The complete chloroplast genomes of seventeen Aegilops tauschii: Genome characteristic and comparative analysis
- Published
- Accepted
- Subject Areas
- Agricultural Science, Genetics, Genomics, Plant Science
- Keywords
- chloroplast genome, Aegilops tauschii, Common wheat D progenitor, Genome characteristic, genome comparative, phylogenetic analysis, cpDNA markers, genetic differentiation, Next-generation sequencing, Synonymous (Ks) and Non-synonymous (KA) substitution rates
- Copyright
- © 2019 Su et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. The complete chloroplast genomes of seventeen Aegilops tauschii: Genome characteristic and comparative analysis. PeerJ Preprints 7:e27932v1 https://doi.org/10.7287/peerj.preprints.27932v1
Abstract
As the diploid progenitor of common wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14) is regarded to be a potential genetic resource for improving common wheat, which is naturally distributed in central Eurasia, spreading from northern Syria and Turkey to western China. In this work, the chloroplast genomes of seventeen Ae. tauschii accessions showed 135 551~ 136 009 bp in length and contained the typical quadripartite structure of angiosperms. Meanwhile, a total of 127 functional genes, including 78 protein-coding genes, 4 rRNAs, 26 tRNAs, and 19 duplicated genes were identified. Overall genomic structure including gene number, gene order were well conserved with identical IR/SC boundary regions, but few variations predominantly were detected in non-coding regions (intergenic spacer regions). IR expansion and contraction with identical structure among 17 Aegilops tauschii accessions were not influence chloroplast genomes in length. Four cpDNA markers including rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20 showed high nucleotide polymorphisms，which may be used to study on inter- and intra-specific genetic structure and diversity of Ae. tauschii. The ndhF gene in AY46 accession appeared the highest ω value, which might be involved in the adaptation to high altitude ecological environment during the evolution of AY46 accession. The phylogenetic relationships constructed by the complete genome sequences strongly support that Ae. tauschii in the Yellow River region might be directly originated from Central Asia rather than Xinjiang. The specific spreading route of Ae. tauschii revealed in this work, reflects the frequent cultural exchange through the silk road from one point of view. We confirmed that Ae. tauschii derived from monophyletic speciation rather than hybrid speciation at the chloroplast genome level.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
List of genes present in the Aegilops tauschii chloroplast genome
Sequences alignment of the chloroplast genomes between T093 (L1 lineage) and AY81 (L2 lineage) using AL8/78 as the reference genome
The vertical scale of mVISTA visualization image denotes the percentage of identity, ranging from 50% to 100%. The horizontal axis marked color code as protein-coding genes, rRNA, tRNA or conserved non-coding regions.