a","added_by":"auto","created_at":"2026-04-08 09:17:17","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":170714,"visible":true,"origin":"","legend":"\u003cp\u003eGenomeScope profile of the white star apple (\u003cem\u003eGambeya albida\u003c/em\u003e) genome. A k-mer (21-mer) distribution curve for estimating genome size, heterozygosity, and repeat content.\u003c/p\u003e","description":"","filename":"Picture2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-9271727/v1/d1fad7cdf0c3f016bf64f739.jpg"},{"id":106387342,"identity":"a7d3c6c3-5712-4452-b2ee-2f8fde0fe7dd","added_by":"auto","created_at":"2026-04-08 06:33:07","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":55878,"visible":true,"origin":"","legend":"\u003cp\u003eProportion and distribution of transposable elements (TEs) across the chromosomes of the white star apple (\u003cem\u003eGambeya albida\u003c/em\u003e) genome (a) Proportion of the percentage TEs covering the genome \u0026nbsp;(b) Distribution of TEs across all chromosomes.\u003c/p\u003e","description":"","filename":"Picture3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-9271727/v1/266e65f528f7841dc75b8069.jpg"},{"id":106406093,"identity":"ae76edf3-dd09-4c92-b4a2-a99652b92590","added_by":"auto","created_at":"2026-04-08 09:29:49","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1640088,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9271727/v1/2cf5349c-501d-4f63-8f47-1918be43f5eb.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Chromosome-scale genome assembly and annotation of the white star apple (Gambeya albida)","fulltext":[{"header":"Background \u0026 Summary","content":"\u003cp\u003eWhite star apple (\u003cem\u003eGambeya albida\u003c/em\u003e (G. Don) Aubr\u0026eacute;v. \u0026amp; Pellegr., syn. \u003cem\u003eChrysophyllum albidum\u003c/em\u003e G. Don) is a woody plant species belonging to the family Sapotaceae, with its native range across the lowland rainforests of Central, East, and West Africa\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e. Commonly called Agbalumo (Yoruba), Udara (Igbo), and Agwaliba (Hausa) in Nigeria and Alasa in Ghana\u003csup\u003e\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e, it can grow up to 45m in height, with mature girth varying from 1.5 to 2m\u003csup\u003e3\u003c/sup\u003e. The fruit is five-celled, enclosing five brown, bean-shaped seeds within a yellowish, pleasantly acidic pulp. These seeds are shiny when ripe and are distinctively arranged in a star pattern inside the fruits, hence the tree\u0026rsquo;s unique name.\u003c/p\u003e \u003cp\u003eThe tree is indigenous to West and Central Africa with numerous nutritional, medicinal, socio-cultural, and economic benefits\u003csup\u003e\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e,\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e\u003c/sup\u003e. It plays a crucial role in food security, particularly in rural and urban areas of West Africa, serving as a vital food source and snack. Its fruit is a significant contributor to the diets of many communities, especially during its peak fruiting season from December to March\u003csup\u003e\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e.The fleshy pulp of the fruit is highly relished by both young and old. Beyond direct consumption, the fruit is also utilized in the production of various food products such as stewed fruit, marmalade, syrup, and soft drinks, highlighting its versatility in food processing. Nutritionally, the white star apple fruit is rich in ascorbic acid, alkaloids, tannins, carbohydrates, crude fibre, lipids, potassium, and calcium\u003csup\u003e\u003cspan additionalcitationids=\"CR7\" citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e. For example, Amusa et al.\u003csup\u003e9\u003c/sup\u003e found that white star apple fruits have a higher vitamin C content than oranges and 10 times that of guava or cashew. Its proximate analysis has shown the presence of moisture (73.33%), ash (2.64%), fiber (3.61%), protein (16.99%), and vitamins A, B1, and B2\u003csup\u003e10\u003c/sup\u003e. The presence of pectin, polyphenols, and various minerals further enhances its nutritional value, with potential for detoxification and reducing sugar absorption\u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u003c/sup\u003e. Studies have also indicated that the nutritional content can vary between sweet and sour fruits, though lipid and crude fiber values remain similar\u003csup\u003e\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e. This rich nutritional profile underscores its importance in combating malnutrition and enhancing dietary diversity in regions where it is consumed\u003csup\u003e\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eTraditional African medicine widely utilizes different parts of the white star apple for treating a wide range of ailments. Every part of the plant, including its leaf, seed, pulp, peel, bark, and root, is essentially considered valuable because of its