Chromosome‐based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides

Abstract

SummaryWild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome‐based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein‐coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small‐scale evolutionary rearrangements, in addition to providing evidence for the 4AL‐5AL‐7BS translocation in wild emmer wheat. Chromosome‐based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.

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

“…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. Akpinar et al (2018) predicted lncRNA genes in the T. turgidum ssp. dicoccoides genome and investigated potential lncRNA-miRNA-mRNA networks.…”

Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms

“…The second allopolyploidization event that occurred ~10,000 years ago included hybridization of the domesticated emmer and Aegilops tauschii (donor of the D genome) and led to the generation of the bread wheat T. aestivum (genome AABBDD) [2,6]. Domestication, together with allopolyploidization, is a key event shaping the wheat genome through selection [5,7]. Wheat allopolyploids are relatively young species and thus are expected to show limited genetic variation due to the "polyploidy diversity bottleneck".…”

Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms

“…Domestication, together with allopolyploidization, is a key event shaping the wheat genome through selection (Avni et al 2017;Akpinar et al 2018). To better assess when the structural variations identified in this study occurred, site-specific PCR analyses were performed for 4 tested accessions, namely a sequenced accession of wild emmer (Zavitan), an accession of durum (Svevo) and two accessions of bread wheat (accessions CS46 and TAA01).…”