Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships

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However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa, Protium javanicum, and Dysoxylum mollissimum. Additional tools such as molecular approaches can be used to verify whether it is true or not that Kayu bawang is scientifically named as Azadirachta excelsa based on previous morphological identification. This study aimed to construct draft chloroplast genome and verify the scientific name based on molecular identification using a single rbcL gene marker. Genomic DNA was extracted from bark cambium originated from three different provenances in Bengkulu, Indonesia, namely TBT-A, TBT-K, and TBT-S. MinION from Oxford Nanopore Technologies was used to sequence the samples following manufacture protocols SQK-LSK109 yielding 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S, respectively. Generated data were assembled and constructed, namely 58,780 bp (14 tRNAs and 47 encoding genes) for TBT-A, 142,139 bp (4 rRNAs, 24 tRNAs, and 78 encoding genes) for TBT-K, and 84,906 bp (24 tRNAs and 53 encoding genes) for TBT-S. Based on the phylogenetic tree, Azadirachta excelsa from three identified tree stands were placed in the same group with other Azadirachta excelsa accessions." } { "@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/13-254/v1", "name": "Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs)..." } } ] } Home Browse Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs)... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Depari EK, Wijayanto N, Karlinasari L et al. Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.12688/f1000research.144155.1 ) 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 Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] Efratenta Katherina Depari https://orcid.org/0009-0000-3270-6786 1,2 , Nurheni Wijayanto 3 , Lina Karlinasari 4 , Mohamad Rafi 5,6 , Iskandar Zulkarnaen Siregar https://orcid.org/0000-0003-0278-5887 3,5 Efratenta Katherina Depari https://orcid.org/0009-0000-3270-6786 1,2 , Nurheni Wijayanto 3 , [...] Lina Karlinasari 4 , Mohamad Rafi 5,6 , Iskandar Zulkarnaen Siregar https://orcid.org/0000-0003-0278-5887 3,5 PUBLISHED 05 Apr 2024 Author details Author details 1 Department of Forestry, Faculty of Agriculture, University of Bengkulu, Bengkulu, Bengkulu, 38371, Indonesia 2 Tropical Silviculture Study Program, Faculty of Forestry and Environment, IPB University, Bogor, West Java, 16680, Indonesia 3 Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, West Java, 16680, Indonesia 4 Department of Forest Product, Faculty of Forestry and Environment, IPB University, Bogor, West Java, 16680, Indonesia 5 Advanced Research Laboratory, IPB University, Bogor, West Java, 16680, Indonesia 6 Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, West Java, 16680, Indonesia Efratenta Katherina Depari Roles: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Resources, Visualization Nurheni Wijayanto Roles: Investigation, Supervision, Writing – Review & Editing Lina Karlinasari Roles: Supervision, Validation, Writing – Review & Editing Mohamad Rafi Roles: Resources, Supervision, Writing – Review & Editing Iskandar Zulkarnaen Siregar Roles: Conceptualization, Funding Acquisition, Methodology, Resources, Supervision, Validation, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Plant Science gateway. This article is included in the Genomics and Genetics gateway. This article is included in the Nanopore Analysis gateway. Abstract Abstract* Azadirachta excelsa (Jack) Jacobs, Kayu bawang (Meliaceae) is economically valuable and widely used by the local community in Bengkulu (Sumatra) as carpentry and construction wood because of its good durability class. However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa , Protium javanicum , and Dysoxylum mollissimum. Additional tools such as molecular approaches can be used to verify whether it is true or not that Kayu bawang is scientifically named as Azadirachta excelsa based on previous morphological identification. This study aimed to construct draft