anti-nociceptive, anti-inflammatory, and antioxidant properties\u003csup\u003e\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e,\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u003c/sup\u003e. Extracts from these various parts have demonstrated good antimicrobial and antifungal activities. For example, Eleagnine, an alkaloid isolated from white star apple seed cotyledon, has been found to exhibit these properties\u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e. The fruit's rich sources of natural antioxidants have been established to promote health by acting against oxidative stress-related diseases such as diabetes, cancer, and coronary heart diseases\u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e\u003c/sup\u003e. The plant's therapeutic value is attributed to its rich phytochemical composition, including alkaloids, tannins, flavonoids, phenols, anthocyanins, and proanthocyanidins. In addition, the socio-economic usefulness of the white star apple has been reported in several studies\u003csup\u003e\u003cspan additionalcitationids=\"CR18\" citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u003c/sup\u003e, highlighting its high value as a tree of support, financial profitability, and monetary returns, especially for African rural dwellers. The fruit also contains anacardic acid, industrially used for wood protection and as a resin source, while the seeds are a source of oil used for diverse purposes and for local games\u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe numerous uses of star apple in tropical Africa have led to its unsustainable exploitation, which is the greatest threat to this species, combined with other factors such as habitat loss, deforestation, urbanisation, and climate change\u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e. This has led to its classification as a \u0026lsquo;Near Threatened\u0026rsquo; species by the International Union for Conservation of Nature\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e. Thus, conservation efforts aimed at reviving the declining populations of the white star apple are necessary\u003csup\u003e\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eHere, we present a high-quality chromosome-level genome of the white star apple. In addition, we report one of the first plant genome sequenced and assembled 100% locally in Africa, utilising highly accurate PacBio HiFi and Omni-C chromatin conformation data. As at 2022, of the 798 plant species sequenced globally, only 20 are endemic to Africa, and none of these were sequenced locally in Africa\u003csup\u003e\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u003c/sup\u003e. Previous plant species sequenced in Africa either utilised Oxford Nanopore Technologies (ONT) and chromosome conformation capture (Hi-C) sequencing lablab (\u003cem\u003eLablab purpureus\u003c/em\u003e) and African yam bean (\u003cem\u003eSphenostylis stenocarpa\u003c/em\u003e)\u003csup\u003e\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e,\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e\u003c/sup\u003e. This white star apple genome will facilitate breeding and conservation efforts, enhance our understanding of important metabolic pathways and underlying genes for nutritional and pharmacological applications and showcase the possibility of genomic studies fully implemented in Africa.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eEthics statement\u003c/h2\u003e \u003cp\u003e Sample collection procedure, including processing and handling of the plant used in this study followed and Collection Policy for tree propagation at the International Institute of Tropical Agriculture (IITA), was approved by the Manager of the IITA Forest Center. Approval for the collection, handling, and international transfer of plant genetic material was granted via a legally binding Material Transfer Agreement (MTA) executed between the Federal Ministry of Environment of the Federal Republic of Nigeria, and Inqaba Biotec West Africa Ltd. These were guided by the African BioGenome Project (AfricaBP) Ethical Legal, and Social Issues Subcommittee practical guide on accessing and sharing biological materials and data\u003csup\u003e\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e, enabling the later-stage processes that were carried out in accordance with local biodiversity, biosafety, and access‑and‑benefit‑sharing regulations of the Federal Republic of Nigeria, including adherence to the Nagoya Protocol. The transfer of DNA samples for sequencing was conducted strictly under this MTA, and no materials were used outside of the agreed scope.