Eight soybean reference genome resources from varying latitudes and agronomic traits
Open Access
- 1 July 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Scientific Data
- Vol. 8 (1), 1-8
- https://doi.org/10.1038/s41597-021-00947-2
Abstract
Comparative analysis of multiple reference genomes representing diverse genetic backgrounds is critical for understanding the role of key alleles important in domestication and genetic breeding of important crops such as soybean. To enrich the genetic resources for soybean, we describe the generation, technical assessment, and preliminary genomic variation analysis of eight de novo reference-grade soybean genome assemblies from wild and cultivated accessions. These resources represent soybeans cultured at different latitudes and exhibiting different agronomical traits. Of these eight soybeans, five are from new accessions that have not been sequenced before. We demonstrate the usage of these genomes to identify small and large genomic variations affecting known genes as well as screening for genic PAV regions for identifying candidates for further functional studies.Funding Information
- Ministry of Science and Technology of the People's Republic of China (2016YFD0101900)
- Chinese Academy of Sciences Key Project (593-ZDRW-ZS-2019-2-02)
This publication has 51 references indexed in Scilit:
- Infernal 1.1: 100-fold faster RNA homology searchesBioinformatics, 2013
- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing dataNature Methods, 2013
- Multiple reference genomes and transcriptomes for Arabidopsis thalianaNature, 2011
- Whole-genome sequencing and intensive analysis of the undomesticated soybean ( Glycine soja Sieb. and Zucc.) genomeProceedings of the National Academy of Sciences of the United States of America, 2010
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationNature Biotechnology, 2010
- TopHat: discovering splice junctions with RNA-SeqBioinformatics, 2009
- LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposonsNucleic Acids Research, 2007
- Identifying bacterial genes and endosymbiont DNA with GlimmerBioinformatics, 2007
- AUGUSTUS: ab initio prediction of alternative transcriptsNucleic Acids Research, 2006
- Basic local alignment search toolJournal of Molecular Biology, 1990