Journal Article

Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

Tinker, Nicholas A., Jellen, Eric N., Jackson, Eric W., Bekele, Wubishet A., Schlueter, Jessica A., Walstead, Rachel, Vickerstaff, Robert J., Reid, Robert R., Brouwer, Cory R., Langdon, Tim, Lee, Rebekah, Maughan, Peter J., Fogarty, Melissa C., Jay, Jeremy J.

2019

Overview

Background Cultivated hexaploid oat (Common oat; Avena sativa ) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the A s - and C p -subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat’s adaptive and food quality characteristics. Results The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species—including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance ( Pc 91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. Conclusions The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Annotations / Assemblies / Avena / Avena - genetics / Avena atlantica / Avena eriantha / Avena sativa / Aveninae / Biomedical and Life Sciences / Chromosomes / Chromosomes, Plant - genetics / Crown rust / Crown rust resistance / Cultivation / Dietary fiber / Diploidy / Flow cytometry / Flowering / Flowering time / Food quality / Gene mapping / Genes / Genetic Linkage / Genetic research / Genetic resources / Genome, Plant / Genomes / Genomics / Gluten / Grain cultivation / Hi-C / Life Sciences / Molecular Sequence Annotation / Nucleotide sequence / Oat / Phylogeny / Plant breeding / Plant genetics / Research Article / Retirement benefits / Skin / Species / Synteny / Transposons