Complete mitogenome and phylogenetic significance of Metoecus javanus (Pic, 1913) (Coleoptera: Ripiphoridae) from Southwest China, with notes on morphological traits of adult and immature stages
Author:
LI JUN,ZHOU ZHENG,MAO CHUYANG,PAN ZHAO,YAO YUHAO,HE JINWU,LIN YAN,DONG ZHIWEI,LIU GUICHUN,ZHAO RUOPING,WANG WEN,LI XUEYAN
Abstract
Wedge-shaped beetles (Ripiphoridae) not only exhibit enigmatic morphological and biological traits but also disputable phylogenetic positions. At present, however, genetic information regarding this family remains limited. In this study, we report on the complete mitogenome of one ripiphorid beetle, Metoecus javanus (Pic, 1913), from Southwest China, as well as its different developmental stages, populations, and morphological variability. The complete mitogenome of M. javanus was 16 109 bp in length, containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a noncoding control region. Of the 37 genes, 23 were located on the majority strand (J-strand) and 14 were located on the minority strand (N-strand). All PCGs started with “ATN” (N represents A, T, G, and C), and terminated with “TAA”, except for NAD1 with “TAG” and COX2 with a single “T”. The five most used codons in the PCGs were UUA(L), UCU(S2), CCU(P), UCA(S2), and GGA(G), indicating a strong bias toward A + T-rich codons. All 22 tRNAs showed typical cloverleaf structures, except trnS1, which lacked a dihydrouridine (DHU) stem. The control region contained five types of tandem repeats, with the repeat units ranging from 17 to 24 bp. Phylogenetic analysis of the concatenated set of 13 PCGs and two rRNAs (rrnL and rrnS) of M. javanus and 17 other Tenebrionoidea species indicated that M. javanus did not cluster with Pelecotoma fennica (Ripiphoridae: Pelecotominae), another wedge-shaped beetle, but was located at the base of the Mordellidae + P. fennica clade. This reconstruction supported the paraphyly of Ripiphoridae with respect to Mordellidae. Using the mitogenome COX1 data, wedge-shaped beetles from different stages (male adult, female adult, and pupa), different geographical populations (Nujiang and Lincang), and different wasp hosts (Vespidae: Vespa velutina Lepeletier, 1836 and Vespa bicolor Fabricius, 1787) were identified as a same species (i.e., M. javanus). Based on morphological observations of all specimens, we identified and described variability in the adult pronotum, male genitalia, and pupa of M. javanus. The present results provide important genetic and morphological information for further investigations on the phylogenetic position of Ripiphoridae and its evolutionary diversity.
Subject
Animal Science and Zoology,Ecology, Evolution, Behavior and Systematics
Reference1 articles.
1. Batelka, J. (2003) New synonym and notes on the distribution of Metoecus javanus (Coleoptera: Ripiphoridae). Klapalekiana, 39, 199–203.
Batelka, J. (2006) New synonymies in the family Ripiphoridae (Coleoptera) from Malaysia. Folia Heyrovskyana, Series A, 13, 195–199.
Batelka, J. (2010) A review of Ripiphoridae in the Arabian Peninsula (Coleoptera: Tenebrionoidea). Acta Entomologica Musei Nationalis Pragae, 50, 157–166.
Batelka, J. & Chaboo, C.S. (2015) Beetles (Coleoptera) of Peru: A Survey of the Families. Ripiphoridae Gemminger and Harold, 1870. Journal of the Kansas Entomological Society, 88 (3), 399–403. https://doi.org/10.2317/kent-88-03-399-403.1
Batelka, J. & Fekrat, L. (2014) New records of Palaearctic species of the genus Metoecus (Coleoptera: Ripiphoridae), with remarks on their variability. Klapalekiana, 50, 1–6.
Batelka, J., Kundrata, R. & Bocak, L. (2016) Position and relationships of Ripiphoridae (Coleoptera: Tenebrionoidea) inferred from ribosomal and mitochondrial molecular markers. Annales Zoologici, 66 (1), 113–123. https://doi.org/10.3161/00034541ANZ2016.66.1.008
Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27 (2), 573–580. https://doi.org/10.1093/nar/27.2.573
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. https://doi.org/10.1016/j.ympev.2012.08.023
Beutel, R.G. & Pohl, H. (2013) The Strepsiptera–Odyssey: the history of the systematic placement of an enigmatic parasitic insect order. Entomologia, e4. https://doi.org/10.4081/entomologia.2013.e4
Cameron, S.L. (2014) Insect mitochondrial genomics: implications for evolution and phylogeny. Annual Review of Entomology, 59, 95–117. https://doi.org/10.1146/annurev-ento-011613-162007
Capella-Gutierrez, S., Silla-Martinez, J.M. & Gabaldon, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25 (15), 1972–1973. https://doi.org/10.1093/bioinformatics/btp348
Du, C., Zhang, L.F., Lu, T., Ma, J.N., Zeng, C.J., Yue, B.S. & Zhang, X.Y. (2017) Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera. BMC Genomics, 18 (1), 698. https://doi.org/10.1186/s12864-017-4102-y
Engel, M.S., Falin, Z.H. & Batelka, J. (2019) A new genus of Pelecotominae from Mexico, with notes on the genera Clinops and Scotoscopus and the description of new species (Coleoptera, Ripiphoridae). Zookeys, 857, 59–84. https://doi.org/10.3897/zookeys.857.34938
Falin, Z.H. (2003) s.n. In: Phylogenetic analysis and revision of the genera and subfamilies of the Ripiphoridae (Coleoptera). University of Kansas, Lawrence, Kansas, pp. 95–148.
