Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

BMC Genomics

Research Article

Robert M. Stupar¹  Junqi Liu¹  Peter Tiffin²  Joseph Guhlin²  Roxanne Denny³  Peng Zhou³  Nevin D. Young⁴  Jason R. Miller⁵  Andrew D. Farmer⁶  Thiruvarangan Ramaraj⁶  Joann Mudge⁶  Kelly P. Steele⁷  Kevin A. T. Silverstein⁸ 

[1] Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA;Department of Plant Biology, University of Minnesota, St. Paul, MN, USA;Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA;Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA;Department of Plant Biology, University of Minnesota, St. Paul, MN, USA;J. Craig Venter Institute, Rockville, MD, USA;National Center for Genome Resources, Santa Fe, NM, USA;Science and Mathematics Faculty, Arizona State University, Mesa, AZ, USA;Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN, USA;

关键词: Ortholog Group;    Syntenic Block;    Short InDels;    Dispensable Genome;    Pairwise Genome Comparison;   

DOI  :  10.1186/s12864-017-3654-1

 received in 2016-10-04, accepted in 2017-03-22,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundPrevious studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome.ResultsGenome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation.ConclusionsAnalysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation.

【 授权许可】

CC BY   
© The Author(s). 2017