Multiple Medicago assemblies Enable Analysis of Large Gene Families on a Genome Scale

Medicago truncatula is a model for investigating legume genetics and the evolution of legume-rhizobia symbiosis. Previous studies using whole-genome sequence data to identify sequence polymorphisms (SNPs and short Insertion/Deletions) have relied on mapping short reads to a single reference (ecotype A17). However, limitation of read-mapping approaches has hindered variant detection and characterization in repeat-rich regions as well as highly divergent regions. Studies of large gene families, as a result, are also hindered due to high sequence similarities among family members and high divergence among accessions. Here we report the sequencing, de novo assembly and annotation of the genomes of 15 natural M. truncatula accessions. Genome-wide pairwise alignments and construction of synteny blocks enabled accurate detection of SNPs, short InDels and large structural variants (large InDels, copy number changes, translocations). Nucleotide substitution rates (SNP bp^-1from 0.63% in HM058 to 2.37% in HM340) were found to be dramatically higher than previous reports that were based on aligning next generation reads to the reference genome. Among the most variable genes are two defense-related gene families: the nucleotide-binding site leucine-rich repeat (NBS-LRR) gene family and the nodule-specific, cysteine-rich gene family (CRPs). While gene structural changes are frequently observed in longer genes such as NBS-LRRs, family expansion / contraction is an important source of variation for shorter genes such as CRPs. Here, we describe detection of structural variants using a comparative genomics approach, focusing on their impacts on genome architecture, segregating patterns in natural populations, and functional relevance to important gene families.

This work was supported by NSF Plant Genome grant IOS-1237993.