A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa

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.

Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history

“…Our comparative genomics analyses showed that M. ruthenica and other legume species shared the common Papilionoideae WGD event (Wang et al, 2017), and no additional WGD events occurred specifically in M. ruthenica (Figure 2b), which is consistent with the findings for other diploid Medicago species (Li et al, 2020). We further identified ~619.…”

“…In general, each chromosome of M. ruthenica corresponded to one chromosome of M. sativa and M. truncatula. We also found a pair of large interchomosomal rearrangements between chromosomes 4 and 8 in M. truncatula compared with the M. ruthenica and M. sativa genomes, which was consistent with the previous finding (Li et al, 2020).…”

“…M. ruthenica shared 9962 gene families with four other species (A. thaliana, G. max, M. sativa, and M. truncatula) and contained 2728 unique gene families (Figure 2a). Phylogenetic inferences based on 440 singlecopy orthologous genes showed that M. sativa and M. truncatula were closely related species that diverged approximately 4.80 Ma (Figure 2c and Figure S7), which is consistent with previous studies (Chen et al, 2020;Li et al, 2020). M. ruthenica was found to be a sister to M. sativa and M. truncatula, diverging approximately 6.71 Ma (Figure 2c and Figure S7).…”

“…To understand the genome evolution of the three Medicago species, we conducted synteny analysis among our genome assembly, the diploid alfalfa genome (Li et al, 2020), and the M. truncatula ecotype Jemalong A17 genome v5.0 (Pecrix et al, 2018). High collinearity was revealed between our genome and the other two genomes by visualizing the synteny blocks (Figure 3a and Figure S8), reflecting the high quality of our genome assembly.…”

A global alfalfa diversity panel reveals genomic selection signatures in Chinese varieties and genomic associations with root development

“…The plant then widely spread in China for about two millennia, with wild alfalfa populations distributed in many parts of China (Basigalup et al, 2014). The reference genomes for Medicago sativa , one for autotetraploid alfalfa and the other for diploid blue alfalfa ( Medicago caerulea ), were published, opening the avenue for a global dissection of the species (Chen et al, 2020; Li et al, 2020; Shen et al, 2020; Long et al, 2021). For example, the genome of “Xinjiangdaye”, a main tetraploid landrace in Xinjiang, China, was assembled into 32 allelic chromosomes (Chen et al, 2020).…”