College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao, 266109, China.
BMC Genomics. 2022 Apr 11;23(1):293. doi: 10.1186/s12864-022-08489-6.
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.
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.
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.
沟叶结缕草‘Flugge’是一种二倍体植物，具有 20 条染色体（2n = 20），是原产于南美洲的一种多功能亚热带草本植物，具有很高的生态意义。它目前在热带和亚热带地区广泛种植。尽管沟叶结缕草‘Flugge’的基因库在过去十年中被大量发掘，但有关沟叶结缕草属植物的基因组信息仍未见报道。本研究通过对其基因组进行测序和从头组装，建立并注释了沟叶结缕草的全基因组信息。
最新的 PacBio 第三代 HiFi 组装和测序结果表明，沟叶结缕草‘Flugge’的基因组大小为 541M。该组装结果是目前已发表的禾本科基因组中较高的指标，其连群 N50 = 52Mbp，支架 N50 = 49Mbp，BUSCOs = 98.1%，占估计基因组的 98.5%。基因组注释揭示了 36511 个高可信度的基因模型，为未来的分子育种和进化研究提供了重要资源。与其他密切相关的物种的基因组注释结果进行比较表明，沟叶结缕草与玉米的关系密切，但与短柄草、柳枝稷、水稻、披碱草、稗草的关系并不密切。对基因家族的扩张和收缩分析表明，沟叶结缕草‘Flugge’包含与环境抗性、生殖能力增强和分子进化相关的基因家族，这解释了其优良的农艺性状。
本研究首次报道了利用最新的 PacBio 第三代 HiFi 测序数据组装的沟叶结缕草‘Flugge’高质量染色体水平基因组。该研究为禾本科作物提供了一个极好的遗传资源库，并为禾本科植物的进化提供了宝贵的视角。
