[1].Complete Mitochondrial Genome of the Steppe Ribbon Racer (Psammophis lineolatus): The First Representative from the Snake Family Psammophiidae and its Phylogenetic Implications[J].Asian Herpetological Research,2021,12(3):295-307.[doi:10.16373/j.cnki.ahr.200129]
　Minli CHEN,Jinlong LIU,Jun LI,et al.Complete Mitochondrial Genome of the Steppe Ribbon Racer (Psammophis lineolatus): The First Representative from the Snake Family Psammophiidae and its Phylogenetic Implications[J].Asian Herpetological Research(AHR),2021,12(3):295-307.[doi:10.16373/j.cnki.ahr.200129]
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Complete Mitochondrial Genome of the Steppe Ribbon Racer (Psammophis lineolatus): The First Representative from the Snake Family Psammophiidae and its Phylogenetic Implications()
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Asian Herpetological Research[ISSN:2095-0357/CN:51-1735/Q]

卷:
12
期数:
2021年3期
页码:
295-307
栏目:
出版日期:
2021-09-25

文章信息/Info

Title:
Complete Mitochondrial Genome of the Steppe Ribbon Racer (Psammophis lineolatus): The First Representative from the Snake Family Psammophiidae and its Phylogenetic Implications
文章编号:
AHR-2020-0129
Author(s):
Minli CHEN1; 2 ;  Jinlong LIU2;  Jun LI3 ;  Na WU1; 2 and Xianguang GUO1*
1 Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
2 University of Chinese Academy of Sciences, Beijing 100049, China
3 College of Life Science and Technology, Xinjiang University, Urumqi 830046, Xinjiang, China
Keywords:
mitochondrial genome;  phylogenetic relationships;  Psammophis lineolatus;  Psammophiidae;  purifying selection
DOI:
10.16373/j.cnki.ahr.200129
Abstract:
Comparisons of vertebrate mitochondrial genomes (mitogenomes) may yield significant insights into the evolution of organisms and genomes. However, no complete mitogenome from the snake family Psammophiidae has been reported. In this study, we sequenced and annotated the complete mitogenome of Psammophis lineolatus, representing the first mitogenome of Psammophiidae. The total length is 17 166 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (12S rRNA and 16S rRNA), and duplicate control regions (CRs). This gene arrangement belongs to the Type III pattern, which is a widely shared gene order in Alethinophidian snakes. All tRNAs exhibit cloverleaf structures with the exception of tRNA-SerAGY and tRNA-Pro, which lack a dihydrouridine (DHU) arm/stem and TΨC loop, respectively. The 13 PCGs include five start codons (ATG, GTG, ATA, ATT, and ATC), two complete stop codons (TAA and AGG), and two incomplete stop codon (T-- and TA-). In addition, the Ka/Ks ratios indicate that all PCGs had undergone a strong purifying selection. Four types of CR domains rearrangement occurred among eight species of Elapoidea. The phylogenetic reconstructions with both Bayesian inference and maximum likelihood methods support the placement of Psammophiidae in the Elapoidea superfamily, with Homalopsidae being the sister taxon to Elapoidea and Colubroidea. However, the sister taxon of Psammophiidae is unclear due to the availability of Elapoidea mitogenomes being limited to the family Elapidae. More mitogenomes from different taxonomic groups in Elapoidea are needed to better understand the phylogenetic relationships within Elapoidea.

参考文献/References:

