Published December 31, 2017
| Version v1
Journal article
Restricted
The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea
Authors/Creators
Description
Wang, Ying, Cao, Jinjun, Li, Weihai (2017): The complete mitochondrial genome of the styloperlid stonefly species Styloperla spinicercia Wu (Insecta: Plecoptera) with family-level phylogenetic analyses of the Pteronarcyoidea. Zootaxa 4243 (1): 125-138, DOI: 10.11646/zootaxa.4243.1.5
Files
Linked records
Additional details
References
- Abascal, F., Zardoya, R. & Telford, M.J. (2010) TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Research, 38, 7-13.
- Altschup, S., Gish, W., Miller, W., Myers, E. & Lipman, D. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
- https://doi.org/10.1016/S0022-2836(05)80360-2
- Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27, 573-580. https://doi.org/10.1093/nar/27.2.573
- Cameron, S.L. (2014) Insect mitochondrial genomics: implications for evolution and phylogeny. Annual Review of Entomology, 59, 95-117.
- Cameron, S.L. & Whiting, M.F. (2008) The complete mitochondrial genome of the tobacco hornworm, Manduca sexta (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene, 408, 112-123.
- Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540-552.
- Chen, Z.T. & Du, Y.Z. (2015) Comparison of the complete mitochondrial genome of the stonefly Sweltsa longistyla (Plecoptera: Chloroperlidae) with mitogenomes of three other stoneflies. Gene, 558 (1), 82-87. https://doi.org/10.1016/j.gene.2014.12.049
- Chen, Z.T., Wu, H.Y. & Du, Y.Z. (2016) The nearly complete mitochondrial genome of a stonefly species, Styloperla sp. (Plecoptera: Styloperlidae). Mitochondrial DNA Part A, 27, 2728-2729.
- Dai, X., Xun, H.Z., Chang, J., Zhang, J.G., Hu, B.W., Li, H., Yuan, X.Q. & Cai, W.Z. (2012) The complete mitochondrial genome of the plant bug Nesidiocoris tenuis (reuter)(Hemiptera: Miridae: Bryocorinae: Dicyphini). Zootaxa, 3554, 30-44.
- Elbrecht, V. & Leese, F. (2015) The mitochondrial genome of the Arizona Snowfly Mesocapnia arizonensis (Plecoptera, Capniidae). Mitochondrial DNA, 27 (5), 1-2.
- Elbrecht, V., Poettker, L., John, U. & Leese, F. (2015) The complete mitochondrial genome of the stonefly Dinocras cephalotes (Plecoptera, Perlidae). Mitochondrial DNA, 26, 469-470.
- Gao, J.Y., Li, H., Truong, X.L., Dai, X., Chang, J. & Cai, W.Z. (2013) Complete nucleotide sequence and organization of the mitochondrial genome of Sirthenea flavipes (Hemiptera: Reduviidae: Peiratinae) and comparison with other assassin bugs. Zootaxa, 3669 (1), 1-16.
- Hall, T.A. (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
- Hebert, P.D.N., Ratnasingham, S. & DeWaard, J.R. (2003) Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society Biological Sciences, 270 (Supplement), S96-S99. https://doi.org/10.1098/rsbl.2003.0025
- Huang, M.C., Wang, Y.Y., Liu, X.Y., Li, W.H., Kang, Z.H., Wang, K., Li, X.K. & Yang, D. (2015) The complete mitochondrial genome and its remarkable secondary structure for a stonefly Acroneuria hainana Wu (Insecta: Plecoptera, Perlidae). Gene, 557, 52-60.
- Illies, J. (1966) Katalog der rezenten Plecoptera, In Das Tierreich, 82. Walter de Gruyter and Company Press, Berlin, xxx + 632 pp.
- James, B.S. & Andrew, T.B. (2006) Insect mitochondrial genomics 2: the complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A + T-region elements. Genome, 49, 815-824.
- Johns, G.C. & Avise, J.C. (1998) A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution, 15, 1481-1490.
- Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment sofware version 7: improvements in performance and usability. Molecular Biology and Evolution, 30, 772-780.
- Kearse, M., Richard, M., Amy, W., Steven, S.H., Matthew, C., Shane, S., Simon, B., Alex, C., Sidney, M., Chris, D., Tobias, T., Bruce, A., Peter, M. & Alexei, D. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28 (12), 1647-1649. https://doi.org/10.1093/bioinformatics/bts199
- Li, H., Liu, H., Shi, A.M., Stys, P., Zhou, X.G. & Cai, W.Z. (2012a) The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae). PLoS ONE, 7, e29419. https://doi.org/10.1371/journal.pone.0029419
- Li, H., Liu, H.Y., Cao, L.M. & Cai, W.Z. (2012b) The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae). International Journal of Biological Sciences, 8 (1), 93-107. https://doi.org/10.7150/ijbs.8.93
- Li, H., Shao, R., Song, F., Zhou, X.G., Yang, Q.Q., Li, Z.H. & Cai, W.Z. (2013) Mitochondrial genomes of two barklice, Psococerastis albimaculata and Longivalvus hyalospilus (Psocoptera: Psocomorpha): contrasting rates in mitochondrial gene rearrangement between major lineages of Psocodea. PLoS ONE, 8, e61685. https://doi.org/10.1371/journal.pone.0061685
- Lohse, M., Bolger, A.M., Nagel, A., Fernie, A.R., Lunn, J.E., Stitt, M. & Usadel, B. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seqbased transcriptomics. Nucleic Acids Research, 40, W622-W627. https://doi.org/10.1093/nar/gks540
- 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, 955-964.
- McMahon, D.P., Hayward, A. & Kathirithamby, J. (2009) The mitochondrial genome of the 'twisted-wing parasite' Mengenilla australiensis (Insecta, Strepsiptera): a comparative study. BMC Genomics, 10, 603. https://doi.org/10.1186/1471-2164-10-603
- Park, D.S., Foottit, R., Maw, E. & Hebert, P.D. (2011) Barcoding bugs: DNA-based identification of the true bugs (Insecta: Hemiptera: Heteroptera). PLoS ONE, 6, e29419.
- Peng, Y., Leung, H.C.M., Yiu, S.M. & Chin, F.Y.L. (2012) IBDA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28, 1420-1428.
- Perna, N.T. & Kocher, T.D. (1995) Patterns of nucleotide composition at four-fold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution, 41, 353-358.
- Posada, D. (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256. https://doi.org/10.1093/molbev/msn083
- Qian, Y.H., Wu, H.Y., Ji, X.Y., Yu, W.W. & Du, Y.Z. (2014) Mitochondrial genome of the stonefly Kamimuria wangi (Plecoptera: Perlidae) and phylogenetic position of Plecoptera based on mitogenomes. PLoS ONE, 9 (1), e86328-e86328. https://doi.org/10.1371/journal.pone.0086328
- Ronquist, F., Teslenko, M., van der Mark, P.V.D., Ayres, D.L., Darling, A., Hohna, 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. Systematic Biology, 61, 539-542.
- Shi, A.M., Li, H., Bai, X.S., Dai, X., Chang, J., Guilbert, E. & Cai, W.Z. (2012). The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae). Zootaxa, 3238, 23-38.
- Simon, C., Buckley, T.R., Frati, F., Stewart, J.B. & Beckenbach, A.T. (2006) Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annual Review of Ecology and Systematics, 37, 545-579.
- Sproul, J.S., Houston, D.D., Nelson, C.R., Evans, P., Crandall, K.A. & Shiozawa, D.K. (2015) Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia, (Plecoptera), in Western North America. BMC Evolutionary Biology, 15 (1), 1-18. https://doi.org/10.1186/s12862-015-0553-4
- Stamatakis, A. (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
- Stark, B.P. & Sivec, I. (2007) A Synopsis of Styloperlidae (Insecta, Plecoptera) with description of Cerconychia sapa, a new stonefly from Vietnam. Illiesia, 3, 10-16.
