Abstract
In this study, we reported the complete mitochondrial genome (mitogenome) of Sinopodisma pieli by polymerase chain reaction method for the first time, the type species of the genus Sinopodisma. Its mitogenome was a circular DNA molecule of 15,625 bp in length, with 76.0% A+T, and contained 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes and one A+T control region. The overall base composition of the S. pieli mitogenome was 42.8% for A, 33.2% for T, 13.5% for C, and 10.5% for G, respectively. All 13 mitochondrial PCGs shared the start codon ATN. Twelve of the PCGs ended with termination codon TAA and TAG, while cytochrome coxidase subunit 1 (COI) utilized an incomplete T as terminator codon. All tRNA genes could be folded into the typical cloverleaf secondary structure, except trnS(AGN) lacking of dihydrouridine arm. The sizes of the large and small ribosomal RNA genes were 1379 bp and 794 bp, respectively. The A+T rich region was 798 bp in length and contained 88.5% AT content. A phylogenetic analysis based on 13 PCGs by using Bayesian inference (BI) and maximum likelihood (ML) revealed that Sinopodisma is not monophyletic group. We think that the name and taxonomic status of S. tsinlingensis are right, and it should not be moved into the genus Pedopodisma. These data will provide important information for a better understanding of the population genetics and species identification for Sinopodisma.
References
Boore, J.L. (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27, 1767–1780.
https://doi.org/10.1093/nar/27.8.1767Chen, Z.N. & Xu, S.Q. (2016) The complete mitochondrial DNA genome sequence of a terrestrial grasshopper, Curvipennis wixiensis (Acrididae: Podismini). Conservation Genetics Resources, 9 (1), 115–118.
https://doi.org/10.1007/s12686-016-0634-8Cheng, T.M. (1974) A new species of Sinopodisma Chang and description of the male of Chorthippus louguanensis Cheng et Tu (Orthoptera: Acrididae). Acta Entomologica Sinica, 2 (4), 335–350.
Cigliano, M.M., Braun, H., Eades, D.C. & Otte, D. (2017) Orthoptera Species File. Version 5.0/5.0. Available from: http://Orthoptera.Species File.org (accessed 28 November 2017)
Dirsh, V.M. (1961) A preliminary revision of the families and subfamilies of Acridoidea (Orthoptera, Insecta). Bulletin of the British Museum Entomology, 10 (9), 351–418.
https://doi.org/10.5962/bhl.part.16264
Dong, L.J., Shi, J.P., Zhang, X.H., Zhang, Y.L., Li, X.J. & Yin, H. (2015) Molecular phylogenetic analysis of Acridoidea (Orthoptera: Caelifera) based on mitochondrial cytochrome oxidase subunit sequences. Zootaxa, 4018 (3), 411–425.
https://doi.org/10.11646/zootaxa.4018.3.5.Duchêne, S., Archer, F.I., Vilstrup, J., Caballero, S. & Morin, P.A. (2011) Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS ONE, 6, e27138.
https://doi.org/10.1371/journal.pone.0027138
Felsenstein, J. (1985) CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP. Evolution, 39 (4), 783–791.
https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O. (2005) PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research, 33 (Supplement 2), W557–W559.
https://doi.org/10.1093/nar/gki352
Hassanin, A., Leger, N. & Deutsch, J. (2005) Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences. Systematic Biology, 54, 277–98.
https://doi.org/10.1080/10635150590947843
Hwang, U.W., Friedrich, M., Tautz, D., Park, C.J. & Kim, W. (2001) Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature, 413 (6852), 154.
https://doi.org/10.1038/35093090Huang, J., Zhang, A., Mao, S. & Huang, Y. (2013) DNA barcoding and species boundary delimitation of selected species of Chinese Acridoidea (Orthoptera: Caelifera). PLoS ONE, 8 (12), e82400.
https://doi.org/10.1371/journal.pone.0082400
Huelsenbeck, J.P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17 (8), 754–755.
https://doi.org/10.1093/bioinformatics/17.8.754Huelsenbeck, J.P., Ronquist, F., Nielsen, R. & Bollback, J.P. (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294 (5550), 2310–2314.
https://doi.org/10.1126/science.1065889Li, H.C., Xia, K.L., Bi, D.Y., Jin, X.B., Huang, C.M., Yin, X.C., Zheng, Z.M., Lian, Z.M., You, Q.J., Zhang, F.L. & Li, T.S. (2006) Orthoptera, Acridoidea, Catantopidae. Fauna Sinica, Insecta. Science Press, Beijing, 43, 1–736.
Li, X.J., Zhi, Y.C., Lang, L. & Yin, X.C. (2014) The complete mitochondrial genome of Filchnerella beicki Ramme, 1931 (Orthoptera: Acridoidea: Pamphagidae). Mitochondrial DNA, 25, 348–349.
https://doi.org/10.3109/19401736.2013.803087
Li, X.J., Zhi, Y.C., Xiao, J.T. & Yin, X.C. (2008) Generic Fauna of Catantopidae from China (Orthoptera: Acridoidea). Sichuan Journal of Zoology, 5, 035.
