Medicago Genome Assembly with Long-Read and Short-Read Sequencing

Medicago is a model plant for the study of legume symbioses. The Medicago HapMap project is creating resources for analysis of genetic variation within the M. truncatula clade. The resources include high-quality de novo genome assemblies for 3 accessions, high-throughput de novo genome assemblies for 30 accessions, and re-sequencing data for 300 accessions. These data will complement the community’s reference sequence that captures the A17 accession. Our high-throughput pipeline uses Illumina PE and MP sequence and the ALLPATHS-LG assembler. The high-quality assembly pipeline, called ALPACA, exploits Illumina and PacBio sequence with a hybrid combination of three software packages: ALLPATHS-LG, ECtools, Celera Assembler. The high-quality assemblies present larger scaffolds and significantly larger contigs. While the high-throughput assemblies reveal many accession-specific differences, the high-quality assemblies capture a greater degree of chromosomal re-arrangement, gene family expansion, and tandem duplication events from M. truncatula evolution.