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eSampling and botanical information\u003c/h3\u003e\n\u003cp\u003eIn 2012, white star apple seeds were collected from an elite mother tree, recognized for producing the sweetest fruits of the species, on the IITA campus in Ibadan, Nigeria (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ec). These seeds were sown and nurtured in the IITA Botanical Nursery in Ibadan before being planted out in the area in 2013. Among the 10 seedlings planted, this tree produced its first fruit in 2019, ahead of all others which fruited for the first time in 2020. Leaf samples were collected from the lower branches of this tree located at N7\u0026deg;30.183' E3\u0026deg;53.582' (147 m above sea level). The tree measured 8.9 m in height and 15.92 cm in diameter at breast height on 27 June 2025.\u003c/p\u003e\n\u003ch3\u003eDNA Extraction and Sequencing\u003c/h3\u003e\n\u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003eDNA Extraction\u003c/h2\u003e \u003cp\u003eHealthy young leaves of white star apple were collected from mature trees at the IITA Botanical Nursery. Immediately after collection as described above, the leaves were placed on ice and stored at -20\u0026deg;C. All the samples were processed within 24 hours of collection to ensure DNA integrity. Approximately 2.5 g of the leaves were thoroughly cleaned and finely ground into a homogeneous powder using a porcelain mortar and pestle. During grinding, liquid nitrogen was added continuously for 20 minutes to keep the sample frozen and enhance the cell lysis efficiency. After grinding, 1.5 g of the leaf powder was transferred into a pre-cooled 50 mL centrifuge tube. The homogenized sample was processed for ultra-pure, high molecular weight DNA isolation using the NucleoBond HMW DNA Kit (Macherey-Nagel, Germany), following the manufacturer\u0026rsquo;s instructions for chemical lysis, incubation, RNA digestion, column equilibration, binding, flushing and washing, elution, precipitation, and resuspension. The purity and concentration of the DNA were assessed using a NanoDrop spectrophotometer. DNA quality was further verified by electrophoresis on a 1% agarose gel.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eHiFi SMRTbell Library Construction and Sequencing\u003c/h3\u003e\n\u003cp\u003eThe initial evaluation of the quantity and size distribution of the purified gDNA was performed using the Agilent 2200 TapeStation Nucleic Acid System (G2965AA), operated with Agilent 2200 TapeStation Software A.01.05. Analysis was conducted using the Agilent Genomic DNA ScreenTape (5067\u0026ndash;5365) and Agilent Genomic DNA Reagents (5067\u0026ndash;5366), with samples drawn from a 96-well plate. The isolated high molecular weight (HMW) gDNA yielded a concentration of 96 ng/\u0026micro;l in a total volume of 150 \u0026micro;l. High molecular weight genomic DNA was sheared into 15\u0026ndash;25 kb fragments using the Megaruptor\u0026reg; 3 system (Diagenode, Cat# B06010003) according to the manufacturer\u0026rsquo;s specifications. An input of 66 ng/\u0026micro;l gDNA in a 30 \u0026micro;l volume was used for library preparation. HiFi SMRTbell libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences). Sequencing was performed on two SMRT cells, with the first SMRT cell producing 1,916,709 reads, while the second generated 1,775,843 reads. The raw sequence reads were assessed for quality using the default settings of FastQC version 0.11.5 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/\u003c/span\u003e\u003cspan address=\"https://www.bioinformatics.babraham.ac.uk/projects/fastqc/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e to determine the parameters for the subsequent filtering step. Filtering of the raw reads was performed using Fastp version 0.23.1\u003csup\u003e27\u003c/sup\u003e (parameters: --length_required 10000,--length_limit 30000, -f 15). The read length was set at an acceptable read length between 10 Kbp and 30 Kbp to enhance genome assembly performance. The filtered reads were merged, resulting in a total of 3,668,683 reads (99.36%).\u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eOmni-C Library Construction and Sequencing\u003c/h2\u003e \u003cp\u003eFrozen plant leaves (300 mg) were crushed into fine powder with a mortar and pestle in liquid nitrogen and transferred into a 50 mL Falcon tube. Formaldehyde (37% solution), PBS, and DSG were added to the ground tissue to facilitate chromatin crosslinking. After a series of washes, the enzyme mix was added to the sample for enzymatic digestion, followed by lysate QC assessment using the Tapestation D5000 kit (Agilent). The ideal fragment distribution is 100 to 2,500 bp for successful crosslinking and digestion. The next step involved performing proximity ligation by capturing the chromatin with chromatin capture beads, followed by end polishing and bridge ligation. Reverse crosslinking and DNA fragment purification were then performed. Post-DNA fragment purification and Illumina library prep (part of Dovetail Omni-C kits) were performed according to the manufacturer's protocol. For sequencing on the PacBio Onso system, the library was converted by adding PacBio A and P1 adapter sequences in a limited PCR cycle. Sequencing was performed on the PacBio Onso system using a 300-cycle kit (2\u0026times;150 bp), generating a total of 107,723,424 paired-end Omni-C reads. Quality control was conducted with FastQC (v0.11.3), and reads were filtered using fastp (v0.23.4) (parameters: \u003cem\u003e-\u003c/em\u003e-length_required 50 -f 14 -F 14). After filtering, 91,493,006 (98.5%) high-quality Omni-C reads were retained and used for genome scaffolding.