Liu, F. & Qiu, Z. (2016) The complete mitochondrial genome of Fruhstorferiola huayinensis (Orthoptera: Catantopidae). Mitochondrial DNA, 1 (1), 1–2.
https://doi.org/10.1080/23802359.2016.1159936
Liu, Z.W., Li, B.P. & Zheng, Z.M. (2011) Phylogeny and classification of the Catantopidae at the tribal level (Orthoptera, Acridoidea). Zookeys, 148 (148), 209–255.
https://doi.org/10.3897/zookeys.148.2081
Lowe, T.M. & Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer rna genes in genomic sequence. Nucleic Acids Research, 25 (5), 955–964.
https://doi.org/10.1093/nar/25.5.0955Nylander, J. (2004) MrModeltest. Version 2. Computer program distributed by the author. Uppsala. Evolutionary Biology Centre, Uppsala University. [software]
Perna, N.T. & Kocher, T.D. (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution, 41 (3), 353–358.
https://doi.org/10.1007/BF00186547
Posada, D. & Crandall, K.A. (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics (Oxford, England), 14 (9), 817–818.
https://doi.org/10.1093/bioinformatics/14.9.817
Taanman, J.W. (1999) The mitochondrial genome: structure, transcription, translation and replication. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1410 (2), 103–123.
https://doi.org/10.1016/S0005-2728(98)00161-3
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution, 30 (12), 2725–2729.
https://doi.org/10.1093/molbev/mst197
Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25 (24), 4876–4882.
https://doi.org/10.1093/nar/25.24.4876
Wang, W., Li, X. & Yin, X. (2004) Taxonomic study on Sinopodisma Chang from China (Orthoptera: Acridoidea: Catantopidae). Journal of Hebei University (Natural Science Edition), 24 (1), 99–106.
Wolstenholme, D.R. (1992) Animal mitochondrial DNA: structure and evolution. International Review of Cytology, 141, 173–216.
https://doi.org/10.1016/S0074-7696(08)62066-5
Yang, R., Guan, D.L. & Xu, S.Q. (2015) Complete mitochondrial genome of the Chinese endemic grasshopper Fruhstorferiola kulinga (Orthoptera: Acrididae: Podismini). Mitochondrial DNA, Part A, 27 (5), 3240–3241.
https://doi.org/10.3109/19401736.2015.1007364
Zhang, D.X. & Hewitt, G.M. (1997) Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochemical Systematics and Ecology, 25 (2), 99–120.
https://doi.org/10.1016/S0305-1978(96)00042-7
Zhang, D.X., Szymura, J.M. & Hewitt, G.M. (1995) Evolution and structural conservation of the control region of insect mitochondrial DNA. Journal of Molecular Evolution, 40 (4), 382–391.
https://doi.org/10.1007/BF00164024
Zhang, D.C., Zhi, Y.C., Yin, H., Li, X.J. & Yin, X.C. (2011) The complete mitochondrial genome of Thrinchus schrenkii (Orthoptera: Caelifera, Acridoidea, Pamphagidae). Molecular Biology Reports, 38 (1), 611–619.
https://doi.org/10.1007/s11033-010-0147-6Zhang, H.L., Zeng, H.H., Huang, Y. & Zheng, Z.M. (2013) The complete mitochondrial genomes of three grasshoppers, Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis (Orthoptera: Pamphagidae). Gene, 517 (1), 89–98.
https://doi.org/10.1016/j.gene.2012.12.080
Zhang, X., Li, X., Liu, F., Yuan, H. & Huang, Y. (2017) The complete mitochondrial genome of Tonkinacris sinensis (Orthoptera: Acrididae): A tRNA-like sequence and its implications for phylogeny. Biochemical Systematics and Ecology, 70, 147–154.
https://doi.org/10.1016/j.bse.2016.11.002
Zhang, X. & Lin, L. (2016) The complete mitochondrial genome of Fruhstorferiola tonkinensis (Orthoptera: Catantopidae). Mitochondrial DNA Part B, 1 (1), 434–435.
https://doi.org/10.1080/23802359.2016.1180555
Zhang, X.H., Hao, J.F., Xia, Y., Chang, Y., Zhang, D.C. & Yin, H. (2017) Molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) based on Hexamerin sequences. Zootaxa, 4232 (4), 523–534.
https://doi.org/10.11646/zootaxa.4232.4.4
Zheng, Z.M. (1980) New genera and new species of grasshoppers from Sichuan, Shaanxi and Yunnan. Entomotaxonomia, 17 (1), 97–99.
Zhi, Y.C., Liu, B., Han, G., Yin, H. & Zhang, D.C. (2012) The complete mitochondrial genome of Kingdonella bicollina (Orthoptera: Acridoidea: Catantopidae). Mitochondrial DNA, 27 (1), 391–392.
https://doi.org/10.3109/19401736.2014.896000