chloroplast genome and verify the scientific name based on molecular identification using a single rbc L gene marker. Genomic DNA was extracted from bark cambium originated from three different provenances in Bengkulu, Indonesia, namely TBT-A, TBT-K, and TBT-S. MinION from Oxford Nanopore Technologies was used to sequence the samples following manufacture protocols SQK-LSK109 yielding 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S, respectively. Generated data were assembled and constructed, namely 58,780 bp (14 tRNAs and 47 encoding genes) for TBT-A, 142,139 bp (4 rRNAs, 24 tRNAs, and 78 encoding genes) for TBT-K, and 84,906 bp (24 tRNAs and 53 encoding genes) for TBT-S. Based on the phylogenetic tree, Azadirachta excelsa from three identified tree stands were placed in the same group with other Azadirachta excelsa accessions. READ ALL READ LESS Keywords Azadirachta excelsa, chloroplast genome, identification, identified seed stand, long-reads, phylogenetics, gene marker Corresponding Author(s) Iskandar Zulkarnaen Siregar ( [email protected] ) Close Corresponding author: Iskandar Zulkarnaen Siregar Competing interests: No competing interests were disclosed. Grant information: Beasiswa Pendidikan Pascasarjana Dalam Negeri (BPPDN) 2019 Copyright: © 2024 Depari EK 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: Depari EK, Wijayanto N, Karlinasari L et al. Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.12688/f1000research.144155.1 ) First published: 05 Apr 2024, 13 :254 ( https://doi.org/10.12688/f1000research.144155.1 ) Latest published: 05 Apr 2024, 13 :254 ( https://doi.org/10.12688/f1000research.144155.1 ) Introduction Azadirachta excelsa (Jack) Jacobs or known as Kayu bawang (Meliaceae) is a main local wood in Bengkulu Province that is cultivated in private forests, mainly found in North Bengkulu and Central Bengkulu Districts ( Depari et al . 2015 ; Siahaan & Sumadi 2015 ). Kayu bawang has been used for carpentry wood. Historically, this wood has been a favorite one of the local community as the primary material for building. In addition, the wood is also known for its resistance to attack by destructive organisms ( Krisdianto et al . 2015 ). Despite kayu bawang is widely used for building wood and furniture, but some references are still ambiguous with respect to its scientific naming. Some references mentioned the naming of kayu bawang tree in Bengkulu as Protium javanicum Burm F ( Adfa et al . 2013 ). In some other references, kayu bawang is named differently such as Dysoxylum mollissimum Blume ( Ishiguri et al . 2016 ), Azadirachta excelsa (Jack) M Jacobs ( Premono & Lestari 2014 ). In addition, in the identified seed stand (TBT) in Bengkulu as registered under No. 002/BPSMBK/SSB/2016, No. 001/BPTH.I-3/SSB/2016, and No. 006/P2STH/SSB/2018, kayu bawang is named respectively as Azadirachta exelsa , Dysoxylum molissimum , and Melia excelsa (synonym of Azadirachta excelsa ). Based on morphological identification on Herbarium Bogoriense under National Research and Innovation Agency (BRIN), kayu bawang has been confirmed as Azadirachta excelsa (Jack) Jacobs. We used three specimens from different identified seed stands, namely TBT-A, TBT-K, and TBT-S, that were collected with the specimen numbers BO1991351 (TBT-A), BO1991352;1991353;1991354 (TBT- K), and BO1991350 (TBT-S) for genome sequencing using Oxford Nanopore Technologies. The objectives of the research were to assembly long-read DNA sequences and to construct a phylogeny for verifying species identification. Methods Genomic DNA was extracted from kayu bawang ( Azadirachta excelsa ) cambium samples which were taken from three different identified seed stands namely Talang Boseng (TBT-A, -3.66890°S, 102.292122°E), Batu Ampar (TBT-K, -4.394333°S, 103.138056°E), and Penyangkak (TBT-S, -3.531333°S, 102.252861°E) in Bengkulu Province, Indonesia. The modified CTAB (cetyl trimethyl ammonium bromide) method was used to extract the genomic DNA from each A. excelsa cambium ( Doyle & Doyle 1987 ). The DNA extract buffer contained 200 μL of 10% CTAB (CAT NO. 194004, LOT NO. QR15741, MP Biomedicals, LLC), 100 μL of 1 M Tris-HCL, 280 μL of 5M NaCl, 40 μL of 0.5 M EDTA, 100 μL of 1% PVP, 280 μL of aquades. 