Background White clover (Trifolium repens L.), an excellent perennial legume forage, is an allotetraploid native to southeastern Europe and southern Asia. It has high nutritional, ecological, genetic breeding, and medicinal values and exhibits excellent resistance to cold, drought, trample, and weed infestation. Thus, white clover is widely planted in Europe, America, and China; however, the lack of reference genome limits its breeding and cultivation. This study generated a white clover de novo genome assembly at the chromosomal level and annotated its components. Results The PacBio third-generation Hi-Fi assembly and sequencing methods generated a 1096 Mb genome size of T. repens, with contigs of N50 = 14 Mb, scaffolds of N50 = 65 Mb, and BUSCO value of 98.5%. The newly assembled genome has better continuity and integrity than the previously reported white clover reference genome; thus provides important resources for the molecular breeding and evolution of white clover and other forage. Additionally, we annotated 90,128 high-confidence gene models from the genome. White clover was closely related to Trifolium pratense and Trifolium medium but distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum. The expansion, contraction, and GO functional enrichment analysis of the gene families showed that T. repens gene families were associated with biological processes, molecular function, cellular components, and environmental resistance, which explained its excellent agronomic traits. Conclusions This study reports a high-quality de novo assembly of white clover genome obtained at the chromosomal level using PacBio Hi-Fi sequencing, a third-generation sequencing. The generated high-quality genome assembly of white clover provides a key basis for accelerating the research and molecular breeding of this important forage crop. The genome is also valuable for future studies on legume forage biology, evolution, and genome-wide mapping of quantitative trait loci associated with the relevant agronomic traits.

Background Multiprotein bridging factor 1 are transcription factors that play critical roles in plant life cycle and in plant tolerance to environmental stresses. Medicago sativa is an important perennial legume forage grass, whereas the potential information in the MBF1 genes associated with stress resistance remains poorly understood. Results Three MBF1 genes were identified from each of the M. truncatula and M. sativa genomes. Multiple sequence alignment analysis showed that all these members contain conserved MBF1 and HTH domains. The MBF1 genes showed similar exon-intron organizations, and similar architectures in their conserved motifs. A number of cis-acting elements associated with drought, MeJA and light stress were identified in their promoter regions. In addition, these MBF1 genes were shown in genechip and transcriptome data to exhibit divergent expression patterns in various tissues or in response to drought and salt treatments. In particular, qRT-PCR results showed that the expression of MtMBF1b and MtMBF1c were significantly induced by NaCl treatment, indicating that they are likely to play a role in salt stress response. Conclusions Our comprehensive analysis provides valuable information for elucidating the evolutionary process of MBF1 genes and their expression patterns in different tissues and under four stresses. This work will facilitate the application of MBF1 genes in molecular breeding of highly resistant alfalfa.

Background: White clover (Trifolium repens L.), an excellent perennial legume forage, is a heterotetraploid native to southeastern Europe and southern Asia. It has high feeding, ecological, genetic breeding, and medicinal values and exhibits excellent resistance to cold, drought, trample, and weed infestation. Thus, white clover is widely planted in Europe, America, and China. However, the lack of reference genome limits white clover breeding and cultivation. This study generated a white clover de novo genome assembly at the chromosomal level and annotated its components. Results: The PacBio third-generation Hi-Fi assembly and sequencing methods were used to generate a 1096 Mb genome size of T. repens, with contigs of N50 = 14 Mb, scaffolds of N50 = 65 Mb, and BUSCOs value of 98.5%. The newly assembled genome has better continuity and integrity than the previously reported white clover reference genome; thus provides important resources for the molecular breeding and evolution of white clover and other forage. Additionally, we annotated 90,128 high-confidence gene models from the genome. White clover was most closely related to Trifolium pratense and Trifolium medium but distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum. The expansion, contraction, and GO functional enrichment analysis of the gene families showed that T. repens gene families were associated with biological processes, molecular function, cellular components, and environmental resistance, which explained its excellent agronomic traits. Conclusions: This study reports a high-quality de novo assembly for white clover obtained at the chromosomal level using PacBio third-generation Hi-Fi sequencing. The generated high-quality genome assembly of white clover provides a key basis for accelerating the research and molecular breeding of this important forage crop. The genome is also valuable for future studies on legume forage biology, evolution, and genome-wide mapping of quantitative trait loci associated with the relevant agronomic traits.