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Issue: Vol. 5369 No. 4: 13 Nov. 2023
Type: Article
Published: 2023-11-13
DOI: 10.11646/zootaxa.5369.4.6
Page range: 576-584
Abstract views: 278
PDF downloaded: 18

Mitogenome of Xya pfaendleri (Orthoptera: Caelifera): Its comparative description and phylogenetic position within Tridactylidea

Department of Biology; Faculty of Science; Akdeniz University; Antalya; Turkey
Department of Biology; Faculty of Art & Science; Gaziantep University; Gaziantep; Turkey
Department of Biology; Faculty of Science; Akdeniz University; Antalya; Turkey
Department of Biology; Faculty of Art & Science; Hatay Mustafa Kemal University; Hatay; Turkey
Department of Biology; Faculty of Science; Akdeniz University; Antalya; Turkey
Orthoptera Mitophylogeny Tridactyloidea Dated phylogeny

Abstract

We report the comparative examination of the complete mitochondrial genome of the pygmy mole cricket Xya pfaendleri (Orthoptera: Caelifera: Tridactylidae). The mitogenome consists of 13 protein-coding regions, 22 tRNAs, two rRNAs, and one control region, following the gene order of the ancestral pancrustacean mitogenome. The length of the mitogenome in Xya pfaendleri is 15352 bp. The start and stop codons of the protein-coding genes exhibit the general pattern observed in orthopterans. The data indicate that the pattern of gene overlapping/intergenic sequences exhibits a significant phylogenetic signal. A phylogenetic tree inferred using 12 mitogenomes (seven belonging to Tridactylidea, three to Acrididea, and two to Ensifera) confirms the sister group relationship of Acrididea and Tridactylidea. The relationship among the families of Tridactylidea is Cylindrachetidae + (Ripipterygidae + Tridactylidae). The mitogenome sequences of Xya and Tridactylus constitute a single clade, sharing a last common ancestor 94 million years ago, and rendering the first genus paraphyletic. The present preliminary data suggest that we still have much to learn about the evolution and diversity of Tridactylidea.

 

