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Chromosome-scale assembly and annotation of the perennial ryegrass genome

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  • Istvan Nagy
  • ,
  • Elisabeth Veeckman, Ghent University, ILVO (Flanders Research Institute for Agricultural Fisheries and Food), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium
  • ,
  • Chang Liu, University of Tübingen
  • ,
  • Michiel Van Bel, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Klaas Vandepoele, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Christian Sig Jensen, DLF Seeds A/S
  • ,
  • Tom Ruttink, ILVO (Flanders Research Institute for Agricultural Fisheries and Food), Plant Sciences Unit, Caritasstraat 39, 9090 Melle, Belgium
  • ,
  • Torben Asp

Background: The availability of chromosome-scale genome assemblies is fundamentally important to advance genetics and breeding in crops, as well as for evolutionary and comparative genomics. The improvement of long-read sequencing technologies and the advent of optical mapping and chromosome conformation capture technologies in the last few years, significantly promoted the development of chromosome-scale genome assemblies of model plants and crop species. In grasses, chromosome-scale genome assemblies recently became available for cultivated and wild species of the Triticeae subfamily. Development of state-of-the-art genomic resources in species of the Poeae subfamily, which includes important crops like fescues and ryegrasses, is lagging behind the progress in the cereal species. Results: Here, we report a new chromosome-scale genome sequence assembly for perennial ryegrass, obtained by combining PacBio long-read sequencing, Illumina short-read polishing, BioNano optical mapping and Hi-C scaffolding. More than 90% of the total genome size of perennial ryegrass (approximately 2.55 Gb) is covered by seven pseudo-chromosomes that show high levels of collinearity to the orthologous chromosomes of Triticeae species. The transposon fraction of perennial ryegrass was found to be relatively low, approximately 35% of the total genome content, which is less than half of the genome repeat content of cultivated cereal species. We predicted 54,629 high-confidence gene models, 10,287 long non-coding RNAs and a total of 8,393 short non-coding RNAs in the perennial ryegrass genome. Conclusions: The new reference genome sequence and annotation presented here are valuable resources for comparative genomic studies in grasses, as well as for breeding applications and will expedite the development of productive varieties in perennial ryegrass and related species.

OriginalsprogEngelsk
Artikelnummer505
TidsskriftBMC Genomics
Vol/bind23
Nummer1
Antal sider20
ISSN1471-2164
DOI
StatusUdgivet - jul. 2022

Bibliografisk note

Funding Information:
This work was supported by a grant from Innovation Fund Denmark (6150-00020B).

Funding Information:
The authors are grateful to Dr. Philip Howard (Queen Mary University London, UK) for his help in BioNano optical mapping and to Stephan Hentrup for his skilful technical assistance.

Publisher Copyright:
© 2022, The Author(s).

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