Bernt M., Bleidorn C., Braband A., Dambach J., Donath A., Fritzsch G., Golombek A., Hadrys H., Jühling F., Meusemann K., Middendorf M., Misof B., Perseke M., Podsiadlowski L., von Reumont B., Schierwater B., Schlegel M., Schr?dl M., Simon S., Stadler P. F., St?ger I., Struck T. H. 2013a. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol Phylogenet Evol, 69: 352–364
Bernt M., Braband A., Schierwater B., Stadler P. F. 2013b. Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol, 69: 328–338
Bernt M., Donath A., Jühling F., Externbrink F., Florentz C., Fritzsch G., Pütz J., Middendorf M., Stadler P. F. 2013c. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol, 69: 313–319
Boore J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res, 27: 1767–1780
Boore J. L., Brown W. M. 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev, 8: 668–674
Bourgeois M. 1968. Contribution à la morphologie comparée du cr?ne des Ophidiens de l’Afrique Centrale. Publications de l’Université Officielle du Congo vol. XVIII: 1–293
Brandt J. F. 1838. Note sur quatre nouvelles espèces de serpents de la c?te occidentale de la mer Caspienne et de la Perse septentrionale, découvertes par M. Kareline; par M. Brandt (in le 22 dècembre 1837). Bulletin de l’Académie Impériale des Sciences de Saint Pétersbourg, 3: 241–244
Cai Y., Li Q., Zhang J., Storey K. B., Yu D. 2020. Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses. PeerJ, 8: e8901
Chen N., Zhao S. 2009. New progress in snake mitochondrial gene rearrangement. Mitochondrial DNA, 20: 69–71
Doda J. N., Wright C. T., Clayton D. A. 1981. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA, 78: 6116–6120
Dong S., Kumazawa Y. 2005. Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features. J Mol Evol, 61: 12–22
Douglas D. A., Gower D. J. 2010. Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution. BMC Genomics, 11: 14
Douglas D. A., Jank A., Arnason U. 2006. A mitogenomic study on the phylogenetic position of snakes. Zool Scr, 35: 545–558
Dowling H. G., Duellman W. E. 1978. Systematic herpetology: A synopsis of families and higher categories. HISS Publications, New York
Dubey B., Meganathan P. R., Haque I. 2012. Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae). Mol Biol Rep, 39: 7403–7412
Figueroa A., McKelvy A. D., Grismer L. L., Bell C. D., Lailvaux S. P. 2016. A species-level phylogeny of extant snakes with description of a new colubrid subfamily and genus. PLoS ONE, 11: e0161070
Gouy M., Guindon S., Gascuel O. 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol, 27: 221–224
Gravlund P. 2001. Radiation within the advanced snakes (Caenophidia) with special emphasis on African Opistoglyph colubrids, based on mitochondrial sequence data. Biol J Linn Soc, 72: 99–114
Greiner S., Lehwark P., Bock R. 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res, 47: W59–W64
Hurst L. D. 2002. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet, 18: 486–487
Hurst L. D. 2009. Evolutionary genomics and the reach of selection. J Biol, 8: 12
Jiang Z. J., Castoe T. A., Austin C. C., Burbrink F. T., Herron M. D., McGuire J. A., Parkinson C. L., Pollock D. D. 2007. Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region. BMC Evol Biol, 7: 123
Katoh K., Standley D. M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 30: 772–780
Kelly C. M. R., Barker N. P., Villet M. H. 2003. Phylogenetics of advanced snakes (Caenophidia) based on four mitochondrial genes. Syst Biol, 52: 439–459
Kelly C. M. R., Barker N. P., Villet M. H., Broadley D. G., Branch W. R. 2008. The snake family Psammophiidae (Reptilia: Serpentes): Phylogenetics and species delimitation in the African sand snakes (Psammophis Boie, 1825) and allied genera. Mol Phylogenet Evol, 47: 1045–1060
Kelly C. M. R., Barkera N. P., Villetb M. H., Broadley D. G. 2009. Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the late Eocene. Cladistics, 25: 38–63
Knaus B. J., Cronn R., Liston A., Pilgrim K., Schwartz M. K. 2011. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore. BMC Ecol, 11: 10
Kumar S., Stecher G., Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol, 33: 1870–1874
Kumazawa Y. 2004. Mitochondrial DNA sequences of five squamates, phylogenetic affiliation of snakes. DNA Res, 11: 137–144
Kumazawa Y., Ota H., Nishida M., Ozawa T. 1996. Gene rearrangements in snake mitochondrial genomes, highly concerted evolution of control region-like sequences duplicated and inserted into a tRNA gene cluster. Mol Biol Evol, 13: 1242–1254
Kumazawa Y., Ota H., Nishida M., Ozawa, T. 1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics, 150: 313–329
Lanfear R., Frandsen P. B., Wright A. M., Senfeld T., Calcott B. 2017. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol, 34: 772–773
Lawson R., Slowinski J. B., Crother B. I., Burbrink F. T. 2005. Phylogeny of the Colubroidea (Serpentes): New evidence from mitochondrial and nuclear genes. Mol Phylogenet Evol, 37: 581–601
Levinson G., Gutman G. A. 1987. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol Biol Evol, 4: 203–221
Lowe T. M., Chan P. P. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA gene. Nucleic Acids Res, 44: W54–W57
Macey J. R., Larson A., Ananjeva N. B., Fang Z., Papenfuss T. J. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol Biol Evol, 14: 91–104
Mauro D. S., Gower D. J., Zardoya R., Wilkinson M. 2006. A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. Mol Biol Evol, 23: 227–234
