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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

ABSTRACT: Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.

SUBMITTER: Rabanus-Wallace MT

PROVIDER: S-EPMC8035072 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

Rabanus-Wallace M Timothy MT Hackauf Bernd B Mascher Martin M Lux Thomas T Wicker Thomas T Gundlach Heidrun H Baez Mariana M Houben Andreas A Mayer Klaus F X KFX Guo Liangliang L Poland Jesse J Pozniak Curtis J CJ Walkowiak Sean S Melonek Joanna J Praz Coraline R CR Schreiber Mona M Budak Hikmet H Heuberger Matthias M Steuernagel Burkhard B Wulff Brande B Börner Andreas A Byrns Brook B Čížková Jana J Fowler D Brian DB Fritz Allan A Himmelbach Axel A Kaithakottil Gemy G Keilwagen Jens J Keller Beat B Konkin David D Larsen Jamie J Li Qiang Q Myśków Beata B Padmarasu Sudharsan S Rawat Nidhi N Sesiz Uğur U Biyiklioglu-Kaya Sezgi S Sharpe Andy A Šimková Hana H Small Ian I Swarbreck David D Toegelová Helena H Tsvetkova Natalia N Voylokov Anatoly V AV Vrána Jan J Bauer Eva E Bolibok-Bragoszewska Hanna H Doležel Jaroslav J Hall Anthony A Jia Jizeng J Korzun Viktor V Laroche André A Ma Xue-Feng XF Ordon Frank F Özkan Hakan H Rakoczy-Trojanowska Monika M Scholz Uwe U Schulman Alan H AH Siekmann Dörthe D Stojałowski Stefan S Tiwari Vijay K VK Spannagl Manuel M Stein Nils N

Nature genetics 20210318 4

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye ge ...[more]

PMID: 33737754

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Project description:Chromosome evolution drives species evolution, speciation, and adaptive radiation. Accurate genome assembly is crucial to understanding chromosome evolution of species, such as dikaryotic fungi. Rust fungi (Pucciniales) in dikaryons represent the largest group of plant pathogens, but the evolutionary process of adaptive radiation in Pucciniales remains poorly understood. Here, we report a gapless genome for the wheat leaf rust fungus Puccinia triticina determined using PacBio high-fidelity (HiFi) sequencing. This gapless assembly contains two sets of chromosomes, showing that one contig represents one chromosome. Comparisons of homologous chromosomes between the phased haplotypes revealed that highly frequent small-scale sequence divergence shapes haplotypic variation. Genome analyses of Puccinia triticina along with other rusts revealed that recent transposable element bursts and extensive segmental gene duplications synergistically highlight the evolution of chromosome structures. Comparative analysis of chromosomes indicated that frequent chromosomal rearrangements may act as a major contributor to rapid radiation of Pucciniales. This study presents the first gapless, phased assembly for a dikaryotic rust fungus and provides insights into adaptive evolution and species radiation in Pucciniales. IMPORTANCE Rust fungi (Pucciniales) are the largest group of plant pathogens. Adaptive radiation is a predominant feature in Pucciniales evolution. Chromosome evolution plays an important role in adaptive evolution. Accurate chromosome-scale assembly is required to understand the role of chromosome evolution in Pucciniales. We took advantage of HiFi sequencing to construct a gapless, phased genome for Puccinia triticina. Further analyses revealed that the evolution of chromosome structures in rust lineage is shaped by the combination of transposable element bursts and segmental gene duplications. Chromosome comparisons of Puccinia triticina and other rusts suggested that frequent chromosomal arrangements may make remarkable contributions to high species diversity of rust fungi. Our results present the first gapless genome for Pucciniales and shed light on the feature of chromosome evolution in Pucciniales.

Dataset Information

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

Publications

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

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