Complete chloroplast DNA sequences of Zanduri wheat (Triticum spp.)
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Georgia plays an important role in wheat formation. In the past, the Zanduri population of Georgia was a set of diploid—Triticum monococcum var. hornemanii (2n = 14) (Gvatsa Zanduri), tetraploid Triticum timopheevii (2n = 28) (Chelta Zanduri) and hexaploid Triticum zhukovskyi Men. et Er. (2n = 42). It is a Zanduri puzzle that wild T. araraticum was not found in Georgia, though cultivated T. timopheevii was only detected here. Next-generation sequencing technologies, which have been developed in recent years, enable the determination of complete nucleotide sequences of both chloroplast and mitochondrial DNA of many higher plants, including wheat. The genetic structure of Zanduri wheat is more accurately inferred by the complete sequences of chloroplast DNA. In the present investigation, the complete sequences of three Zanduri wheats (T. timopheevii, T. zhukovskyi, and T. monococcum var. hornemanii) and wild T. araraticum are presented. Sequencing of chloroplast DNA was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. In comparison to T. araraticum, there are 12 SNPs, a 25 bp inversion in the ccsA-ndhD intergenic sequence, and a 38-bp inversion in the intergenic sequence rbcL-rpl23 pseudogene identified in T. timopheevii and T. zhukovskyi. In addition, a 24 bp repeat of trnG-trnI intergenic sequence is present as a double copy in T. araraticum, whereas in T. timopheevii and T. zhukovskyi, it is present as a triple copy. Unlike T. araraticum, T. timopheevii and T. zhukovskyi have a 6 bp repeat in the gene ndhH, which results in a dipeptide duplication in the corresponding protein. Gvatsa Zanduri (T. monococcum var. hornemanii) chloroplast DNA slightly differs from other einkorn chloroplast DNA. In comparison to T. monococcum, four SNPs can be identified in T. monococcum (Gvatsa Zanduri), two in gene matK and one in gene ndhD. The sequenced chloroplast DNA molecules were compared to other Triticum and Aegilops species, and a phylogenetic tree was constructed. T. araraticum, T. timopheevii and T. zhukovskyi chloroplast DNA showed the closest phylogenetic relationship with the chloroplast DNA of Ae. speltoides. The most significant difference was in the 114-bp deletion within the gene ndhH in the Timopheevi species.
KeywordsChloroplast DNA Illumina Indels Phylogeny Sequencing SNP Triticum spp. Wheat
The authors wish to acknowledge the constant interest and support of Mr. K. Bendukidze who untimely passed away on 13th November, 2014. This research was funded by the Knowledge Fund. The Knowledge Fund is a funding organization of the Free University of Tbilisi and Agricultural University of Georgia. Correction of the manuscript in terms of English was funded through the University Research Program by the U.S. Embassy in Georgia, grant No S-GE800-13-GR-122.
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