The Experts below are selected from a list of 2514 Experts worldwide ranked by ideXlab platform
Tianxiang Gao - One of the best experts on this subject based on the ideXlab platform.
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The complete mitochondrial genome of Thryssa kammalensis (Clupeiformes: Engraulidae).
Mitochondrial DNA. Part B Resources, 2016Co-Authors: Jing Zhang, Tianxiang GaoAbstract:AbstractIn this study, the complete mitochondrial genome (mitogenome) sequence of Thryssa kammalensis has been determined by long polymerase chain reaction and Primer Walking methods. The mitogenome is a circular molecule of 16 968 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, two ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence (TAS) domain, the central conserved sequence block domains (CSB-F, CSB-E and CSB-D) and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3). There are eight copies of tandem repeats of 38 bp in the control region, which contain TAS.
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the complete mitochondrial genome of the tessellated leatherjacket thamnaconus tessellatus tetraodontiformes monacanthidae
Mitochondrial DNA, 2016Co-Authors: Zhiyang Wang, Zhaohui Zhang, Longshan Lin, Tianxiang GaoAbstract:AbstractThe long PCR and Primer Walking methods were applied for obtaining the complete mitochondrial genome of the tessellated leatherjacket Thamnaconus tessellatus. The complete mitochondrial genome was 16,437 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication and a control region. The arrangements and characteristics of these segments shared common features with other teleosts. Extended termination associated sequence domain (TAS, cTAS), central conserved sequence block domain (CSB-F, CSB-E, CSB-D) and conserved sequence block domain (CSB-1, CSB-2, CSB-3) were identified in the control region.
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the complete mitochondrial genome of sebastes koreanus scorpaeniformes scorpaenidae from china
Mitochondrial DNA, 2016Co-Authors: Yalu Fang, Na Song, Tianxiang Gao, Zhaohui ZhangAbstract:In this study, the complete mitochondrial genome (mitogenome) sequence of Sebastes koreanus was determined by long PCR and Primer Walking methods. The complete mitochondrial genome is 17,606 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) as well as a control region (CR) as other bony fishes. The overall base composition of the S. koreanus mitogenome was estimated to be 28.56% for A, 27.77% for C, 16.83% for G and 26.85% for T, respectively, indicating an obvious anti-guanine bias. Twelve of the 13 mitochondrial protein-coding genes have an ATG start codon while COX1 had a GTG start codon; the incomplete stop codon (T/TA) was present in the COII, COIII, ND2, ND3, ND4 and Cytb genes. The complete mitogenome sequence of S. koreanus will contribute to molecular phylogenetic and evolutionary analyses of Sebastinae.
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the complete mitochondrial genome of coilia nasus clupeiformes engraulidae from ariake sea
Mitochondrial DNA, 2016Co-Authors: Nan Zhang, Na Song, Tianxiang GaoAbstract:In this study, the complete mitochondrial genome (mitogenome) sequence of Coilia nasus has been determined by long polymerase chain reaction and Primer Walking methods. The mitogenome is a circular molecule of 16,900 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).
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The complete mitochondrial genome of Coilia grayii (Clupeiformes: Engraulidae)
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2015Co-Authors: Zhaohui Zhang, Nan Zhang, Ming Liu, Tianxiang GaoAbstract:In this study, the complete mitochondrial genome (mitogenome) sequence of Coilia grayii has been determined by long polymerase chain reaction and Primer Walking methods. The mitogenome is a circular molecule of 16,851 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNAs (tRNAs) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).
Mutsumi Nishida - One of the best experts on this subject based on the ideXlab platform.
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PCR-Based Approach for Sequencing Mitochondrial Genomes of Decapod Crustaceans, with a Practical Example from Kuruma Prawn (Marsupenaeus japonicus)
Marine Biotechnology, 2004Co-Authors: Mitsugu M Yamauchi, Ryuji J Machida, Masaki U. Miya, Mutsumi NishidaAbstract:An approach for sequencing the entire mitochondrial genomes (mitogenomes) of decapod crustaceans using 79 newly designed and 7 published polymerase chain reaction (PCR) Primers is described. The approach comprises the following steps: (1) the entire mitogenome is amplified in 2 or 3 long PCRs; (2) the 86 Primers are used in different combinations to amplify contiguous, overlapping short segments of the entire mitogenome with the diluted long PCR products as templates; (3) direct cycle sequencing is conducted using the short PCR products. This strategy allows a more rapid determination of decapod mitogenomic sequences than a traditional method using cloned mitochondrial DNA and Primer Walking strategy. As a practical example, the mitogenomic sequence for a kuruma prawn Marsupenaeus japonicus (Crustacea: Decapoda), was determined using the PCR-based approach.
