PT  - JOURNAL ARTICLE
AU  - Qing Liu
AU  - Hongyu Yuan
AU  - Mingzhi Li
AU  - Ziwei Wang
AU  - Dongli Cui
AU  - Yushi Ye
AU  - Zongyi Sun
AU  - Xukai Tan
AU  - Trude Schwarzacher
AU  - John Seymour Heslop-Harrison
TI  - Chromosome-scale genome assembly of the diploid oat <em>Avena longiglumis</em> reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses
AID  - 10.1101/2022.02.09.479819
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.02.09.479819
4099  - http://biorxiv.org/content/early/2022/02/10/2022.02.09.479819.short
4100  - http://biorxiv.org/content/early/2022/02/10/2022.02.09.479819.full
AB  - Background Oat (Avena sativa, 2n=6x=42) is an important crop, and with its wild relatives including A. longiglumis (ALO, 2n=6x=14), has advantageous agronomic and nutritional traits. A de-novo chromosome-level ALO genome assembly was made to investigate diversity and structural genome variation between Avena species and other Poaceae in an evolutionary context, and develop genomic resources to identify the pangenome and economic traits within Pooideae.Results The 3.85 gigabase ALO genome (seven pseudo-chromosomes), contained 40,845 protein-coding genes and 87% repetitive sequences (84.21% transposable elements). An LTR retrotransposon family was abundant at all chromosome centromeres, and genes were distributed without major terminal clusters. Comparisons of synteny with A. eriantha and A. strigosa showed evolutionary translocations of terminal segments including many genes. Comparison with rice (x=12) and the ancestral grass karyotype showed synteny and features of chromosome evolution including fusions, translocations and insertions of syntenic blocks across Pooideae species. With a genome size 10 times larger than rice, ALO showed relatively uniform expansion along the chromosome arms, with few gene-poor regions along arms, and no major duplications nor deletions. Linked gene networks were identified (mixed-linkage glucans and cellulose synthase genes), and CYP450 genes may be related to salt-tolerance.Conclusions The high-continuity genome assembly shows gene, chromosomal structural and copy number variation, providing a reference for the Avena pangenome, defining the full spectrum of diversity. Chromosomal rearrangements and genome expansion demonstrate features of evolution across the genus and grass BOP-clade, contributing to exploitation of gene and genome diversity through precision breeding.Competing Interest StatementThe authors have declared no competing interest.