45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

Abstract

The genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity–A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5’ external transcribed spacer (5’-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5’-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5’-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5’-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5’-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways.

Oat evolution revealed in the maternal lineages of 25 Avena species

“…First, based on the asymmetrical karyotype with a preponderance of heterobrachial chromosomes species, Rajhathy 51 proposed that A. ventricosa was the C genome donor towards hexaploid oat. Recent studies also provided support for A. ventricosa being the ancestral Avena genome based on 45 S rDNA external transcribed spacer organization variability 52 and based on ITS1-5.8 SITS2 sequence variability 53 . Second, A. canariensis was the only diploid oat species with denticulate lemma tips, which is a morphological feature in common with hexaploid oat 54 .…”

Genomic relationships among sixteen species of Avena based on (ACT)6 trinucleotide repeat FISH

“…Kellogg and Bennetzen (2004) put forward that this variation was the outcome of a set of highly active processes, including gene duplication and deletion, chromosomal duplication followed by gene loss, amplification of retrotransposons separating genes, and genome rearrangement; the latter process often follows hybridization or polyploidy. Rodrigues et al (2017) suggested that the loss of the C genome sequence might be correlated with differences in the parental genome size in polyploid species of Avena. Indeed, the C genome is larger than the A genome (Bennett and Leitch 2012).…”

Molecular cytogenetics of valuable Arctic and sub-Arctic pasture grass species from the Aveneae/Poeae tribe complex (Poaceae)

“…Despite widespread occurrence and economic value of most cereals from the Aveneae / Poeae tribe, their genomes still remain insufficiently studied [14, 15]. Due to the agricultural significance, oat species have become the subject of complex investigation, and extensive molecular studies have largely clarified diversity and evolution of the genus Avena [16–20]. Phylogenetic studies in recent decades, mostly based on analyses of different DNA sequences from both plastid regions and nuclear ribosomal regions, have helped to clarify the evolutionary relationships within the Aveneae / Poeae complex [4, 5, 15, 21–23].…”