Journal of Phylogenetics & Evolutionary Biology

Grape (Vitis vinifera) is a genus of tree in the family of Vitaceae. V. vinifera's species belong to Eurasian grapes. The genome of chloroplast is the most comprehensive genome in plants, and it has many features for evolution analyses due to the unique molecular structure and single-parent inheritance. The goals of this research were study and compare of the complete sequences chloroplast genomes of Saperavi and Meskhuri mtsvane from Caucasia subspecies with common grape (Vitis vinifera), as well as genomes structure analysis, gene content, organization and repetitive sequences, codon usage and comparison among genomes. The chloroplast genome of Vitis vinifera is a circular DNA molecule with 160928 base pairs (bp), which is longer than the chloroplast genomes of Saperavi and Meskhuri mtsvane varieties. The large and small unique regions are separated by two inverted repeat regions a, b. In three genomes, the complete genome contains 131 genes, which include 79 protein coding genes, 4 rRNA genes and 30 tRNA genes. In other words, there are totally 113 single-copy genes and 18 double-copy genes located in inverted repeat region (IR) in the three studied genomes. The SSRs of the chloroplast genomes were identified and the results indicated that the chloroplast genomes of Vitis vinifera and Saperavi both have 74 SSRs and Meskhuri mtsvane has 73 SSRs. The chloroplast SSRs are important and useful for genetic diversity studies. Low GC content is a significant feature of plastidic genomes, which is possibly formed after endosymbiosis by DNA replication and repair.

The genetic origins of European Jewish women remain controversial and new insights may be obtained through the less studied “other European Jews”, the Sephardim. The branch T2e1 of the mitochondrial DNA phylogenetic tree contains two Sephardic branches distant from one another. To investigate further, the largest analysis of T2e1 to date is presented with 40 new complete T2e1 mitochondrial DNA sequences (mitogenomes) from Europeandescended individuals, doubling the number available. Additionally, nearly 8000 control region sequences from 37 studies were re-considered for T2e1 specifically, from areas high in T2e (Near East, Italy) and areas low in T2e but Sephardic related (Spain, Portugal). These revealed unexpectedly an absence of T2e1 in the Near East and a high number in Spain. By contrast, numerous T2e-Other sequences were in the Near East and Italy with considerable overlap. The mitogenomes elucidated new branches of T2e1 at varying distances from the Sephardic branches including the closest, an Irish-specific clade (4107T), the most populous (nonsynonomous 14180C with unknown biological effect) from Norway (also Sweden, Germany, British Isles), and the root node of T2e1a (2308G) . The findings suggest an origin or early arrival of T2e1 in Europe whilst for T2e, strengthens the role of Near East and its early free travel with the Mediterranean. Quiet Judaism (down-low) may have produced T2e1 branches where Jewish identity was lost, such as from Sephardics who took the Northern route after the Iberian expulsion. The Scandinavian branches may reflect Nordic conquest of British Isles and solve a mystery of a T2e1 hot spot in Iceland. The Near East-Mediterranean origins of T2e resemble that reported for Ashkenazi maternal lineages; other Sephardic haplogroups are needed to assess generality of this common origin. Additional insight may be obtained with the first Jews to enter Europe, the Romaniots, the other other European Jews.

Tankwa goats are feral animals initially identified from the Tankwa Karoo National Park in the Northern Cape, South Africa that is reported to be well adapted to their harsh environment. We assessed the genetic diversity of these goats by sequencing the hypervariable segment of the mitochondrial control region (mtDNA HVI D-loop). We additionally clarified genetic origin of the Tankwa goats relative to international breeds. A total of 40 blood samples were collected between 2012 and 2016 from individual unrelated Tankwa goats. Genomic DNA was extracted and the amplified mtDNA D-loop region was used for phylogenetic analysis. A total of 12 haplotypes were identified. Haplotype and nucleotide diversity of Tankwa goat’s population was identified to be low compared to the global goat populations including South African goats, which may be an indication of higher inbreeding in this population. The results obtained from analysis of the mtDNA region in Tankwa goats identified a unique population constructed of two lineages (A 42.5% and B 57.5%).