Mitochondrial Cytochrome b Sequence Variations and Population Structure of Siberian Chipmunk (Tamias sibiricus) in Northeastern Asia and Population Substructure in South Korea

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequ

Mitochondrial control region sequence variation within the argali wild sheep (Ovis ammon): evolution and conservation relevance

The phylogenetic relationship of several subspecies of Ovis ammon were analyzed by comparing DNA sequences within the entire mitochondrial D-loop region. Five putative subspecies of ammon (dalai-lamae, darwini, hodgsoni, sairensis and adamerzi) were sampled from four provinces in China [Xinjiang, Qinghai, Gansu and Xizang (Tibet)] and two (servertzovi and nigrimontana) from Uzbekistan. The argalis sampled represent most of the currently recognized putative Subspecies of argali. Analysis of mtDNA sequences revealed high variability within ammon (7.7%), ranging from 2.4 to 11.5%. MaxiMUM-Parsimony tree indicated that nigrimontana from Uzbekistan diverged First, followed by severtzovi from Uzbekistan. The dispersal of argalis into China gave rise to three clades, suggesting that the argali originated in Western Asia and then dispersed throughout the central Asian highlands on a southeastward course. Among the Chinese argalis, mtDNA analysis places dalailamae genetically closer to hodgsoni than to darwini. Severtzovi and.. nigrimontana are two separate subspecies and genetically distinct from the Chinese argali.

Analysis of the characteristic sequence of intein and revision of its motifs

Since the first intein (Sce VMA) was found in Saccharomydes cerevisiae ATPases gene in 1990, more and more inteins were identified. It is necessary to analyze the new inteins to understand the sequence charateristics of inteins. By searching protein and n

Identification of protein superfamily from structure-based sequence motif

The structure-based sequence motif of the distant proteins in evolution, protein tyrosine phosphatases (PTP) I and II superfamilies, as an example, has been defined by the structural comparison, structure-based sequence alignment and analyses on substitut

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Study morphologic, phylogenic relationships DNA barcoding of of identified decapod group (Crustacean) of Persian Gulf and Oman Sea.

Phylogenetic relationships among all described species (total of 12 taxa) of the decapoda, were examined with nucleotide sequence data from portions of mitochondrial gene and cytochrome oxidase subunit I (COI). The previous works on phylogeny proved that the mitochondrial COI gene in crustacean is a good discriminative marker at both inter- and intra-specific levels. We provide COI barcode sequences of commertial decapoda of Oman Sea, Persian Gulf, Iran. Industrial activities, ecologic considerations, and goals of the decapoda Barcode of Life campaign make it crucial that species of the south costal be identified. The reconstruction of evolut phylogeny of these species are crucial for revealing stock identity that can be used for the management of fisheries industries in Iran. Mitochondrial DNA sequences were used to reconstruct the phylogeny of the Penaeus species of marine shrimp. For this purpose, DNA was extracted using phenol- chloroform well as CTAB method. The evolutionary relationships among 12 species of the decapoda were examined using 610 bp of mitochondrial (mt) DNA from the cytochrome oxidase subunit I gene. Finally the cladograms were compared and the resulted phylogenetic trees confirmed that the Iran's species origin is Indo-west pacific species. Iran's species, which were not grouped with the other decapoda taxa seem to always form a sister clade with Indo-west pacific species with strong bootstrap support 100%. The result completely agrees with the previously defined species using morphological characters.However, we still lack any comprehensive and clear understanding of phylogenetic relationships in this group.

The identity of Schizothorax griseus Pellegrin, 1931, with descriptions of three new species of schizothoracine fishes (Teleostei: Cyprinidae) from China

The identity of Schizothorax griseus Pellegrin, 1931, is clarified and the species redescribed. Three new species previously identified as S. griseus are described: S. nudiventris, from the Lancang Jiang, China; S. heterophysallidos, from the Nanpan Jiang

DNA sequence analysis of the triose phosphate isomerase gene from isolates of Giardia lamblia

Objective To confirm the genetic relation between Giardia lamblia (G. lamblia) isolates from different geographic regions of China and other countries. Methods Genomic DNA were extracted from the trophozoites or cysts of Giardia lamblia. The triose phosphate isomerase (tim) gene was amplified using polymerase chain reaction (PCR) technique. PCR products were digested with endonuclease and sequenced. The data of sequencing were analyzed with the DNAstar software and compared with that of the isolates acquired from GenBank. Results Of nine isolates of Giardia lamblia from China (C1, C2, CH2 and CH3), Cambodia (CAM), Australia (A1 and A2) and America (BP and CDC), respectively, 3 (A1, A2 and CAM) fit into Group 1 (WB), 2 (CH2 and CH3) into Group 2, and 4 (C1, C2, BP and CDC) into Group 3 (GS). The results confirmed the genetic relatedness of G. lamblia isolates from all over the world. Conclusion Genotyping isolates of G. Lamblia provides important information for establishing the phylogenetic relationship or for the epidemiological evaluation of the spreading of this organism.

Identification of triosephosphate isomerase (TIM) genes from Microcystis (Cyanobacteria : Chroococcales) and theoretical analyses of the potential of cyanobacterial TIM as a target for designing specific inhibitors

The genes encoding triosephosphate isomerase (TIM) in three species of Microcystis (M. aeruginosa, M. viridis and M. wesenbergii) were investigated. Reverse transcriptase-polymerase chain reaction indicated that they were transcribed in the cells. Analyses showed that their DNA and deduced amino acid sequences were highly conserved between all the three species, only a single nonsynonymous substitution was seen at position 31, from an Asp in M. aeruginosa and M. viridis to Glu in M. wesenbergii. Sequence alignment of these with 12 other known cyanobacterial TIM sequences showed that all the cyanobacterial TIMs had a very high level of amino acid identity (over 50% between each two). Comparison of the cyanobacterial TIMs with other reported TIMs (from diverse lineages of the three Domains) showed that they possessed common active-site residues and sequence motifs. All cyanobacterial TIMs have two common cysteine residues (Cys127 and Cys176), and the Cys176 is almost cyanobacteria-specific with only one exception in Streptomyces coelicolor. Both secondary structure alignment and comparative modelling of Synechocystis sp. TIM showed that Cys176 was located at the hinge region of the flexible loop-6 and might therefore be critical to the movement of TIM's loop-6, which is important to the function of the enzyme. Thus, the cyanobacterial TIM-specific Cys176 may be a potential site for the discovery of suitable drugs against cyanobacteria, and such drugs may have utility in controlling water blooms due to cyanobacteria.