title: Complete chloroplast genomes of Aegilops tauschii Coss. and Ae. cylindrica Host sheds light on plasmon D evolution.
abstract: Hexaploid wheat (Triticum aestivum L., genomes AABBDD) originated in South Caucasus by allopolyploidization of the cultivated Emmer wheat T. dicoccum (genomes AABB) with the Caucasian Ae. tauschii ssp strangulata (genomes DD). Genetic variation of Ae. tauschii is an important natural resource, that is why it is of particular importance to investigate how this variation was formed during Ae. tauschii evolutionary history and how it is presented through the species area. The D genome is also found in tetraploid Ae. cylindrica Host (2n = 28, CCDD). The plasmon diversity that exists in Triticum and Aegilops species is of great significance for understanding the evolution of these genera. In the present investigation the complete nucleotide sequence of plasmon D (chloroplast DNA) of nine accessions of Ae. tauschii and two accessions of Ae. cylindrica are presented. Twenty-eight SNPs are characteristic for both TauL1 and TauL2 accessions of Ae. tauschii using TauL3 as a reference. Four SNPs are additionally observed for TauL2 lineage. The longest (27 bp) indel is located in the intergenic spacer Rps15-ndhF of SSC. This indel can be used for simple determination of TauL3 lineage among Ae. tauschii accessions. In the case of Ae. cylindrica additionally 7 SNPs were observed. The phylogeny tree shows that chloroplast DNA of TauL1 and TauL2 diverged from the TauL3 lineage. TauL1 lineage is relatively older then TauL2. The position of Ae. cylindrica accessions on Ae. tauschii phylogeny tree constructed on chloroplast DNA variation data is intermediate between TauL1 and TauL2. The complete nucleotide sequence of chloroplast DNA of Ae. tauschii and Ae. cylindrica allows to refine the origin and evolution of D plasmon of genus Aegilops.
authors.affiliation: Institute of Molecular Genetics, Agricultural University of Georgia, #240 D. Agmashenebeli Alley, 0159, Tbilisi, Georgia. m.gogniashvili@agruni.edu.ge.
authors.forename: Mari
authors.initials: M
authors.lastname: Gogniashvili
authors.affiliation: Institute of Botany, Ilia State University, Tbilisi, Georgia.
authors.forename: Tamar
authors.initials: T
authors.lastname: Jinjikhadze
authors.affiliation: Institute of Botany, Ilia State University, Tbilisi, Georgia.
authors.forename: Inesa
authors.initials: I
authors.lastname: Maisaia
authors.affiliation: Institute of Botany, Ilia State University, Tbilisi, Georgia.
authors.forename: Maia
authors.initials: M
authors.lastname: Akhalkatsi
authors.affiliation: National Centre for Disease Control and Public Health, Tbilisi, Georgia.
authors.forename: Adam
authors.initials: A
authors.lastname: Kotorashvili
authors.affiliation: National Centre for Disease Control and Public Health, Tbilisi, Georgia.
authors.forename: Nato
authors.initials: N
authors.lastname: Kotaria
authors.affiliation: Institute of Molecular Genetics, Agricultural University of Georgia, #240 D. Agmashenebeli Alley, 0159, Tbilisi, Georgia.
authors.forename: Tengiz
authors.initials: T
authors.lastname: Beridze
authors.affiliation: Institute of Cytology and Genetics, Novosibirsk, Russia.
authors.forename: Alexander Ju
authors.initials: AJ
authors.lastname: Dudnikov
mesh_terms: D005075:Biological Evolution; D054628:Genome, Chloroplast; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000235:genetics; D014908:Triticum / Q000145:classification / Q000235:genetics*
keywords: Aegilops; Chloroplast DNA; Illumina; Indels; SNP; Sequencing