0.1 g cambium mashed using mortar milling was put into a 2 mL tube, 1000 μL of DNA extract buffer that had been incubated at 65°C (60 min), 40 μL of 26% PVP, and 40 μL of β-Mercaptoethanol. The mixture was homogenized using a vortex and subsequently incubated at 65°C (60 min) with rehomogenization performed every 10 min by gently flipping the tube. The cooled mixture was centrifuged for 10 min, at 10,000 rpm. The supernatant was transferred to a 1.5 mL tube, and 500 μL of chloroform: isoamyl alcohol solution (24:1) and 10 μL of phenol were added and centrifuged for 10 min, at 10,000 rpm. Separation of the mixture was done again by adding 500 μL of chloroform: isoamyl alcohol solution (24:1). The obtained supernatant was put into a 1.5 mL tube, then 500 μL cold isopropanol and 250 μL NaCl were added. The mixture was stored in a freezer at 4°C for 1 day so that the DNA precipitation process occurring. After DNA precipitation, the mixture was centrifuged for 10 min, at 10,000 rpm. The mixture was removed gradually to retrieve the DNA pellet. DNA pellet washing using 500 μL of 70% ethanol, centrifuged for 10 min, at 10,000 rpm. The DNA pellet was separated from the mixture and dried in a desiccator containing silica gel (±20 min). 50 μL of TE RNAse buffer was added to dissolve the DNA pellet. The quality of extracted genomic DNA was evaluated using 1% agarose gel electrophoresis. The quality and quantity of the extracted genomic DNA were measured using NanoPhotometer ® NP80 (IMPLEN) and Qubit 1.0 Fluorometer (Thermo Fisher Scientific) with the Qubit dsDNA BR assay kit. The library preparation of long-read sequencing was performed using Oxford Nanopore Technologies (ONT) manufactured protocol SQK-LSK109 version NBE_9065_v109_revZ_14Aug2019 with the MinION R9.4.1 flow cell (FLO-MIN106D, LOT 11001352) on a MinION Mk1C sequencer (Oxford Nanopore Technologies). The chloroplast genome assembly for TBT-A, TBT-K, and TBT-S (Accession number DRA015537; https://ddbj.nig.ac.jp/resource/bioproject/PRJDB14301 ) ( IPB University 2023 ) was performed using Galaxy Server ( https://usegalaxy.eu/ , RRID: SCR_006281, MIT License) v.23.1.1.dev0 following long-read data with some modifications ( Wang et al . 2018 ). Long-read data for each sample was quality checked using NanoPlot ( https://usegalaxy.eu/ , RRID:SCR_024128, MIT License) v1.41.0 ( De Coster et al . 2018 ). Those clean reads data were aligned with the reference NC_023792.1 ( Azadirachta indica ) using Minimap2 ( https://usegalaxy.eu/ , RRID:SCR_018550, MIT License) v.2.26 ( Li 2018 ) and SAMTools ( https://usegalaxy.eu/ , RRID:SCR_002105, MIT License) v.2.05 ( Li et al . 2009 ). Chloroplast reads were assembled using Canu Assembler ( https://usegalaxy.eu/ , RRID:SCR_015880, GPLv2 and others) v.2.1.1+galaxy0 ( Koren et al . 2017 ) involving parameters such as technology Nanopore, estimated genome size 160k, and min read length 1000. Medaka Consensus Pipeline ( https://usegalaxy.eu/ , RRID:SCR_005857, Mozilla Public License 2.0) v1.7.2+galaxy1 was used to polish the assembly result ( Oosterbroek et al. 2021 ). Geseq ( https://chlorobox.mpimp-golm.mpg.de/geseq.html , RRID:SCR_017336, MIT License) ( Tillich et al . 2017 ) was used to annotate the assembled chloroplast genome using all Meliaceae reference in NCBI RefSeq and visualized using OGDRaw ( https://chlorobox.mpimp-golm.mpg.de/OGDraw.html , RRID:SCR_017337, MIT License) in the CHLOROBOX ( https://chlorobox.mpimp-golm.mpg.de/index.html , MIT License) ( Greiner et al . 2019 ). Phylogenetic analysis was performed using MEGAX ( https://www.megasoftware.net/ , RRID:SCR_023471, MIT License) v10.2.2 ( Kumar et al . 2018 ) with Maximum Likelihood method, Tamura-3 model and bootstrap value of 1000 replications. rbc L gene marker was used to construct the phylogenetic tree from TBT-A, TBT-K, and TBT-S samples ( Owenia vernicocsa (DQ238063.1) as an outgroup) ( Muellner et al . 