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

Chromosomes Genome Size Genomics High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Paspalum / genetics
De novo assembly Genome Genome annotation Paspalum notatum ‘Flugge’

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
11 Apr 2022
Historique:
received: 14 09 2021
accepted: 16 03 2022
entrez: 12 4 2022
pubmed: 13 4 2022
medline: 14 4 2022
Statut: epublish

Résumé

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.

Sections du résumé

BACKGROUND 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 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 CONCLUSIONS
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.

Identifiants

DOI: 10.1186/s12864-022-08489-6 PMID: 35410159 PMC: PMC9004155
pubmed: 35410159
doi: 10.1186/s12864-022-08489-6
pii: 10.1186/s12864-022-08489-6
pmc: PMC9004155
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

293

Informations de copyright

© 2022. The Author(s).

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Auteurs

Zhenfei Yan (Z)

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.

Huancheng Liu (H)

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.

Yu Chen (Y)

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.

Juan Sun (J)

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.

Lichao Ma (L)

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.

Aihua Wang (A)

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.

Fuhong Miao (F)

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.

Lili Cong (L)

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.

Hui Song (H)

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.

Xue Yin (X)

College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.

Qi Wang (Q)

College of Animal Science, Qingdao Agricultural University, Qingdao, 266109, China.

Yayun Gong (Y)

Berry Genomics Corporation, Beijing, China.

Guofeng Yang (G)

College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China. yanggf@qau.edu.cn.
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.

Zengyu Wang (Z)

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.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Chromosomes › High-quality chromosome-scale de novo assembly...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Taille du génome › High-quality chromosome-scale de novo assembly...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › High-quality chromosome-scale de novo assembly...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › High-quality chromosome-scale de novo assembly...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › High-quality chromosome-scale de novo assembly...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Poaceae › Paspalum › High-quality chromosome-scale de novo assembly...