References

  1. Andrews, S. (2010) FastQC: a quality control tool for high throughput sequence data. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc (accessed 15 October 2023)
  2. Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A. & Saunders, N.C. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18 (1), 489–522. https://doi.org/10.1146/annurev.es.18.110187.002421
  3. Baehr, M. (1988) On Australian Tridactylidae mainly from Northern Australia (Orthopteroidea, Saltatoria, Caelifera). Spixiana, Munich, 11 (1), 13–26.
  4. Bernt, M., Bleidorn, C., Braband, A., Dambach, J., Donath, A., Fritzsch, G., Golombek, A. Hadrys, H., Jühling, J., Meusemann, K., Middendorf, M., Misof, B., Perseke, M., Podsiadlowski, L., Reumont, B., Schierwater, B., Schlegel, M., Schrödl, M., Simon, S., Stadler, P.F., Stöger I. & Struck, T.H. (2013) A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Molecular Phylogenetics and Evolution, 69 (2), 352–364. https://doi.org/10.1016/j.ympev.2013.05.002
  5. Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. & Stadler, P.F. (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69 (2), 313–319.
  6. https://doi.org/10.1016/j.ympev.2012.08.023
  7. Boore, J.L. & Brown, W.M. (1998) Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics & Development, 8, 668–674. https://doi.org/10.1016/s0959-437x(98)80035-x
  8. Boore, J.L. (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27 (8), 1767–1780. https://doi.org/10.1093/nar/27.8.1767
  9. Cameron, S. (2014a) How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research. Systematic Entomology, 39 (3), 400–411. https://doi.org/10.1111/syen.12071
  10. Cameron, S.L. (2014b) Insect mitochondrial genomics: implications for evolution and phylogeny. Annual Review of Entomology, 59, 95–117. https://doi.org/10.1146/annurev-ento-011613-162007
  11. Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
  12. Chang, H., Qiu, Z., Yuan, H., Wang, X., Li, X., Sun, H., Guo, X., Lu, Y., Feng, X., Majid, M. & Huang, Y. (2020) Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types. Molecular Phylogenetics and Evolution, 145, 106734. https://doi.org/10.1016/j.ympev.2020.106734
  13. Chikhi, R. & Rizk, G. (2013) Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms for Molecular Biology, 8, 1–9. https://doi.org/10.1186/1748-7188-8-22
  14. Cigliano, M.M., Braun, H., Eades, D.C. & Otte, D. (2023) Orthoptera Species File. Version 5.0/5.0. Available from: http://orthoptera.speciesfile.org (accessed 3 July 2023)
  15. Fenn, J.D., Song, H., Cameron, S.L. & Whiting, M.F. (2008) A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Molecular Phylogenetics and Evolution, 49, 59–68. https://doi.org/10.1016/j.ympev.2008.07.004
  16. Günther, K.K. (1979) Einige Bemerkungen über die Gattungen der Familie Tridactylidae Brunner und zur Klassifi kation der Tridactylodea. Deutsche Entomologische Zeitschrift, 26, 255–264. https://doi.org/10.1002/mmnd.19790260408
  17. Günther, K.K. (1980) Katalog der Caelifera-Unterordnung Tridactyloidea (Insecta). Deutsche Entomologische Zeitschrift, 27, 149–178. https://doi.org/10.1002/mmnd.19800270114
  18. Günther, K.K. (1990) Zwei neue Xya-Arten aus dem Mittelmeergebiet (Orthoptera, Tridactylidae). Deutsche Entomologische Zeitschrift, 37, 119–136. https://doi.org/10.1002/mmnd.19900370125
  19. Günther, K.K., (1994) Die Tridactyloidea-Fauna Kolumbiens (Orthoptera, Caelifera). Deutsche Entomologische Zeitschrift, 41, 1–56. https://doi.org/10.1002/mmnd.19940410102
  20. 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 (2), 277–298. https://doi.org/10.1080/10635150590947843
  21. Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K., von Haeseler, A. & Jermiin, L.S. (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14 (6), 587–589. https://doi.org/10.1038/nmeth.4285
  22. Karakaş, M.Y., Yahyaoğlu, Ö., Uluar, O., Budak, M. & Çiplak, B. (2023) Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions. Zootaxa, 5263 (1), 141–147. https://doi.org/10.11646/zootaxa.5263.1.9
  23. Karşi, U. & Ciplak, B. (2019) Mitogenome of Anterastes babadaghi (Orthoptera: Tettigoniinae; Platycleidini): frequent conserved overlapping regions within Tettigoniinae. Zootaxa, 4651 (1), 173–190. https://doi.org/10.11646/zootaxa.4651.1.11
  24. Katoh, K., Rozewicki, J. & Yamada, K.D. (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics, 20 (4), 1160–1166. https://doi.org/10.1093/bib/bbx108
  25. Kim, I., Cha, S.Y., Yoon, M.H., Hwang, J.S., Lee, S.M., Sohn, H.D. & Jin, B.R. (2005) The complete nucleotide sequence and gene organization of the mitochondrial genome of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae). Gene, 353 (1), 155–168. https://doi.org/10.1016/j.gene.2005.04.019
  26. Laslett, D. & Canbäck, B. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 24 (2), 172–175. https://doi.org/10.1093/bioinformatics/btm573
  27. Li, R. (2021) First record of the complete mitochondrial genome of Coptotettix longtanensis (Orthoptera: Tetrigidae) and its phylogenetic analysis. Available from: https://www.ncbi.nlm.nih.gov/nuccore/OK540319 (accessed 3 June 2023)
  28. Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., Von Haeseler, A. & Lanfear, R. (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37 (5), 1530–1534. https://doi.org/10.1093/molbev/msaa015
  29. Öztürk, P.N. & Çıplak, B. (2019) Phylomitogenomics of Phaneropteridae (Orthoptera): Combined data indicate a poorly conserved mitogenome. International Journal of Biological Macromolecules, 132, 1318–1326. https://doi.org/10.1016/j.ijbiomac.2019.04.011
  30. Park, B., Choi, E.H., Kim, G., Shin, C.R., Hwang, J., Baek, S.Y. & Hwang, U.W. (2021) The complete mitochondrial genome of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae) from South Korea. Mitochondrial DNA Part B, 6 (3), 1144–1146. https://doi.org/10.1080/23802359.2021.1901617
  31. Ramesh, A., Small, S.T., Kloos, Z.A., Kazura, J.W., Nutman, T.B., Serre, D. & Zimmerman, P.A. (2012) The complete mitochondrial genome sequence of the filarial nematode Wuchereria bancrofti from three geographic isolates provides evidence of complex demographic history. Molecular and Biochemical Parasitology, 183, 32–41. https://doi.org/10.1016/j.molbiopara.2012.01.004
  32. Sheffield, N.C., Hiatt, K.D., Valentine, M.C., Song, H. & Whiting, M.F. (2010) Mitochondrial genomics in Orthoptera using MOSAS. Mitochondrial DNA, 21 (3–4), 87–104. https://doi.org/10.3109/19401736.2010.500812
  33. Song, H., Amédégnato, C., Cigliano, M.M., Desutter-Grandcolas, L., Heads, S.W., Huang, Y., Otte, D. & Whiting, M.F. (2015) 300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling. Cladistics, 31 (6), 621–651. https://doi.org/10.1111/cla.12116
  34. Song, N., Li, H., Song, F. & Cai, W. (2016) Molecular phylogeny of Polyneoptera (Insecta) inferred from expanded mitogenomic data. Scientific Reports, 6 (1), 36175. https://doi.org/10.1038/srep36175
  35. Song, H., Béthoux, O., Shin, S., Donath, A., Letsch, H., Liu, S., McKenna, D.D., Meng, G., Misof, B., Podsiadlowski, L., Zhou, X., Wipfler, B. & Simon, S. (2020) Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera. Nature communications, 11(1), 4939. https://doi.org/10.1038/s41467-020-18739-4
  36. Suchard, M.A., Lemey, P., Baele, G., Ayres, D.L., Drummond, A.J. & Rambaut, A. (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4 (1), vey016. https://doi.org/10.1093/ve/vey016
  37. Talavera, G. & Castresana, J. (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56, 564–577. https://doi.org/10.1080/10635150701472164
  38. Xu, H., Mao, B., Storozhenko, S.Y., Huang, Y., Chen, Z. & Huang, J. (2021) Phylogenetic position of the genus Alulacris (Orthoptera: Acrididae: Melanoplinae: Podismini) revealed by complete mitogenome evidence. Insects, 12 (10), 918. https://doi.org/10.3390/insects12100918
  39. Wang, P., Zhi, Y. & Zhang, D. (2013) The complete mitochondrial genome of Tridactylus japonicus (Orthoptera: Tridactyloidea). Available from: https://www.ncbi.nlm.nih.gov/nuccore/KC555032 (accessed 3 June 2023)