2006 ). Results The library yielded 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S. Based on the statistics, TBT-A has 3,339 bp of N50, 3,103 bp for TBT-K, and 3,882 bp for TBT-S ( Figure 1 ). Chloroplast draft genomes of the TBT-A sample (36% GC content) produces 58,780 bp containing 14 tRNAs and 47 encoding genes, TBT-K sample (37% GC content) produced 142,139 bp containing 4 rRNAs, 24 tRNAs, and 78 encoding genes, also TBT-S sample (36% GC content) produced 84,906 bp containing 24 tRNAs and 53 encoding genes ( Table 1 ). Based on the constructed phylogenetic tree, Azadirachta excelsa from three identified tree stands (TBT-A, TBT-K, and TBT-S) were placed in the same group with other Azadirachta excelsa accessions ( Figure 2 ). We can confirm that all those samples belong to Azadirachta excelsa. Figure 1. Chloroplast draft genome of Azadirachta excelsa (TBT-A, TBT-K, and TBT-S samples). Table 1. List of genes in the chloroplast draft genomes of Azadirachta excelsa. Gene groups TBT-A genes TBT-K genes TBT-S genes RNAs transfer trn D-GUC, trn E-UUC, trn F-GAA, trn G-GCC, t rn L-UAA * , trn M-CAU, trn P-UGG, trn S-GGA, trn S-UGA, trn T-GGU, trn T-UGU, trn V-UAC * , trn W-CCA, trn Y-GUA trn A-UGC * , trn C-GCA, trn D-GUC, trn E-UUC d * , trn F-GAA, trn G-GCC, trn H-GUG, trn K-UUU * , trn L-CAA, trn L-UAA * , trn L-UAG, trn M-CAU, trn N-GUU, trn P-UGG, trn Q-UUG, trn R-ACG, trn R-UCU, trn S-CGA d * , trn T-GGU, trn T-UGU, trn V-GAC, trn V-UAC d * , trn W-CCA, trn Y-GUA trn C-GCA, trn D-GUC, trn E-UUC d , trn F-GAA, trn fM-CAU, trn G-GCC * , trn H-GUG, trn I-CAU, trn K-UUU * , trn L-UAA * , trn M-CAU, trn P-GGG, trn P-UGG, trn Q-UUG, trn R-UCU, trn S-CGA * , trn S-GCU, trn S-GGA, trn S-UGA, trn T-GGU, trn T-UGU d , trn V-UAC * , trn V-fragment, trn W-CCA, trnY-GUA RNAs ribosomal rrn 4.5, rrn 5, rrn 5-fragment, rrn 16, rrn 23 Small subunit ribosomal proteins (SSU) rps 3, rps 4, rps 8, rps 11, rps 12-fragment, rps 14, rps 18, rps 19 rps 2, rps 3, rps 4, rps 7, rps 8, rps 11, rps 12 * , rps 14, rps 15, rps 16 * , rps 18, rps 19 rps 2, rps 4, rps 12, rps 12-fragment, rps 14, rps 16 d * , rps 18, rps 19 Large subunit ribosomal proteins (LSU) rpl 2 * , rpl 14, rpl 16 * , rpl 20, rpl 22, rpl 23, rpl 33, rpl 36 rpl 2 d * , rpl 14, rpl 16 * , rpl 20, rpl 22, r pl 23, rpl 32, rpl 33, rpl 36 rpl 2 d * , rpl 20, rpl 22, rpl 23, rpl 33 RNA polymerase rpo A rpo A, rpo B, rpo C2, rpo C1 * rpo B, rpo C1 * , rpo C2 ATP synthase atp B, atp E atp A, atp B, atp E, atp F * , atp H, atp I atp A, atp B, atp E, atp F d * , atp H, atp I Subunit of Photosystem I psa A, psa B, psa I, psa J psa A, psa B, psa C, psa I, psa J psa A, psa B, psa I, psa J Subunit of Photosystem II psb B, psb C, psb D, psb E, psb F, psb H, psb J, psb L, psb T, psb Z psb A, psb B, psb C, psb D, psb E, psb F , psb H, psb I, psb J, psb K, psb L, psb M, psb T, psb Z psb A, psb B, psb C, psb D, psb E, psb F, psb I, psb J, psb K, psb L, psb M, psb Z Subunit of rubisco rbc L rbc L rbc L NADH dehydrogenase ndh C, ndh J, ndh K ndh A * , ndh B * , ndh C, ndh D, ndh E, ndh F, ndh G, ndh H, ndh I, ndh J, ndh K, ndh C, ndh J, ndh K Subunit of cytochrome b/f complex pet A, pet B * , pet D * , pet G, pet L pet A, pet B * , pet D * , pet G, pet L, pet N pet A, pet G, pet L, pet N Photosystem assembly factors paf I * * , paf II paf II, paf I * * paf I d ** , paf II Cytochrome c synthesis ccs A Photosystem biogenesis factor pbf 1 pbf 1 Transitional initiation factor inf A inf A ATP-dependent protease subunit P clp P1 ** clp P1 ** clp P1 ** Fatty metabolic acid acc D acc D acc D Carbon metabolism cem A cem A cem A Maturase mat K mat K Conserved open reading frames ycf 1, ycf 2 ycf 2 d Gene duplication. * Single intron. ** Double intron. Figure 2. Phylogenetic tree based on Maximum Likelihood method. GenBank accession numbers are listed beside the scientific name. The bootstrap value of 1000 replications is shown next to the nodes. Azadirachta excelsa (TBT-A, TBT-K, and TBT-S samples) are marked in coloring red. Author roles Efratenta Katherina Depari : Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Resources, Visualization, Writing-Original Draft; Nurheni Wijayanto : Investigation, Supervision, Writing-Review & Editing; Lina