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Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection
BACKGROUND: The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for th...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6652137/ https://www.ncbi.nlm.nih.gov/pubmed/31337332 http://dx.doi.org/10.1186/s12859-019-2859-5 |
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author | Ha, Jungmin Jeon, Ho Hwi Woo, Dong U. Lee, Yejin Park, Halim Lee, Joohyeong Kang, Yang Jae |
author_facet | Ha, Jungmin Jeon, Ho Hwi Woo, Dong U. Lee, Yejin Park, Halim Lee, Joohyeong Kang, Yang Jae |
author_sort | Ha, Jungmin |
collection | PubMed |
description | BACKGROUND: The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment. MAIN BODY: Here, we developed a web-application, “Soybean-VCF2Genomes”, http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix. CONCLUSION: The information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2859-5) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6652137 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-66521372019-07-31 Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection Ha, Jungmin Jeon, Ho Hwi Woo, Dong U. Lee, Yejin Park, Halim Lee, Joohyeong Kang, Yang Jae BMC Bioinformatics Research BACKGROUND: The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment. MAIN BODY: Here, we developed a web-application, “Soybean-VCF2Genomes”, http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix. CONCLUSION: The information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2859-5) contains supplementary material, which is available to authorized users. BioMed Central 2019-07-24 /pmc/articles/PMC6652137/ /pubmed/31337332 http://dx.doi.org/10.1186/s12859-019-2859-5 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Ha, Jungmin Jeon, Ho Hwi Woo, Dong U. Lee, Yejin Park, Halim Lee, Joohyeong Kang, Yang Jae Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection |
title | Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection |
title_full | Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection |
title_fullStr | Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection |
title_full_unstemmed | Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection |
title_short | Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection |
title_sort | soybean-vcf2genomes: a database to identify the closest accession in soybean germplasm collection |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6652137/ https://www.ncbi.nlm.nih.gov/pubmed/31337332 http://dx.doi.org/10.1186/s12859-019-2859-5 |
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