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

Abstract

BackgroundCultivated 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 As- and Cp-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.ResultsThe 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 (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species.ConclusionsThe 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.

Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci

“…Very few Pc genes have been mapped to the A . sativa consensus (Mrg) linkage groups and assigned to a chromosomal location [ 24 , 25 , 51 , 52 ]. For the group Pc48 / 52 / 57 / 61 only Pc48 has been mapped to A .…”

The Brittle Rachis Trait in Species Belonging to the Triticeae and Its Controlling Genes Btr1 and Btr2

“…longissima (unpublished data provided by A Sharon [Tel Aviv University]), Ae. tauschii ( Luo et al, 2017 ), T. dicoccoides ( Avni et al, 2017 ), Lolium perenne ( Byrne et al, 2015 ), Avena eriantha (provided by Maughan et al, 2019 , [Brigham Young University, Provo, UT, USA]), and Brachypodium distachyon ( International Brachypodium Initiative, 2010 ). A BLASTp search (E-value threshold: 1E-2 and identity threshold: 30%) was used to identify homologs present in rice ( Kawahara et al, 2013 ), foxtail millet ( Setaria italica ) ( Bennetzen et al, 2012 ), sorghum ( Paterson et al, 2009 ), maize ( Jiao et al, 2017 ), and Arabidopsis thaliana ( Swarbreck et al, 2008 ).…”

Genome‐wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.)

“…Four of the GBS tag sequences had perfect matches on the draft assembly. Only avgbs_6K_95238.1 had a perfect GBS match with the A. atlantical genome sequence (Maughan et al., 2019). The markers avgbs_100100.1.64 and avgbs_114613.1.46 have perfect matches on the same scaffold, and inside a genomic region predicted to code for an antioxidant gene.…”