Karlinasari : Supervision, Validation, Writing-Review & Editing; Rafi M : Resources, Supervision, Writing-Review & Editing; Iskandar Zulkarnaen Siregar : Conceptualization, Funding Acquisition, Methodology, Resources, Supervision, Validation, Writing-Review & Editing. Data availability Underlying data DNA Data Bank of Japan (DDBJ): Characterization of kayu bawang in agroforestry system in Bengkulu: species name, wood quality, and metabolite profile. Accession number DRA015537; https://ddbj.nig.ac.jp/resource/bioproject/PRJDB14301 ( IPB University 2023 ). This project contains the following underlying data: • DRR437487 (TBT-A). • DRR437488 (TBT-K). • DRR437489 (TBT-S). Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0). Software availability statement Galaxy server available from: https://usegalaxy.eu/ (MIT license). CHLOROBOX available from: https://chlorobox.mpimp-golm.mpg.de/index.html (MIT license). MEGAX available from: https://www.megasoftware.net/ (MIT license). Acknowledgements Special thanks to the Forest Genetics and Molecular Forestry Laboratory, Department of Silviculture, Faculty of Forestry and Environment, IPB University and Molecular Science Laboratory, Advanced Research Laboratory, IPB University, Bogor, Indonesia, for providing lab facilities during this study. References Adfa M, Hattori Y, Ninomiya M, et al. : Chemical constituents of Indonesian plant Protium javanicum Burm. f. and their antifeedant activities against Coptotermes formosanus Shiraki. Nat. Prod. Res. 2013; 27 (3): 270–273. PubMed Abstract | Publisher Full Text De Coster W, D’Hert S, Schultz DT, et al. : NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018; 34 (15): 2666–2669. PubMed Abstract | Publisher Full Text | Free Full Text Depari EK, Wiryono W, Susatya A: Potensi tegakan kayu bawang ( Dysoxylum mollissimum Blume) pada sistem agroforestri sederhana di Kabupaten Bengkulu Utara. Jurnal Hutan Tropis. 2015; 3 (2). 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PubMed Abstract | Publisher Full Text | Free Full Text Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 05 Apr 2024 ADD YOUR COMMENT Comment Author details Author details 1 Department of Forestry, Faculty of Agriculture, University of Bengkulu, Bengkulu, Bengkulu, 38371, Indonesia 2 Tropical Silviculture Study Program, Faculty of Forestry and Environment, IPB University, Bogor, West Java, 16680, Indonesia 3 Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, West Java, 16680, Indonesia 4 Department of Forest Product, Faculty of Forestry and Environment, IPB University, Bogor, West Java, 16680, Indonesia 5 Advanced Research Laboratory, IPB University, Bogor, West Java, 16680, Indonesia 6 Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, West Java, 16680, Indonesia Efratenta Katherina Depari Roles: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Resources, Visualization Nurheni Wijayanto Roles: Investigation, Supervision, Writing – Review & Editing Lina Karlinasari Roles: Supervision, Validation, Writing – Review & Editing Mohamad Rafi Roles: Resources, Supervision, Writing – Review & Editing Iskandar Zulkarnaen Siregar Roles: Conceptualization, Funding Acquisition, Methodology, Resources, Supervision, Validation, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information Beasiswa Pendidikan Pascasarjana Dalam Negeri (BPPDN) 2019 Article Versions (1) version 1 Published: 05 Apr 2024, 13:254 https://doi.org/10.12688/f1000research.144155.1 Copyright © 2024 Depari EK 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 Depari EK, Wijayanto N, Karlinasari L et al. Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.12688/f1000research.144155.1 ) 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 05 Apr 2024 Views 0 Cite How to cite this report: Dwiyanti MS. Reviewer Report For: Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.5256/f1000research.157909.r269396 ) The direct URL for this report is: https://f1000research.com/articles/13-254/v1#referee-response-269396 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 09 May 2024 Maria Stefanie Dwiyanti , Laboratory of Applied Plant Genome, Hokkaido University, Sapporo, Japan Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.157909.r269396 This study sequenced three samples of Kayu bawang ( Azadirachta excelsa) obtained from three stands in Bengkulu Province, Indonesia. Since there is no genomic information about A. excelsa, this will help science community to use the information for sample authentication and further genetic ... Continue reading READ ALL This study sequenced three samples of Kayu bawang ( Azadirachta excelsa) obtained from three stands in Bengkulu Province, Indonesia. Since there is no genomic information about A. excelsa, this will help science community to use the information for sample authentication and further genetic analysis. The authors have provided detailed DNA extraction, sequencing and data analysis procedures to be replicated by others. Since the authors want to prove that Kayu bawang is indeed A. excelsa , I will suggest to add Protium and Dysoxylum rbcL sequences in the phylogenetic analysis to show that the difference between A. excelsa and the other two species. In addition, the chloroplast sequence sizes obtained from the three samples are different. If there is any estimated chloroplast genome sequence size for A. excelsa , or closely related species, the information can be added as estimation for the completeness of A. excelsa chloroplast genome sequences obtained in this study. 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: My research area is plant genetics especially soybean and wild soybean, analysis of whole genome sequence, genotyping-by-sequencing, and SNP genotyping, GWAS and QTL analysis using SNP data. 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 Dwiyanti MS. Reviewer Report For: Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.5256/f1000research.157909.r269396 ) The direct URL for this report is: https://f1000research.com/articles/13-254/v1#referee-response-269396 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: Do HDK. Reviewer Report For: Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.5256/f1000research.157909.r266729 ) The direct URL for this report is: https://f1000research.com/articles/13-254/v1#referee-response-266729 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 06 May 2024 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.157909.r266729 Dear Authors, Thank you very much for adding new genomic data of Azadirachta excelsa (Jack) Jacobs, generated by long-read sequencing method of Oxford Nanopore Technologies. The content of the manuscript is suitable for F1000research. Please check my ... Continue reading READ ALL Dear Authors, Thank you very much for adding new genomic data of Azadirachta excelsa (Jack) Jacobs, generated by long-read sequencing method of Oxford Nanopore Technologies. The content of the manuscript is suitable for F1000research. Please check my below comments. 1/ Why the chloroplast genomes of three samples were not completed? Please add some reason for this issue in the main text. 2/ There are several genes in the draft genomes. However, only rbcL was used for phylogenetic analysis. Please add the reason in the main text. 3/ In the Abstract, the authors mentioned that "However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa , Protium javanicum , and Dysoxylum mollissimum .". However, in the phylogenetic analysis, the authors used only " Azadirachta excelsa " for comparison. It is better if the authors add the data of Protium and Dysoxylum species to make a strong and reliable conclusion for the identification of three samples in this study. 4/ The draft genomes were constructed from three samples of one species. Therefore, the authors might add information about the pairwise identity of those genomes. Thank you. 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, Plant systematics. 