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eGenome size and heterozygosity estimation\u003c/h3\u003e\n\u003cp\u003eTo estimate the genome size, heterozygosity, and ploidy of the white star apple genome, k-mer analysis was performed using high-quality filtered PacBio HiFi reads. The k-mer frequency distribution was generated using Jellyfish (v2.2.8)\u003csup\u003e28\u003c/sup\u003e (parameters: count -C -m 21 -s 1000000; histo). The resulting histogram was visualised with the default parameters of GenomeScope (v2.0)\u003csup\u003e29\u003c/sup\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). The analysis estimated the haploid genome size to be approximately 822 Mbp. The k-mer distribution displays a strong unimodal peak centered around a k-mer coverage of ~\u0026thinsp;60\u0026times;, representing the homozygous portion of the genome. A minor peak near ~\u0026thinsp;30\u0026times; coverage corresponds to a very small proportion of heterozygous k-mers. The ploidy level of the genome was estimated as diploid. The low heterozygosity rate of 0.317%, combined with a higher homozygosity, indicates that the white star apple genome is highly homozygous.\u003c/p\u003e\n\u003ch3\u003eGenome assembly\u003c/h3\u003e\n\u003cp\u003eFiltered HiFi sequence reads of approximately 75X genome coverage with an average read length of 16,951 bp were assembled \u003cem\u003ede novo\u003c/em\u003e using three assembly tools. Hifiasm v0.16.1-r375 (parameter: --primary), HiCanu v2.3 (parameters: -pacbio-hifi genomeSize=800m -useGrid=false -merylThreads\u0026thinsp;=\u0026thinsp;4 -merylMemory\u0026thinsp;=\u0026thinsp;8 corOverlapper\u0026thinsp;=\u0026thinsp;ovl), and Flye v2.9.6-b1802 (parameters: --pacbio-hifi --genome-size 800 m)\u003csup\u003e30\u0026ndash;32\u003c/sup\u003e. The genome statistics from the three assemblies were compared using the default settings of QUAST\u003csup\u003e\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e (v5.1.0rc1) (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eGenome assembly quality metrics\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003e\u003cb\u003eTotal length\u003c/b\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHiFiasm\u003c/p\u003e \u003cp\u003eassembly\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eHiCanu assembly\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eFlye assembly\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eHiFiasm assembly purged\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHiFiasm assembly purged (second round)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eHi-C scaffolded assembly\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eFinal assembly\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2,407,389,064\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2,832,626,671\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1,532,658,079\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003e901,469,050\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003e821,339,754\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003e821,384,454\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003e813,971,461\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003e#Contig/scaffold\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e7111\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e28200\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e26505\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1114\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e1023\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e596\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e586\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eN50\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e1,359,676\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e236,513\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e106,680\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3,005,615\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e3,111,027\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e57,681,698\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e57,681,045\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eL50\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e454\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1707\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e3420\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e95\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e84\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eN90\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e147,003\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e35,005\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e27,602\