A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis

Abstract

Background Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. Results The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism. Conclusions We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.

Recent Advances in Assembly of Complex Plant Genomes

“…As a typical example, purge_haplotigs software [52] utilizes the RD-based strategy for identifying and removing these redundant sequences from a heterozygous assembly and eventually retains primary contigs to construct the monoploid genome ( Figure 4 A). The RD-based strategy has been successfully applied to several highly heterozygous genomes, namely, golden buckwheat ( Fagopyrum dibotrys ) [53] , red clover ( Trifolium pratense L.) [54] , lilacs ( Syringa oblata L.) [55] , and carnation ( Dianthus caryophyllus ) [56] . However, the RD-based strategy consumes time and money due to the need for large-scale global alignment of genome sequences.…”

Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics

“…The data suggest that both sweet yellow clover and white clover in the self-comparisons had peaks at approximately 0.75 (Fig. 4 C) [ 37 , 38 ]. In addition, the WGD event occurred when the KS value of sweet yellow clover was 0.75 (Fig.…”

De novogenome assembly ofMyricaria laxifloraprovides insights into its molecular mechanisms under flooding stress

“…High quality reference genomes are of great significance for the basic biological research of a species [34,35]. With the continuous updates of sequencing technology, reference genomes of more and more species have been assembled one after another [36].…”

“…The clean Hi-C reads were mapped to the genome assembly through BWA align. HiC-Pro was used for repetitive reading removal, classification and quality assessment [34]. Raw counts of Hi-C links were aggregated and separately by using Juicer [35] and 3D-DNA [36].…”