Minh B. Q., Nguyen M. A. T., Haeseler A. V. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol, 30: 1188–1195
Nagy Z. T., Joger U., Wink M., Glaw F., Vences M. 2003. Multiple colonization of Madagascar and Socotra by colubrid snakes: evidence from nuclear and mitochondrial gene phylogenies. Proc Biol Sci, 270: 2613–2621
Nguyen L., Schmidt H. A., Arndt V. H., Minh B. Q. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol, 32: 268–274
Ojala D., Montoya J., Attardi G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature, 290: 470–474
Okajima Y., Kumazawa Y. 2010. Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications. BMC Evol Biol, 10: 141
Pereira S. L. 2000. Mitochondrial genome organization and vertebrate phylogenetics. Genet Mol Biol, 23: 745–752
Perna N. T., Kocher T. D. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol, 41: 353–358
Pruitt K. D., Tatusova T., Maglott D. R. 2007. NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res, 35: D61–D65
Pyron R. A., Burbrink F. T., Colli G. R., de Oca A. N. M., Vitt L. J., Kuczynski C. A., Wiens J. J. 2011. The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Mol Phylogenet Evol, 58: 329–342
Pyron R. A., Hendry C. R., Chou V. M., Lemmon E. M., Lemmon A. R., Burbrink F. T. 2014. Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia). Mol Phylogenet Evol, 81: 221–231
Qian L. 2018. Evolution of the mitochondrial genome structure in snake, with the biogeography analysis of Protobothrops. Doctoral Dissertation, Anhui University, Hefei, Anhui Province, China (In Chinese with English abstract)
Qian L., Wang H., Yan J., Pan T., Jiang S., Rao D., Zhang B. 2018. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes. BMC Genomics, 19: 354
Raina S. Z., Faith J. J., Disotell T. R., Seligmann H., Stewart C., Pollock D. D. 2005. Evolution of base-substitution gradients in primate mitochondrial genomes. Genome Res, 15: 665–673
Reeder T. W., Townsend T. M., Mulcahy D. G., Noonan B. P., Wood Jr P. L., Sites Jr J. W., Wiens J. J. 2015. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa. PLoS ONE, 10: e0118199
Ronquist F., Teslenko M., Mark P. V. D., Ayres D. L., Darling A., H?hna S., Larget B., Liu L., Suchard M. A., Huelsenbeck J. P. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol, 61: 539–542
Rozas J., Ferrer-Mata A., Sánchez-DelBarrio J. C., Guirao-Rico S., Librado P., Ramos-Onsins S. E., Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol, 34: 3299–3302
Sbisa E., Tanzariello F., Reyes A., Pesole G., Saccone C. 1997. Mammalian mitochondrial D-loop region structural analysis: Identification of new conserved sequences and their functional and evolutionary implications. Gene, 205: 125–140
Streicher J. W., Wiens J. J. 2016. Phylogenomic analyses reveal novel relationships among snake families. Mol Phylogenet Evol, 100: 160–169
Sun C., Liu H., Lu C. 2020. Five new mitogenomes of Phylloscopus (Passeriformes, Phylloscopidae): Sequence, structure, and phylogenetic analyses. Int J Biol Macromol, 146: 638–647
Uetz P., Freed P., Ho?ek J. 2020. The Reptile Database, http://www.reptile-database.org (accessed 1st October 2020)
Vidal N., Hedges S. B. 2002a. Higher-level relationships of snakes inferred from four nuclear and mitochondrial genes. C R Biol, 325: 977–985
Vidal N., Hedges S. B. 2002b. Higher-level relationships of caenophidian snakes inferred from four nuclear and mitochondrial genes. C R Biol, 325: 987–995
Wang G. L., He S. P., Huang S., He M., Zhao E. M. 2009. The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata). Chin Sci Bull, 54: 1713–1724
Wiens J. J., Hutter C. R., Mulcahy D. G., Noonan B. P., Townsend T. M., Sites Jr J. W., Reeder T. W. 2012. Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biol Lett, 8: 1043–1046
Wilcox T. P., Zwickl D. J., Heath T. A., Hillis D. M. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol Phylogenet Evol, 25: 361–371
Xia Y., Zheng Y., Miura I., Wong P. B. Y., Murphy R. W., Zeng X. 2014. The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization. BMC Genomics, 15: 691
Xia Y., Zheng Y., Murphy R. W., Zeng X. 2016. Intraspecific rearrangement of mitochondrial genome suggests the prence of the tandem duplication random loss (TDLR) mechanism in Quasipaa boulengeri. BMC Genomics, 17: 965
Yan J., Li H., Zhou K. 2008. Evolution of the mitochondrial genome in snakes: Gene rearrangements and phylogenetic relationships. BMC Genomics, 9: 569
Yang Z., Bielawski J. P. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol, 15: 496–503
Yu X., Du Y., Fang M., Li H., Lin L. 2018. The mitochondrial genome of Pseudocalotes microlepis (Squamata: Agamidae) and its phylogenetic position in agamids. Asian Herpetol Res, 9: 24–34
Zaher H. 1999. Hemipenial morphology of the South American Xenodontine snakes, with a proposal for a monophyletic Xenodontinae and a reappraisal of colubroid hemipenes. Bull Am Mus Nat Hist, 240: 1–168
Zaher H., Murphy R. W., Arredondo J. C., Graboski R., Machado-Filho P. R., Mahlow K., Montingelli G. G., Quadros A. B., Orlov N. L., Wilkinson M., Zhang Y. P., Grazziotin F. G. 2019. Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes). PLoS ONE, 14: e0216148
Zheng Y., Wiens J. J. 2016. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol Phylogenet Evol, 94: 537–557

更新日期/Last Update: 2021-09-25