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e683,202\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e778,075\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e30,446,293\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e46,682,311\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eL90\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e2353\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e16719\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e14831\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e322\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e280\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eGaps\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e1153\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e146\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eOn the basis of the N50 value and the number of contigs, we selected the hifiasm primary assembly. This assembly had an N50 of 1.3 Mbp and the fewest number of contigs (7,111), making it the most contiguous draft genome among the outputs of the three assemblers. However, its total size of the draft genome was larger than the estimated genome size, likely due to a high level of duplication (87.6%) (Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). We implemented a two-round purging strategy using the purge_dups pipeline\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e. First, PacBio clean HiFi reads were aligned to the draft primary assembly using Minimap2 (v2.24-r1122)\u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e, and coverage statistics along with cutoff thresholds were computed to inform the purging process. The assembly was then split and self-aligned with Minimap2 to identify and remove redundant haplotigs. The final purged genome (draft genome) had an N50 of 3.1 Mbp and a total size of 821 Mbp and was subsequently used for scaffolding.\u003c/p\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eOmni-C scaffolding, manual curation and gap filling\u003c/h2\u003e \u003cp\u003eA chromosome-scale assembly comprising thirteen chromosomes was constructed by integrating Omni-C data with the contig-level draft assembly, followed by manual curation and gap filling (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea). Filtered high-quality paired-end Omni-C reads were aligned to the draft genome using bwa (v0.7.19-r1273)\u003csup\u003e\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e\u003c/sup\u003e (parameters: mem -SP -T0). The resulting alignments were processed using the pairtools (v1.1.2)\u003csup\u003e37\u003c/sup\u003e, which performed parsing, sorting, duplicate marking, and splitting of read pairs to generate a contact map. The final alignment file was sorted and indexed using samtools (v1.15.1)\u003csup\u003e38\u003c/sup\u003e and was used for scaffolding with YaHS (v1.2.2)\u003csup\u003e39\u003c/sup\u003e with default parameters, which incorporated the proximity ligation data to reorder and orient contigs into scaffolds. YaHS\u0026rsquo;s alignment matrix was subsequently converted into a contact map in pairs format using PretextMap (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/sanger-tol/PretextMap\u003c/span\u003e\u003cspan address=\"https://github.com/sanger-tol/PretextMap\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) (parameters: --sortby length --sortorder descend --mapq 0), which was then visualized in PretextView (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/sanger-tol/PretextView\u003c/span\u003e\u003cspan address=\"https://github.com/sanger-tol/PretextView\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) for manual curation. The PretextView enabled inspection of Omni-C read contact patterns against the scaffolds, allowing correction of mis-assemblies and refinement of scaffold anchoring and orientation into chromosome-scale pseudomolecules, guided by the genomic proximity signal of the Omni-C data.\u003c/p\u003e \u003cp\u003eTo reduce assembly fragmentation, gaps introduced during scaffolding and manual curation were filled using LR_GapCloser\u003csup\u003e\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u003c/sup\u003e. LR_Gapcloser employs a tiling path-based approach by fragmenting long reads into short tags and aligning them using bwa (v0.7.19-r1273) to the assembly to identify and fill gaps. Before gap filling, the curated genome contained 1,153 gaps. Using default parameters, LR_Gapcloser reduced the number of gaps to 146. The final chromosome-scaled genome had an improved contiguity of N50 value of 57 Mbp and an L90 value of 12 (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eGenome annotation\u003c/h2\u003e \u003cdiv id=\"Sec13\" class=\"Section3\"\u003e \u003ch2\u003eTransposable Elements (TE) annotation\u003c/h2\u003e \u003cp\u003eThe repeat landscape of \u003cem\u003eG. albida\u003c/em\u003e was characterized and annotated using Extensive \u003cem\u003ede novo\u003c/em\u003e TE Annotator (EDTA) v2.2.2\u003csup\u003e41\u003c/sup\u003e (parameters: \u0026ndash;genome \u0026ndash;overwrite 1 \u0026ndash;sensitive 1 \u0026ndash;anno 1 \u0026ndash;evaluate 1). This pipeline integrates structure-based and homology-based approaches to detect primary TEs within the assembled genome. It employs a combination of specialized tools, including HelitronScanner, LTR_FINDER, LTRHarvest, LTR_retriever, TIR-Learner, RepeatModeler2, and RepeatMasker, to classify and annotate novel TE sequences\u003csup\u003e\u003cspan additionalcitationids=\"CR43 CR44 CR45 CR46\" citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e\u003c/sup\u003e. The repeats accounted for 58.62% of the genome. EDTA was able to categorise the repeats into major categories such as LTR transposons (38.97%), LINE transposons (4.22%), TIR (6.93%), nonTIR (4,71%), nonLTR (0.41%) and other repeats (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ea). LTR transposons were the most abundant repeats identified across the genome (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eb). After repeat identification and annotation, the genome was soft-masked using the \u003cem\u003emake_masked.pl\u003c/em\u003e utility from the EDTA pipeline, and the masked genome was subsequently used for gene prediction.\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eGene Prediction and Functional Annotation\u003c/h2\u003e \u003cp\u003eGene prediction was performed using BRAKER (v2.0)\u003csup\u003e48\u003c/sup\u003e, which integrates ab initio predictions from AUGUSTUS\u003csup\u003e\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e\u003c/sup\u003e with evidence of external homologous proteins. The protein evidence was sourced from the Viridiplantae dataset in OrthoDB version 11\u003csup\u003e50\u003c/sup\u003e. The protein dataset was processed for compatibility with the BRAKER2 pipeline. BRAKER2 predicted 75,057 gene models (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). The functional information was then transferred onto the protein coding models, interrogating the eggNOG database (v5.0.2) using eggNOG-mapper (v2.1.12) and the InterPro member databases using InterProScan\u003csup\u003e\u003cspan additionalcitationids=\"CR52 CR53\" citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e\u003c/sup\u003e(v5.66-98.0). As a final step, the annotated clusters of orthologous groups (COGs) from eggNOG, the resulting InterProScan outputs and the original gene models from BRAKER2 were parsed to funannotate annotate\u003csup\u003e\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e\u003c/sup\u003e (v1.8.1) (parameters: --eggnog, --iprscan and \u0026ndash;gff) for final functional annotation in the form of a gff3 file.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eAnnotation counts and gene models supported with functional annotation\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"2\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eFeature\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCount\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eGenes\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e75,057\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eCDS complete\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e81,156\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eTotal exons\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e292,568\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eTotal introns\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e211,405\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eTotal protein\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e81,163\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eNumber of genes with GO terms\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e33,767\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eNumber of genes with InterProScan annotations\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e48,771\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eNumber of genes with eggnog annotations\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e61,085\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eNumber of genes with Pfam annotations\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e38,601\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eNumber of genes with Cazyme annotations\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e1,504\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec15\" class=\"Section2\"\u003e \u003ch2\u003eData Records\u003c/h2\u003e \u003cp\u003eThe raw PacBio HiFi reads and Omni-C reads used for the assembly are available from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under the BioProject PRJNA1255872 with accession numbers SRR33323859\u003csup\u003e56\u003c/sup\u003e and SRR33422445\u003csup\u003e57\u003c/sup\u003e, respectively. The genome has been submitted under the same BioProject with the accession number JBNXVW000000000\u003csup\u003e58\u003c/sup\u003e. The genome annotation files are uploaded to