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

Zhenfei Yan; Lijun Sang; Yue Ma; Yong He; Juan Sun; Lichao Ma; Shuo Li; Fuhong Miao; Zixin Zhang; Jianwei Huang; Zengyu Wang; Guofeng Yang

doi:10.1186/s12870-022-03707-5

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

BMC Plant Biol. 2022 Jul 11;22(1):332. doi: 10.1186/s12870-022-03707-5.

Authors

Zhenfei Yan^{1

2}, Lijun Sang^{1

2}, Yue Ma^{1

2}, Yong He^{1

2}, Juan Sun^{1

2}, Lichao Ma^{1

2}, Shuo Li^{1

2}, Fuhong Miao^{1

2}, Zixin Zhang¹, Jianwei Huang³, Zengyu Wang^{4

5}, Guofeng Yang^{6

7}

Affiliations

¹ College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
² Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
³ Berry Genomics Corporation, Beijing, China.
⁴ College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China. zywang@qau.edu.cn.
⁵ Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China. zywang@qau.edu.cn.
⁶ College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China. yanggf@qau.edu.cn.
⁷ Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China. yanggf@qau.edu.cn.

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.

Keywords: De novo assembly; Genome; Genome annotation; PacBio HiFi; Trifolium pretense.

MeSH terms

Chromosomes
Genome, Plant / genetics
Phylogeny
Plant Breeding
Trifolium* / genetics

Abstract

MeSH terms

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