High-quality chromosome-scale de novo assembly of the Paspalum notatum 'Flugge' genome

Zhenfei Yan; Huancheng Liu; Yu Chen; Juan Sun; Lichao Ma; Aihua Wang; Fuhong Miao; Lili Cong; Hui Song; Xue Yin; Qi Wang; Yayun Gong; Guofeng Yang; Zengyu Wang

doi:10.1186/s12864-022-08489-6

High-quality chromosome-scale de novo assembly of the Paspalum notatum 'Flugge' genome

BMC Genomics. 2022 Apr 11;23(1):293. doi: 10.1186/s12864-022-08489-6.

Authors

Zhenfei Yan^{1

2}, Huancheng Liu^{1

2}, Yu Chen^{1

2}, Juan Sun^{1

2}, Lichao Ma^{1

2}, Aihua Wang^{1

2}, Fuhong Miao^{1

2}, Lili Cong^{1

2}, Hui Song^{1

2}, Xue Yin¹, Qi Wang³, Yayun Gong⁴, Guofeng Yang^{5

6}, Zengyu Wang^{1

2}

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

Abstract

Background: Paspalum notatum 'Flugge' is a diploid with 20 chromosomes (2n = 20) multi-purpose subtropical herb native to South America and has a high ecological significance. It is currently widely planted in tropical and subtropical regions. Despite the gene pool of P. notatum 'Flugge' being unearthed to a large extent in the past decade, no details about the genomic information of relevant species in Paspalum have been reported. In this study, the complete genome information of P. notatum was established and annotated through sequencing and de novo assembly of its genome.

Results: The latest PacBio third-generation HiFi assembly and sequencing revealed that the genome size of P. notatum 'Flugge' is 541 M. The assembly result is the higher index among the genomes of the gramineous family published so far, with a contig N50 = 52Mbp, scaffold N50 = 49Mbp, and BUSCOs = 98.1%, accounting for 98.5% of the estimated genome. Genome annotation revealed 36,511 high-confidence gene models, thus providing an important resource for future molecular breeding and evolutionary research. A comparison of the genome annotation results of P. notatum 'Flugge' with other closely related species revealed that it had a close relationship with Zea mays but not close compared to Brachypodium distachyon, Setaria viridis, Oryza sativa, Puccinellia tenuiflora, Echinochloa crusgalli. An analysis of the expansion and contraction of gene families suggested that P. notatum 'Flugge' contains gene families associated with environmental resistance, increased reproductive ability, and molecular evolution, which explained its excellent agronomic traits.

Conclusion: This study is the first to report the high-quality chromosome-scale-based genome of P. notatum 'Flugge' assembled using the latest PacBio third-generation HiFi sequencing reads. The study provides an excellent genetic resource bank for gramineous crops and invaluable perspectives regarding the evolution of gramineous plants.

Keywords: De novo assembly; Genome; Genome annotation; Paspalum notatum ‘Flugge’.

MeSH terms

Chromosomes
Genome Size
Genomics
High-Throughput Nucleotide Sequencing
Molecular Sequence Annotation
Paspalum* / genetics