Zenodo\u003csup\u003e\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003eTechnical Validation\u003c/h2\u003e \u003cp\u003eTo assess the accuracy and completeness of the white star apple genome assembly, we conducted a Benchmarking Universal Single-Copy Orthologs (BUSCO)\u003csup\u003e\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e\u003c/sup\u003e analysis using the eudicots lineage dataset. This analysis identified 2,267 complete BUSCO genes out of 2,326, indicating a genome completeness of 97.5% (Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). We aligned clean PacBio HiFi reads to the final assembly using Minimap2 to evaluate assembly accuracy, yielding a mapping rate of 99.29%. Additionally, a \u003cem\u003ek-mer-\u003c/em\u003ebased quality assessment using merqury\u003csup\u003e\u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e61\u003c/span\u003e\u003c/sup\u003e (v1.3) (\u003cem\u003ek-mer\u003c/em\u003e\u0026thinsp;=\u0026thinsp;21) produced a quality value (QV) score of 58.14 and a k-mer completeness of 88.10% (Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). These assessments confirmed the high quality and completeness of the white star apple genome assembly.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eBUSCO assessment of the \u003cem\u003eG.albida\u003c/em\u003e genome assembly\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"5\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e\u0026nbsp;\u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003eDraft assembly\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eFinal assembly\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNumber\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003ePercent (%)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eNumber\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003ePercent (%)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eComplete BUSCOs (C)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2296\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e98.7%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2267\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e97.5%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eComplete and single-copy BUSCOs (S)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e258\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e11.1%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2124\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e91.3%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eComplete and duplicated BUSCOs (D)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2038\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e87.6%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e143\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e6.1%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eFragmented BUSCOs (F)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0.4%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0.3%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eMissing BUSCOs (M)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e21\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0.9%\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e51\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e2.2%\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eTotal BUSCO groups searched\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003e2326\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e2326\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab4\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eQuality value scores of the \u003cem\u003eG.albida\u003c/em\u003e genome assembly\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"3\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eQuality Value (QV) score\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eK-mer completeness\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eWhite star apple genome\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e58.1437\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e88.1048\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e "},{"header":"Declarations","content":"\u003cp\u003e \u003ch2\u003eCompeting interests\u003c/h2\u003e \u003cp\u003eK.B., A.M., and L.A.A. are employees of Inqaba Biotec (Nigeria and South Africa). The remaining authors declare no competing interests.\u003c/p\u003e \u003c/p\u003e\u003ch2\u003eFunding\u003c/h2\u003e \u003cp\u003eDeclaration\u003c/p\u003e \u003cp\u003eThis work was supported by no external funding.