The chromosome-level genome assembly of Astragalus Sinicus and comparative genomic analyses provide new resources and insights for understanding legume-rhizobial interactions

Abstract The legume species Astragalus sinicus (Chinese milk vetch, CMV) has been widely cultivated for centuries in southern China as one of the most important green manures/cover crops to improve rice productivity and prevent soil degeneration. In this study, we generated the first chromosome-scale reference genome of CMV using a combination of PacBio, Illumina sequencing, and high-throughput chromatin conformation capture(Hi-C) technology. The CMV genome was 595.52 Mb, with a contig N50 size of 1.50 Mb. Long terminal repeats (LTR) were amplified and contributed to the genome size expansion in CMV. CMV underwent two whole-genome duplication (WGD) events, and the retained genes following WGD, which were shared by Papilionoideae species, shaped the hormonal regulation of nodulation and the symbiosis with rhizobia. The chalcone synthase (CHS) gene family was expanded and expressed primarily in the root of CMV. Intriguingly, we found that R genes were highly expressed in root than in the nodules of legume species, suggesting that they may be hired to increased plant immunity in root to cope with pathogen infection in legume species. Our work sheds light on the genetic basis of nodulation and symbiosis in CMV and provides a benchmark for accelerating genetic research and molecular breeding in the future.