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      Complete mitochondrial genomes of Boigakraepelini and Hebiuscraspedogaster (Reptilia, Squamata, Colubridae) and their phylogenetic implications

      research-article
      1 , 1 ,
      ZooKeys
      Pensoft Publishers
      Colubrinae, mitogenomes, Natricinae, phylogenetic analysis, protein-coding genes

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          Abstract

          The complete sequence of the mitochondrial genome is a powerful tool for studying phylogenetic relationships and molecular evolution in various species. In this work, the mitogenomes of Boiga kraepelini and Hebius craspedogaster were sequenced and characterized for the first time. The lengths of the B. kraepelini and H. craspedogaster mitogenomes were 17,124 bp and 17,120 bp, respectively, and both included 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. The arrangements of these mitochondrial genes were the same in B. kraepelini and H. craspedogaster . In addition, both genome compositions showed A+T bias (59.03%, 60.93%) and had positive AT skews (0.179, 0.117) and negative GC skews (-0.397, -0.348). The phylogenetic results illustrated a close relationship between B. kraepelini and the genus Lycodon . Moreover, H. craspedogaster was clustered with other Hebius snakes and closely related to other Natricinae species. These results will provide references for further research on the phylogeny of Colubridae .

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          Most cited references44

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

            Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
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              MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

              K Katoh (2002)
              A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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                Author and article information

                Contributors
                Role: Writing - original draft
                Role: Data curationRole: Writing - review and editing
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2022
                17 October 2022
                : 1124
                : 191-206
                Affiliations
                [1 ] College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China Zhejiang Normal University Jinhua China
                [2 ] Key Laboratory of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, China Zhejiang Normal University Jinhua China
                Author notes
                Corresponding author: Yu Wang (yuwang@zjnu.edu.cn)

                Academic editor: Robert Jadin

                Author information
                https://orcid.org/0000-0001-9478-3998
                https://orcid.org/0000-0002-2972-3881
                Article
                87861
                10.3897/zookeys.1124.87861
                9836618
                1dd973b4-deeb-4e7f-91bf-aac0e6aafeee
                Shuangshuang Shan, Yu Wang

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 16 June 2022
                : 25 September 2022
                Funding
                Zhejiang Provincial Natural Science Foundation of China
                Categories
                Research Article
                Serpentes
                Phylogeny
                China

                Animal science & Zoology
                colubrinae,mitogenomes,natricinae,phylogenetic analysis,protein-coding genes

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