Falin, Z.H., Arneson, L.C. & Wcislo, W.T. (2000) Night-flying sweat bees Megalopta genalis and Me. ecuadoria (Hymenoptera: Halictidae) as hosts of the parasitoid beetle Macrosiagon gracilis (Coleoptera: Rhipiphoridae). Journal of the Kansas Entomological Society, 73 (3), 183–185.
Falin, Z.H. & Engel, M.S. (2014) A new genus and two new extant species closely allied with the fossil genus Pauroripidius (Coleoptera: Ripiphoridae). Journal of the Kansas Entomological Society, 87(4), 333–344. https://doi.org/10.2317/JKES130924.1
Gautheret, D., Konings, D. & Gutell, R.R. (1995) G.U base pairing motifs in ribosomal RNA. RNA, 1(8), 807–814.
Gunter, N.L., Levkanicova, Z., Weir, T.H., Slipinski, A., Cameron, S.L. & Bocak, L. (2014) Towards a phylogeny of the Tenebrionoidea (Coleoptera). Molecular Phylogenetics and Evolution, 79, 305–312. https://doi.org/10.1016/j.ympev.2014.05.028
Hao, Y.J., Zou, Y.L., Ding, Y.R., Xu, W.Y., Yan, Z.T., Li, X.D., Fu, W.B., Li, T.J. & Chen, B. (2017) Complete mitochondrial genomes of Anopheles stephensi and An. dirus and comparative evolutionary mitochondriomics of 50 mosquitoes. Scientific Reports, 7(1), 7666. https://doi.org/10.1038/s41598-017-07977-0
Hattori, T. & Yamane, S. (1975) Notes on Metoecus paradoxus and Metoecus vespae parasitic on the Vespula species in northern Japan (Coleoptera, Rhipiphoridae; Hymenoptera Vespidae). New entomologist, 21, 1–7.
Heitmans, W.R. & Peeters, T.M. (1996) Metoecus paradoxus in The Netherlands (Coleoptera: Rhipiphoridae). Entomologische Berichten, 56 (7), 109–117.
Hsiao, Y., Yu, Y.L., Deng, C.S. & Pang, H. (2017) The first fossil wedge-shaped beetle (Coleoptera, Ripiphoridae) from the middle Jurassic of China. European Journal of Taxonomy, 227, 1–13. https://doi.org/10.5852/ejt.2017.277
Kergoat, G.J., Soldati, L., Clamens, A.L., Jourdan, H., Jabbour-Zahab, R., Genson, G., Bouchard, P. & Condamine, F.L. (2014) Higher level molecular phylogeny of darkling beetles (Coleoptera: Tenebrionidae). Systematic Entomology, 39 (3), 486–499. https://doi.org/10.1111/syen.12065
Kôno, H. (1927). Beitrag zu den Rhipiphoriden-arten von Japan. Insecta matsumurana, 1 (4), 177–182.
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. (2018) MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35 (6), 1547–1549. https://doi.org/10.1093/molbev/msy096
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. Molecular Biology and Evolution, 34 (3), 772–773. https://doi.org/10.1093/molbev/msw260
Lawrence, J.F., Falin, Z.H. & Slipinski, A. (2010) Ripiphoridae Gemminger and Harold, 1870. Handbook of zoology. Coleoptera, Beetles, vol. 2: Morphology and systematics, 538–548pp.
