Abstract
Alfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.
Highlights
Alfalfa (Medicago sativa ssp. sativa L.) is a perennial legume forage that is widely cultivated for hay, pasture and silage production (e.g., Fig. 1a)
We used the Benchmarking Universal Single-Copy Orthologs (BUSCO) evaluation score[26] to assess the quality of the assembly, which resulted in 97.7% gene set completeness (Supplementary Table S2), indicating a very complete and high-quality genome assembly
We further detected a pair of large interchromosomal rearrangements between chromosome 4 and chromosome 8 and a large inversion on chromosome 1, as evident in the dot plots comparing our genome and the A17 genome (Fig. 4a and Supplementary Fig. 4). Such rearrangements and inversions were found between the genomes of two ecotypes, A17 and R10830, but not between the PI464715 and R108 genomes. These results indicate that the large interchromosomal rearrangements and inversion may have occurred in A17 after the divergence between M. truncatula and M. sativa, but this needs further investigation
Summary
Alfalfa (Medicago sativa ssp. sativa L.) is a perennial legume forage that is widely cultivated for hay, pasture and silage production (e.g., Fig. 1a). Alfalfa exhibits a relatively high level of disease resistance potential compared to that of other food crops[13]. It provides disease prevention between planting stages and increases the stock carrying capacity. In China, the cultivated area of alfalfa reached 3.6 million hectares in 2017; China still imports more than 1.3 million tons per year, accounting for ~85% of the total imported hay. Low production and a lack of multiple improved varieties with strong resistance and quality may be some of the factors accounting for such a large supply gap in the alfalfa industry[14]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