\u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eL.A.A. conceived the overall project idea and led the project. A.O.A. and A.G.A. conducted the literature review and produced the manuscript's first draft. T.R.O, A.D.A and A.G.A. handled sample collections of the plant materials. L.A.A., A.O.M. T.R.O., A.G.A., and T.E.E. carried out ethical compliance functions/consultations. A.M. T.R.O and K.B. carried out library preparation and sequencing involving long and short reads. M.L. and A.G. performed the sequence quality check and assembly. M.L., A.G, S.M. and T.E.E advised ways to improve overall genome quality, assembly, and completion. S.M. performed manual genome curation. L.O. conducted the genome annotation workflow and Y.A.B.Z generated the circos plot diagram. L.A.A., T.E.E., A.G., and S.M. provided overall supervision throughout the analysis. All authors reviewed, edited, and approved the final manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eThe sequencing data were generated with funding from the Malimbe Foundation and Inqaba Biotec West Africa. Computational resources for genome assembly and annotation, including storage and processing, were provided by the IITA Bioinformatics Unit. IITA Forest Center granted permission for collecting leaf samples. The African BioGenome Project (AfricaBP) contributed to project coordination, implementation, and ELSI guidance as well as negotiating sponsorship for Omni-C sequencing. We would like to thank Inqaba Biotec West Africa, IITA, and SolveLean for sponsoring capacity-building training as part of the ethical and permit approval process described in the ethics section of this work. The authors thank Zahra Mungloo-Dilmohamud, University of Mauritius, Mauritius, Adetutu E. Olumeh, Inqaba Biotec West Africa, and Uchenna N. Urom, Inqaba Biotec West Africa for their assistance in editing the initial manuscript draft. Thanks to Sally Katee Mueni, International Livestock Research Institute (ILRI), Nairobi, Kenya, and Marietjie Botes, School of Law, University of KwaZulu-Natal, Durban, South Africa and University of Texas at Austin, Austin, United States for reviewing the ethics of this work and providing feedback. We thank Laurent Falquet from the University of Fribourg for his contributions to discussions on the genome assembly.\u003c/p\u003e\u003ch2\u003eData Availability\u003c/h2\u003e\u003cp\u003eThe raw PacBio HiFi reads and Omni-C reads used for the assembly are available from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under the BioProject PRJNA1255872 with accession numbers SRR3332385956 and SRR3342244557, respectively. The genome has been submitted under the same BioProject with the accession number JBNXVW00000000058. 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Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. \u003cem\u003eGenome Biol\u003c/em\u003e 21, 245 (2020). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org:10.1186/s13059-020-02134-9\u003c/span\u003e\u003cspan address=\"https://doi.org:10.1186/s13059-020-02134-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":true,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-9271727/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9271727/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eWhite star apple (\u003cem\u003eGambeya albida\u003c/em\u003e) is native to the lowland rainforests of Central, East, and West Africa. This species is highly valued for its nutritious fruits and offers medicinal, socio-cultural, and economic benefits. In West Africa, it contributes to food security for rural and urban communities alike. However, no genomic resources are available to untap the agronomic and medicinal traits of the white star apple. Here, we present its first chromosome-scale genome, generated using PacBio HiFi and Omni-C sequencing. The star apple genome is highly homozygous (0.317%), and we assembled 98.9% of the estimated haploid genome size (822 Mb) into 13 pseudochromosomes. It has a base-level accuracy (QV) of 58.14, an N50 of 57 Mbp, and 97.5% BUSCO completeness, representing a reference-quality assembly. About 58.5% of the genome constitutes repetitive sequences, and homology-based prediction identified 75,057 gene models. This reference-quality genome of the white star apple will serve as a valuable resource to enhance our understanding of its underlying nutritional and pharmacological traits and facilitate improvement research.\u003c/p\u003e","manuscriptTitle":"Chromosome-scale genome assembly and annotation of the white star apple (Gambeya albida)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-04-08 06:32:57","doi":"10.21203/rs.3.rs-9271727/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"5f4fc4b7-03a6-43e1-bdce-4d9603eae83e","owner":[],"postedDate":"April 8th, 2026","published":true,"recentEditorialEvents":[{"type":"editorInvitedReview","content":"","date":"2026-05-07T08:51:49+00:00","index":36,"fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-05-06T11:37:57+00:00","index":35,"fulltext":""},{"type":"reviewerAgreed","content":"92101408296520702799464609453221654947","date":"2026-04-29T09:50:02+00:00","index":33,"fulltext":""}],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-04-15T10:53:17+00:00","versionOfRecord":[],"versionCreatedAt":"2026-04-08 06:32:57","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9271727","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9271727","identity":"rs-9271727","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}