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use of a pcr based approach for sequencing whole mitochondrial genomes of insects two examples cockroach and dragonfly based on the method developed for decapod crustaceans
Insect Molecular Biology, 2004Co-Authors: Mitsugu M Yamauchi, Masaki Miya, Mutsumi NishidaAbstract:Recent development of a PCR-based approach for sequencing vertebrate mitochondrial genomes has attracted much attention as being more rapid and economical than traditional methods using cloned mtDNA and Primer Walking. Such a method has not been available for insect mitochondrial genomes, despite widespread use of them for the molecular phylogenetic, biogeographical and population genetic markers. A recently developed PCR-based approach for sequencing whole mitochondrial genomes of decapod crustaceans, which included the design of many versatile PCR Primers for the latter, was applied with the same Primers sets to mitochondrial genomes of two insects, smoky-brown cockroach Periplaneta fuliginosa (Serville, 1839) and skimmer dragonfly Orthetrum triangulare melania (Selys, 1883). Almost the entire region of the two mitochondrial genomes was successfully sequenced. Features of the two mitochondrial genomes are described and the usefulness of this PCR-based approach for sequencing insect mitochondrial genomes demonstrated.
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large scale gene rearrangements in the mitochondrial genomes of two calanoid copepods eucalanus bungii and neocalanus cristatus crustacea with notes on new versatile Primers for the srrna and coi genes
Gene, 2004Co-Authors: Ryuji J Machida, Masaki Miya, Mutsumi Nishida, Shuhei NishidaAbstract:Partial sequences of the mitochondrial genomes were determined for two calanoid copepods, Eucalanus bungii [9530 bp (base pairs)] and Neocalanus cristatus (7965 bp), using an approach that employs a long polymerase chain reaction (PCR) technique and Primer Walking. In contrast to Tigriopus japonicus (Harpacticoida), in which the complete mitochondrial genome has been determined, genes are encoded on both strands of the genome. In spite of the close relationship between E. bungii and N. cristatus, the gene orders of these calanoid copepods differed greatly from each other. From the sequence we obtained, new copepod-specific versatile Primers were designed for the cytochrome c oxidase I (COI) gene (1200 bp). These Primer pairs, as well as the previously designed Primer pairs for the small ribosomal RNA (srRNA) gene (500 bp), were applied for 20 species representing four orders of both calanoid and non-calanoid copepods and amplification of sequences from at least one species from each order was successful.
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complete mitochondrial dna sequence of the swimming crab portunus trituberculatus crustacea decapoda brachyura
Gene, 2003Co-Authors: Mitsugu M Yamauchi, Masaki Miya, Mutsumi NishidaAbstract:We determined the complete mitochondrial DNA sequence for a swimming crab Portunus trituberculatus (Miers, 1876) (Crustacea: Decapoda: Brachyura). The entire genome was amplified using a long PCR technique, and the products were subsequently used as templates for direct sequencing using a Primer Walking strategy. The genome (16,026 bp) contained the same 37 genes (two rRNAs, 22 tRNAs, and 13 proteins) plus the putative control region as found in other arthropods. The gene order of P. trituberculatus was largely identical to those so far obtained for other arthropods such as Drosophila yakuba, although the relative position of the tRNA(His) gene differed from all other arthropods studied so far. While the tRNA(His) gene in other arthropod mitochondrial genomes is located between the ND4 and ND5 genes, that of P. trituberculatus was found between the tRNA(Glu) and the tRNA(Phe) genes, which were located downstream of the ND5 gene. The present gene order could have resulted from tandem duplication occurring in the tRNA(Phe)-ND5-tRNA(His) region (typical gene order in other arthropods) and following deletions of redundant genes. This is the first report of a mitochondrial genome of a brachyuran crab, one of the most diversified and economically important groups of crustaceans.
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Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda).
Marine biotechnology (New York N.Y.), 2002Co-Authors: Ryuji J Machida, Masaki Miya, Mutsumi Nishida, Shuhei NishidaAbstract:The complete nucleotide sequence of the mitochondrial genome was determined for a harpacticoid copepod, Tigriopus japonicus (Crustacea), using an approach that employs a long polymerase chain reaction technique and Primer Walking. Although the genome (14,628 bp) contained the same set of 37 genes (2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) as found in other metazoan animals, none of the previously reported gene orders were comparable to that of T. japonicus. Furthermore, all genes were encoded on one strand, unlike the mitochondrial genomes of most metazoan animals. Size reductions were notable for tRNA and rRNA genes, resulting in one of the smallest mitochondrial genomes in the arthropod lineage. Although it appears that such large-scale gene rearrangements have occurred in the ancestral species of T. japonicus, none of the proposed mechanisms parsimoniously account for this eccentric gene arrangement.
Rachael E Tarlinton - One of the best experts on this subject based on the ideXlab platform.