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 Do HDK. Reviewer Report For: Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.5256/f1000research.157909.r266729 ) The direct URL for this report is: https://f1000research.com/articles/13-254/v1#referee-response-266729 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 Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 05 Apr 2024 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 Version 1 05 Apr 24 read read Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam Maria Stefanie Dwiyanti , Hokkaido University, Sapporo, Japan 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 © 2024 Dwiyanti M. 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. 09 May 2024 | for Version 1 Maria Stefanie Dwiyanti , Laboratory of Applied Plant Genome, Hokkaido University, Sapporo, Japan 0 Views copyright © 2024 Dwiyanti M. 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 study sequenced three samples of Kayu bawang ( Azadirachta excelsa) obtained from three stands in Bengkulu Province, Indonesia. Since there is no genomic information about A. excelsa, this will help science community to use the information for sample authentication and further genetic analysis. The authors have provided detailed DNA extraction, sequencing and data analysis procedures to be replicated by others. Since the authors want to prove that Kayu bawang is indeed A. excelsa , I will suggest to add Protium and Dysoxylum rbcL sequences in the phylogenetic analysis to show that the difference between A. excelsa and the other two species. In addition, the chloroplast sequence sizes obtained from the three samples are different. If there is any estimated chloroplast genome sequence size for A. excelsa , or closely related species, the information can be added as estimation for the completeness of A. excelsa chloroplast genome sequences obtained in this study. 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 My research area is plant genetics especially soybean and wild soybean, analysis of whole genome sequence, genotyping-by-sequencing, and SNP genotyping, GWAS and QTL analysis using SNP data. 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) Dwiyanti MS. Peer Review Report For: Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.5256/f1000research.157909.r269396) 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/13-254/v1#referee-response-269396 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Do 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. 06 May 2024 | for Version 1 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam 0 Views copyright © 2024 Do 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 Dear Authors, Thank you very much for adding new genomic data of Azadirachta excelsa (Jack) Jacobs, generated by long-read sequencing method of Oxford Nanopore Technologies. The content of the manuscript is suitable for F1000research. Please check my below comments. 1/ Why the chloroplast genomes of three samples were not completed? Please add some reason for this issue in the main text. 2/ There are several genes in the draft genomes. However, only rbcL was used for phylogenetic analysis. Please add the reason in the main text. 3/ In the Abstract, the authors mentioned that "However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa , Protium javanicum , and Dysoxylum mollissimum .". However, in the phylogenetic analysis, the authors used only " Azadirachta excelsa " for comparison. It is better if the authors add the data of Protium and Dysoxylum species to make a strong and reliable conclusion for the identification of three samples in this study. 4/ The draft genomes were constructed from three samples of one species. Therefore, the authors might add information about the pairwise identity of those genomes. Thank you. 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, Plant systematics. 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) Do HDK. Peer Review Report For: Long-read datasets of Kayu Bawang ( Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships [version 1; peer review: 2 approved with reservations] . F1000Research 2024, 13 :254 ( https://doi.org/10.5256/f1000research.157909.r266729) 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/13-254/v1#referee-response-266729 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. 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