Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses

Abstract

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.

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

“…New long-molecule sequencing approaches are allowing assembly of Avena genome sequences, covering nearly 4,000Mbp in the diploids (Maughan et al, 2019; Liu et al 2022; Peng et al, 2022). High coverage shows the reciprocal translocations which are also revealed with the chromosomal probes.…”

“…Chromosome translocations are important for plant evolution (Martin et al, 2020; Wang et al, 2021; Biswas et al, 2022; Liu et al, 2022), and occur in diploids, and after hybrid or amphiploid formation; they lead to exchange of chromosome segments within and between the ancestral genomes. Comparative genetic analysis in the grass family, including major crops, showed that particular taxonomic units are characterized by different chromosome translocations in terms of their position on chromosomes, reciprocity, and number of breaks involved (Bardsley et al 1999).…”

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

“…Chromosome translocations are important for plant evolution ( Martin et al., 2020 ; Biswas et al., 2022 ; Liu et al., 2022 ; Wang et al., 2022 ), and occur in diploids, and after hybrid or amphiploid formation; they lead to exchange of chromosome segments within and between the ancestral genomes. Comparative genetic analysis in the grass family, including major crops, showed that particular taxonomic units are characterized by different chromosome translocations in terms of their position on chromosomes, reciprocity, and number of breaks involved ( Bardsley et al., 1999 ).…”

The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass,Cenchrus ciliaris

“…In Arabidopsis thaliana many Ty3- gypsy retroelements are present in pericentromeric heterochromatin region (Brandes et al, 1997b). Centromeric retroelements in maize (CRM) is a lineage of Ty3- gypsy retroelements (Jin et al, 2004), and the diploid oat Avena longiglumis (2 n =2 × =14; 3,850 Gb genome size) has specific LTR retrotransposons located at the centromeres (Liu et al, 2022), in all cases with other retroelement families dispersed along all chromosomes. Some of these repetitive elements may have a role in centromere functionality, although they may also accumulate in regions of the genome where there are few genes.…”