title: Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.
abstract: Previous 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.
  
  
  
  Genome-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.
  
  
  
  Analysis 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.
authors.affiliation: Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhou
authors.affiliation: Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN, USA.
authors.forename: Kevin A T
authors.initials: KA
authors.lastname: Silverstein
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, USA.
authors.forename: Thiruvarangan
authors.initials: T
authors.lastname: Ramaraj
authors.affiliation: Department of Plant Biology, University of Minnesota, St. Paul, MN, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Guhlin
authors.affiliation: Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
authors.forename: Roxanne
authors.initials: R
authors.lastname: Denny
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
authors.forename: Junqi
authors.initials: J
authors.lastname: Liu
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.affiliation: Science and Mathematics Faculty, Arizona State University, Mesa, AZ, USA.
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Steele
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Stupar
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Miller
authors.affiliation: Department of Plant Biology, University of Minnesota, St. Paul, MN, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Tiffin
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, USA.
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.affiliation: Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA. neviny@umn.edu.|Department of Plant Biology, University of Minnesota, St. Paul, MN, USA. neviny@umn.edu.
authors.forename: Nevin D
authors.initials: ND
authors.lastname: Young
mesh_terms: D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations / Q000235:genetics*; D018745:Genome, Plant; D006360:Heat-Shock Proteins / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D000090263:Leucine-Rich Repeat Proteins; D046913:Medicago truncatula / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D011506:Proteins / Q000235:genetics; D018749:RNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D006360:Heat-Shock Proteins; D000090263:Leucine-Rich Repeat Proteins; D010940:Plant Proteins; D011506:Proteins; D018749:RNA, Plant