Genetic Stability of in vitro Propagated Grapevine (Vitis vinifera L.) cv. Al-Bayadi

Grapevine (Vitis vinifera L.) fruit crops are a significant source of antioxidants, fibre, and nutrients; all are vital for a healthy diet and play a key role in the economy of several advanced and developing countries. It is of great importance to generate true-to-type plant products using in vitro propagation system. Thus, somaclonal variations can multiply very rapidly which leads to loss of the main features of parent rootstocks. In this research, a mixture of three Polymerase Chain Reaction (PCR)-based molecular marker methods – (conserved DNA derived polymorphism) CDDP, (Inter-simple sequence repeat) ISSR, and DNA barcoding – have been used to verify micro propagated grapevine genetic stability. Both ISSR and CDDP primer combinations produced scorable PCR fragments. The total number of bands was 98 and 109, with an average of 9.8 and 10.9 bands/primer in ISSR and CDDP assays, respectively. On the other hand, about 20 polymorphic bands were collected by CDDP primers, of CDDP-3 and CDDP-11produced 1 and 5 bands, with a polymorphism percentage of 11% and 33%, respectively. About 5 different unique PCR bands were detected in the mother plant (control) and were not observed in micro propagated plantlets (MP) samples of grapevine plant or vice versa. The phylogenetic trees were constructed using ISSR and CDDP assays diverged the control from MP samples at 1.3% and 7%, respectively. The phylogenetic tree constructed using (chloroplast gene RNA polymerase1) rpoC1 gene, multiple sequence alignment revealed that rpoC1 gene sequencing detected small genetic differences between control and MP samples of the grapevine and clustered grapevine control and MP samples to a single cluster with other Vitis species. This experiment reveals the potentiality of using CDDP, ISSR, and DNA barcoding in detecting the somaclonal variation of grapevine varieties subjected to tissue culture as a tool for plant conservation and breeding programs.

Nucleotide diversity of a nuclear gene ITS region and chloroplast genes (matK, rbcL, rpoC1) of Canarium nigrum in some provinces in Northern Vietnam

In this study, three chloroplast genes (matK, rbcL and rpoC1) and one nuclear gene (ITS) were used to assess the nucleotide diversity for nine individuals of Canarium nigrum species in Bac Giang, Hoa Binh and Phu Tho provinces (three individuals from each province). The nucleotide sequence of the four regions (ITS, matK, rbcL and rpoC1) of C. nigrum were determined with the results showing their size to be 696 bp, 798 bp, 702 bp and 522 bp, respectively. Results of nucleotide sequence comparison for the studied samples exhibited 100% similarity for all the four gene regions. Sequence comparison with other species in the Canarium genus available in the GenBank revealed that the nucleotide diversity level (π) was the highest for the ITS gene (0.02), followed by matK (0.007), and the lowest for rbcL (0.003). The phylogenetic tree of C. nigrum with the species in Canarium genus indicated that the separation of species was the clearest for the rpoC1 gene, followed by rbcL, matK and ITS gene, with the bootrap values obtained from the branching nodes of each species ranging from 98 to 99%, 35 to 67%, 65 to 98% and 98 to 99%, respectively. The species C. nigrum had the closest nucleotide similarity to C. tramdenum (KP093200) and C. album (KP093198) for the ITS gene and to species C. subulatum (KR530509), C. acutifolium (KR530512) for matK gene region. These results suggests the rpoC1 gene region could be used as barcode for the species in genus Canarium.

Revision of the Synechococcales (Cyanobacteria) through recognition of four families including Oculatellaceae fam. nov. and Trichocoleaceae fam. nov. and six new genera containing 14 species

A total of 48 strains of thin, filamentous cyanobacteria in Synechococcales were studied by sequencing 16S rRNA and rpoC1 sequence fragments. We also carefully characterized a subset of these by morphology. Phylogenetic analysis of the 16S rRNA gene data using Bayesian inference of a large Synechococcales alignment (345 OTU’s) was in agreement with the phylogeny based on the rpoC1 gene for 59 OTU’s. Both indicated that the large family-level grouping formerly classified as the Leptolyngbyaceae could be further divided into four family-level clades. Two of these family-level clades have been recognized previously as Leptolyngbyaceae and Prochlorotrichaceae. Oculatellaceae fam. nov. and Trichocoleaceae fam. nov. are proposed for the other two families. The Oculatellaceae was studied in greater detail, and six new genera containing 14 species were characterized and named. These new taxa are: Pegethrix botrychoides, P. olivacea, P. convoluta, P. indistincta, Drouetiella lurida, D. hepatica, D. fasciculata, Cartusia fontana, Tildeniella torsiva, T. nuda, Komarkovaea angustata, Kaiparowitsia implicata, Timaviella obliquedivisa, and T. radians.

NUCLEOTIDE DIVERSITY OF 15 CONIFER SPECIES IN VIETNAM’ S CENTRAL HIGHLANDS BASED ON THE ANALYSIS OF ITS, trnH-psbA, matK, trnL AND rpoC1 GENE REGIONS

In this study, five DNA sequences from ITS, trnH-psbA, matK, trnL and rpoC1 gene regions were used to explore relationships of 15 conifer species in Highlands of Vietnam. All target gene segments has been cloned at size as predicted by the theory for all 15 species of conifers. Nucleotide-level change of 15 coniferous species in five gene regions showed from the highest to the lowest as follows: the ITS gene region (0.428), the trnH-psbA region (0.378), the trnL (0.354), the matK gene (0.192) and the rpoC1 gene (0.105). The matK gene region showed the highest level of conservation (671 nucleotides) and the trnH-psbA gene region showed the lowest (78 nucleotides). Phylogenetic tree showed that the species in the same family are formatted in a separate evolutionary branch with bootstrap values ​​obtained from the branching nodes of each species ranging from 52 to 97% for the ITS gene, from 50 to 100% for trnH-psbA gene region, from 66 to 100% for matK gene region, from 50 to 100% for trnL gene region and from 57 to 100% for rpoC1 gene region. Of the three gene regions of matK, trnL and rpoC1, the grouping of species in the same family showed the most obvious. This result suggests the three gene regions of matK, trnL and rpoC1 could be used as barcode for the 15 conifer species in central highlands of Vietnam.