ABSTRACT
The Georgian Mountain Cattle (GMC) (Species: Bos taurus Linnaeus, 1758 - aurochs, domesticated cattle, domestic cattle (feral), Aurochs, Subspecies: Bos taurus taurus Linnaeus, 1758) is a local breed from Georgia. It is well adapted to the harsh mountain conditions of the Caucasus, resistant to different pathogens and able to provide milk during the lowest feed rations. In this study, we report for the first time the complete mitochondrial genome sequence of GMC. We selected the five unique control region mitochondrial haplotypes of GMC and sequenced for the complete mitogenome, using Illumina MiSeq platform. The results of our research showed a total of 59 substitutions and seven indels, in comparison to the Bovine Reference Sequence (BRS; V00654), with 15 SNPs never observed before. The complete mitochondrial DNA (mtDNA) phylogenetic analyses revealed hitherto unknown haplotypes falling outside the known taurine diversity. Four mitogenomes fell within haplogroup T (sub-lineages T1, T3, and T5), while one belonged to haplogroup Q (branch Q1). The combination of our results with precision agriculture holds great promises for the identification of genetic variants economically affecting important traits of GMC cattle.
ABSTRACT
Grapevine is the one of the most important fruit species in the world. Comparative genome sequencing of grape cultivars is very important for the interpretation of the grape genome and understanding its evolution. The genomes of four Georgian grape cultivars-Chkhaveri, Saperavi, Meskhetian green, and Rkatsiteli, belonging to different haplogroups, were resequenced. The shotgun genomic libraries of grape cultivars were sequenced on an Illumina HiSeq. Pinot Noir nuclear, mitochondrial, and chloroplast DNA were used as reference. Mitochondrial DNA of Chkhaveri closely matches that of the reference Pinot noir mitochondrial DNA, with the exception of 16 SNPs found in the Chkhaveri mitochondrial DNA. The number of SNPs in mitochondrial DNA from Saperavi, Meskhetian green, and Rkatsiteli was 764, 702, and 822, respectively. Nuclear DNA differs from the reference by 1,800,675 nt in Chkhaveri, 1,063,063 nt in Meskhetian green, 2,174,995 in Saperavi, and 5,011,513 in Rkatsiteli. Unlike mtDNA Pinot noir, chromosomal DNA is closer to the Meskhetian green than to other cultivars. Substantial differences in the number of SNPs in mitochondrial and nuclear DNA of Chkhaveri and Pinot noir cultivars are explained by backcrossing or introgression of their wild predecessors before or during the process of domestication. Annotation of chromosomal DNA of Georgian grape cultivars by MEGANTE, a web-based annotation system, shows 66,745 predicted genes (Chkhaveri-17,409; Saperavi-17,021; Meskhetian green-18,355; and Rkatsiteli-13,960). Among them, 106 predicted genes and 43 pseudogenes of terpene synthase genes were found in chromosomes 12, 18 random (18R), and 19. Four novel TPS genes not present in reference Pinot noir DNA were detected. Two of them-germacrene A synthase (Chromosome 18R) and (-) germacrene D synthase (Chromosome 19) can be identified as putatively full-length proteins. This work performs the first attempt of the comparative whole genome analysis of different haplogroups of Vitis vinifera cultivars. Based on complete nuclear and mitochondrial DNA sequence analysis, hypothetical phylogeny scheme of formation of grape cultivars is presented.
Subject(s)
Genome, Plant , Vitis/genetics , Alkyl and Aryl Transferases/genetics , Chromosomes, Plant , DNA, Mitochondrial/genetics , DNA, Plant/genetics , Polymorphism, Single NucleotideABSTRACT
The nucleotide sequence of 1029 bp BamHI-fragment of leek chloroplast DNA (Allium porrum, fam. Liliaceae) has been determined. The fragment contains the 3'-terminal part of the tRNA-Gly (UCC) gene, the tRNA-Arg (UCU) gene and the 3'-terminal domain of the CF1ATPase alpha-subunit gene. The gene arrangement and the nucleotide sequence of this fragment are similar to those of the tobacco chloroplast DNA but differ significantly from that of other monocots in which the region containing these genes underwent extensive recombination.
Subject(s)
Allium/genetics , Chloroplasts/metabolism , Proton-Translocating ATPases/genetics , RNA, Transfer, Arg/genetics , RNA, Transfer, Gly/genetics , Allium/enzymology , Amino Acid Sequence , Base Sequence , Chloroplasts/enzymology , DNA , Molecular Sequence Data , Nucleic Acid Conformation , RNA, Transfer, Arg/chemistry , RNA, Transfer, Gly/chemistry , Sequence Homology, Amino AcidABSTRACT
The nature of distribution of the chloroplast DNA from three species of higher plants (Sp. oleracea, N. tabacum, P. sativum) in the CsCl density gradient has been investigated DNA preparations isolated from the fractions of chloroplasts completely deprived of the admixtures of nuclei and mitochondria are characterized by symmetric distribution in the density gradient. Fragmentation of chloroplast DNA of higher plants is not accompanied by the appearance of the discrete satellite components. It has been shown that the satellite DNA component found in the fraction of the unpurified chloroplasts are entirely mitochondrial DNA.
