Long non-coding RNAs in wild wheat progenitors

Abstract

Triticum urartu and Aegilops tauschii are the diploid progenitors of the hexaploid Triticum aestivum (A u A u BBDD), donors of the A u and D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives.Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515 T. urartu and 20,908 Ae. tauschii bonafide lncRNA transcripts that show features similar to those of other plant and animal counterparts.Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs. Most of the organ-specific lncRNAs were found associated with transposable elements (TEs), indicating the possible role of TEs in lncRNA origin, differentiation and function. The majority of T. urartu and Ae. tauschii lncRNAs appear to be species-specific; nevertheless, we found some lncRNAs conserved between the two wheat progenitors, highlighting the presence and conservation of exonic splicing enhancers sites in multi-exon conserved lncRNAs.In addition, we found cases of lncRNA conservation and their cis regulatory regions spanning the wheat pre-domestication and post-domestication period. Altogether, these results represent the first comprehensive genome-wide encyclopedia of lncRNAs in wild wheat relatives, and they provide clues as to the hidden regulatory pathway mediated by long noncoding RNAs in these largely unexplored wheat progenitors.

Long Non-coding RNA in Plants in the Era of Reference Sequences

“…One of these classes of crops is the Triticeae tribe, which includes cereal species such as wheat and barley important sources of nutrition in the human diet (Moore et al, 1995). Unraveling cellular mechanisms responsible for gene expression under stress conditions is the objective of ongoing research, in efforts to breed cultivars better able to withstand abiotic and biotic stresses (Pieri et al, 2018). For this purpose, the lncRNA repertoires of two of the three diploid wild ancestors of bread wheat (Triticum aestivum, AABBDD), Triticum urartu (AA) and Aegilops tauschii (DD), whose draft and reference genomes were recently published (Jia et al, 2013;Ling et al, 2013;Luo et al, 2017), were examined.…”

“…tauschii, were also compared to bread wheat and tetraploid wild emmer wheat (Triticum turgidum ssp. dicoccoides, AABB), a wild subspecies of T. turgidum (AABB), the tetraploid ancestor of bread wheat (Pieri et al, 2018). Comparative analyses using RNA sequencing data suggested that the conservation between lncRNA repertoires decreased as the evolutionary distance increased (Pieri et al, 2018).…”

“…dicoccoides, AABB), a wild subspecies of T. turgidum (AABB), the tetraploid ancestor of bread wheat (Pieri et al, 2018). Comparative analyses using RNA sequencing data suggested that the conservation between lncRNA repertoires decreased as the evolutionary distance increased (Pieri et al, 2018). Wild emmer wheat has long been a promising resource for exploration and exploitation of stress responses, due to the remarkable genetic diversity its wild populations retain.…”

Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L.

“…For instance, 65% of Zea mays lncRNAs (Lv et al, 2019) and 53% of Oryza sativa lncRNAs (Zhou et al, 2021) contained sequences that appear to be derived from TEs. On the other hand, some plant species, such as Brachypodium distachyon with 8% (De Quattro et al, 2017), Aegilops tauschii with 19%, and Triticum urartu with 27% (Pieri et al, 2018), exhibited less proportion of lncRNAs which can be attributed to TEs. Regarding these findings, these differences can demonstrate that TEs are likely to be leading actors of the swift evolutionary turnover of lncRNAs among various species (Etchegaray et al, 2021).…”

The regulatory landscape of early maize inflorescence development

“…There is also experimental evidence for the contribution of TEs in the evolution of lncRNAs; for example, TE-derived sequences conferring regulatory activities [61]. In maize and other grasses, retroelements were found to be most associated with lncRNAs [48,62,63]. Coincidently, 36% of the inflorescence-expressed lincRNAs originated from an annotated TE, largely Copia and Gypsy classes (Additional File 1: Figure S15).…”