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retrieval of the complete coding sequence of the uk endemic tatenale orthohantavirus reveals extensive strain variation and supports its classification as a novel species
Viruses, 2020Co-Authors: Joseph G Chappell, Theocharis Tsoleridis, Okechukwu Onianwa, Gabby Drake, Ian Ashpole, Phillipa Dobbs, William Edema, Frederick Kumiansah, Malcolm J Bennett, Rachael E TarlintonAbstract:Orthohantaviruses are globally distributed viruses, associated with rodents and other small mammals. However, data on the circulation of orthohantaviruses within the UK, particularly the UK-endemic Tatenale virus, is sparse. In this study, 531 animals from five rodent species were collected from two locations in northern and central England and screened using a degenerate, pan- orthohantavirus RT-PCR assay. Tatenale virus was detected in a single field vole (Microtus agrestis) from central England and twelve field voles from northern England. Unbiased high-throughput sequencing of the central English strain resulted in the recovery of the complete coding sequence of a novel strain of Tatenale virus, whilst PCR-Primer Walking of the northern English strain recovered almost complete coding sequence of a previously identified strain. These findings represented the detection of a third lineage of Tatenale virus in the United Kingdom and extended the known geographic distribution of these viruses from northern to central England. Furthermore, the recovery of the complete coding sequence revealed that Tatenale virus was sufficiently related to the recently identified Traemersee virus, to meet the accepted criteria for classification as a single species of orthohantavirus.
Wilhelm Ansorge - One of the best experts on this subject based on the ideXlab platform.
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automated low redundancy large scale dna sequencing by Primer Walking
BioTechniques, 1993Co-Authors: Hartmut Voss, Stefan Wiemann, Dietmar Grothues, Christoph Wilhelm Sensen, Jurgen Zimmermann, Christian Schwager, J Stegemann, Holger Erfle, Thomas Rupp, Wilhelm AnsorgeAbstract:Low-redundancy automated DNA sequencing by Primer Walking is described. T7 DNA polymerase is used together with computer-selected Walking Primers and fluorescein-dATP as internal label to sequence large plasmids or cosmids directly on a standard DNA sequencer with an error rate below 1% up to 500 bases (in the unedited raw data). The low error rate allows efficient sequencing with low (2-3 times) redundancy. Plasmid subclones covering 20 kb of a cosmid insert were sequenced with an overall redundancy of 2.7 in the course of the European community Saccharomyces cerevisiae genome sequencing project. Neighboring plasmid subclones were linked by direct cosmid sequencing. Sets of ten Walking Primers are synthesized on the EMBL multiple segmental DNA synthesizer at low costs and used for sequencing with greater than 95% efficiency. The accuracy of the directed approach is improved by simultaneous Walking on both strands by designing two Primers in opposite directions in the same starting region. One Primer is used to confirm sequence data on the opposite strand, and the other Primer to obtain new sequence data.
Waclaw Szybalski - One of the best experts on this subject based on the ideXlab platform.
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genomic dna sequencing by spel 6 Primer Walking using hexamer ligation
Gene, 1998Co-Authors: Tadeusz Kaczorowski, Waclaw SzybalskiAbstract:Abstract DNA sequencing by SPEL-6 (Sequential Primer Elongation by Ligation of 6-mers) Primer Walking is based on the rapid assembly of true Primers by ligation of several (three to 10) contiguous hexamers complementary to a DNA template saturated with Escherichia coli single-stranded DNA-binding protein. To prove the usefulness and to check the reliability of this method, a 3-kb DNA fragment carrying the genes encoding the EcoVIII restriction-modification (RM) system was sequenced with low redundancy (2.8). The use of both single-stranded (ss) and double-stranded (ds) DNA templates was compared. For this project, 27 Primers were assembled by hexamer ligation to form 18–30-nt strings of three to five hexamers. Each Primer was designed based on nucleotide sequence determined in a previous run, and was produced in a matter of minutes. The overall length of the easily readable sequencing ladders was about 300–450 nt. We found that strong secondary structures in the ss DNA tend to interfere with its template function for the Primer assembly by hexamer ligation, especially when they overlap the 3′-end of such a Primer. This was easily overcome either by avoiding such hairpin regions or by using longer strings of hexamers, since we show that their ligation is highly cooperative, and ligation efficiency increases with the length of the string ( Kaczorowski and Szybalski, 1996a ). Some general rules for successful Primer assembly and prospects for using the SPEL-6 method for large-scale, fully automated fluorescent sequencing of large genomes are discussed.
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assembly of 18 nucleotide Primers by ligation of three hexamers sequencing of large genomes by Primer Walking
Analytical Biochemistry, 1994Co-Authors: Tadeusz Kaczorowski, Waclaw SzybalskiAbstract:A novel method (SPEL-6) for sequencing large genomes permits 10-min synthesis of 18-mer Primers and their immediate use in DNA sequencing by Primer Walking. Primers are ligated from three contiguous hexamers complementary to the single-stranded or denatured DNA (150:1 ratio), which is used both as the template for ligation and as the DNA to be sequenced. The complete library consists of 4096 hexamers, but sequencing remains very efficient with a fourfold smaller library composed of 1024 degenerate hexamers containing all four nucleotides at their position 3. The SSB protein (which binds to single-stranded DNA) greatly enhances the quality of sequencing ladders. The SPEL-6 method eliminates the need for subcloning, permits direct sequencing of large DNA fragments (of 50 kb or larger), is ideally suited for automation, and should accelerate the sequencing of large genomes by more than one order of magnitude.