- Stewart, K.W. & Stark, B.P. (2008) Chapter 14, Plecoptera. In: Merritt, R.W., Cummins, K.W. & Berg M.B. (Eds.), An introduction to the aquatic insects of North America. 4th Edition. Kendall-Hunt Publishing Company, Dubuque, Iowa, 1158 pp.
- Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
- Terry, M.D. & Whiting, M.F. (2003) Phylogeny of Plecopter: molecular evidence and evolutionary trends. Entomologische Abhandlungen, 61, 130-131.
- Timmermans, M.J. & Vogler, A.P. (2012) Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea). Molecular Phylogenetics and Evolution, 63, 299- 304.
- Uchida, S. & Isobe, Y. (1989) Styloperlidae, stat. nov. and Microperlinae, subfam. nov. with a revised system of the family group Systellognatha (Plecoptera). Spixiana, 12, 145-182.
- Wang, K., Ding, S.M. & Yang, D. (2016a) The complete mitochondrial genome of a stonefly species, Kamimuria chungnanshana Wu, 1948 (Plecoptera: Perlidae), Mitochondrial DNA Part A, 27, 3810-3811. https://doi.org/10.3109/19401736.2015.1082088
- Wang, K., Wang, Y.Y. & Yang, D. (2016b) The complete mitochondrial genome of a stonefly species, Togoperla sp. (Plecoptera: Perlidae), Mitochondrial DNA Part A, 27, 1703-1704.
- Wang, Y., Li, H., Wang, P., Song, F. & Cai, W.Z. (2014) Comparative mitogenomics of plant bugs (Hemiptera: Miridae): identifying the AGG codon reassignments between serine and lysine. PLoS ONE, 9 (7), e101375. https://doi.org/10.1371/journal.pone.0101375
- Wang, Y.Y., Liu, X.Y., Winterton, S.L., Yan, Y., Chang W.C. & Yang, D. (2013) Comparative Mitogenomic Analysis Reveals Sexual Dimorphism in a Rare Montane Lacewing (Insecta: Neuroptera: Ithonidae). PLoS ONE, 8 (12), e83986-e83986. https://doi.org/10.1371/journal.pone.0083986
- Wolstenholme, D.R. (1992) Genetic novelties in mitochondrial genomes of multicellular animals. Current Opinion in Genetics & Development, 2, 918-925.
- Wu, C.F. (1935) New species of stoneflies from East and South China. Bulletin of the Peking Society of National History, 9, 227-243.
- Wu, C.F. (1938) Plecopterorum sinensium: A monograph of the stoneflies of China (Order Plecoptera). Yenching University, Beijing, 225 pp.
- Wu, C.F. (1962) Results of the Zoologico-Botanical expedition to Southwest China, 1955-1957 (Plecoptera). Acta Entomologica Sinica, 11 (Supplement), 139-153.
- Wu, H.Y., Ji, X.Y., Yu, W.W. & Du, Y.Z. (2014) Complete mitochondrial genome of the stonefly Cryptoperla stilifera Sivec (Plecoptera: Peltoperlidae) and thephylogeny of Polyneopteran insects. Gene, 537, 177-183. https://doi.org/10.1016/j.gene.2013.12.044
- Zhou, C.G., Tan, M. H., Du, S.Y., Zhang, R., Machida, R. & Zhou, X. (2016) The mitochondrial genome of the winter stonefly Apteroperla tikumana (Plecoptera, Capniidae). Mitochondrial DNA Part A, 27, 3030-3032.
- Zwick, P. (2000) Phylogenetic system and zoogeography of the Plecoptera. Annual Review of Entomology, 45, 709-746. https://doi.org/10.1146/annurev.ento.45.1.709
- Zwick, P. (2009) The Plecoptera-who are they? The problematic placement of stoneflies in the phylogenetic system of insects. Aquatic insects, 31 (Supplement), 181-194.