Lawrence, J.F., Ślipiski, A., Seago, A.E., Thayer, M.K., Newton, A.F. & Marvaldi, A.E. (2011).Phylogeny of the Coleoptera based on morphological characters of adults and larvae. Annales zoologici, 61 (1), 115. https://doi.org/10.3161/000345411X576725
Letunic, I. & Bork, P. (2019) Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research, 47 (W1), W256–W259. https://doi.org/10.1093/nar/gkz239
Li, T., Yang, J., Li, Y.W., Cui, Y., Xie, Q., Bu, W.J. & Hillis, D.M. (2016) A mitochondrial genome of Rhyparochromidae (Hemiptera: Heteroptera) and a comparative analysis of related mitochondrial genomes. Scientific Reports, 6, 35175. https://doi.org/10.1038/srep35175
Li, W.J., Wang, Z.Q. & Che, Y.L. (2017) The complete mitogenome of the wood–feeding cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and its phylogenetic relationship among cockroach families. International Journal of Molecular Sciences, 18 (11), 2397. https://doi.org/10.3390/ijms18112397
Liu, L.N. & Wang, C.Y. (2014) Complete mitochondrial genome of yellow meal worm (Tenebrio molitor). Zoological Research, 35 (6), 537–545.
Luo, R.B., Liu, B.H., Xie, Y.L., Li, Z.Y., Huang, W.H., Yuan, J.Y., He, G.Z., Chen, Y.X., Pan, Q., Liu, Y.J., Tang, J.B., Wu, G.X., Zhang, H., Shi, Y.J., Liu, Y., Yu, C., Wang, B., Lu, Y., Han, C.L., Cheung, D.W., Yiu, S.M., Peng, S.L., Zhu, X.Q., Liu, G.M., Liao, X.K., Li, Y.R., Yang, H.M., Wang, J., Lam, T.W. & Wang, J. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1 (1), 18. https://doi.org/10.1186/2047-217X-1-18
McKenna, D.D., Wild, A.L., Kanda, K., Bellamy, C.L., Beutel, R.G., Caterino, M.S., Farnum, C.W., Hawks, D.C., Ivie, M.A., Jameson, M.L., Leschen, R.A.B., Marvaldi, A.E., McHugh, J.V., Newton, A.F., Robertson, J.A., Thayer, M.K., Whiting, M.F., Lawrence, J.F., ŚLipiŃSki, A., Maddison, D.R. & Farrell, B.D. (2015) The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversify during the Cretaceous terrestrial revolution. Systematic Entomology, 40 (4), 835–880. https://doi.org/10.1111/syen.12132
Meng, G.L., Li, Y.Y., Yang, C.T. & Liu, S.L. (2019) MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research, 47 (11), e63. https://doi.org/10.1093/nar/gkz173
Nakamura, T., Yamada, K.D., Tomii, K. & Katoh, K. (2018) Parallelization of MAFFT for large–scale multiple sequence alignments. Bioinformatics, 34 (14), 2490–2492. https://doi.org/10.1093/bioinformatics/bty121
Nakane, T. & Yamane, S. (1990) A new species of the genus Metoecus Gerstaecker (Coleoptera, Rhipiphoridae) from west Sumatra, Indonesia. South Pacific Study, 10 (2), 305–308.
Pan, Z., Wei, J. & Ren, G.D. (2021) Taxonomic note on the genus Metoecus Dejean, 1834 from China (Coleoptera: Ripiphoridae). Journal of Hebei University(Natural Science Edition), 41 (3), 285–289. [in Chinese]
Pan, Z., Duan, J.C., Gao, Q. & Young, D.K. (2021) The adult, larva, and pupa of a new Pseudopyrochroa (Coleoptera: Pyrochroidae: Pyrochroinae) from China, with mmolecular phylogenetic inferences. Insects, 12 (12), 1089. https://doi.org/10.3390/insects12121089
Pentinsaari, M., Hebert, P.D. & Mutanen, M. (2014) Barcoding beetles: a regional survey of 1872 species reveals high identification success and unusually deep interspecific divergences. PLoS One, 9 (9), e108651. https://doi.org/10.1371/journal.pone.0108651
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/BF01215182
Pic, M. (1913) Descriptions de 29 espèces et de plusieurs variétés. Mélanges Exotico-Entomologiques, 5, 7–20.
Pic, M. (1939) Nouveaux Coleopteres de la presqu’ ile Malaise(Ⅵ). Journal of the Federal Malay State Museums, 18, 372–376.
Rittner, O. & Dafny, R. (2018) Metoecus paradoxus (Linnaeus, 1760) (Coleoptera: Ripiphoridae), a new species for the fauna of Israel. Israel Journal of Entomology, 48 (1), 79–83.
Ronquist, F., Teslenko, M., van der Mark, P., 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 (3), 539–542. https://doi.org/10.1093/sysbio/sys029
Roslin, T., Somervuo, P., Pentinsaari, M., Hebert, P.D.N., Agda, J., Ahlroth, P., Anttonen, P., Aspi, J., Blagoev, G., Blanco, S., Chan, D., Clayhills, T., deWaard, J., deWaard, S., Elliot, T., Elo, R., Haapala, S., Helve, E., Ilmonen, J., Hirvonen, P., Ho, C., Itamies, J., Ivanov, V., Jakovlev, J., Juslen, A., Jussila, R., Kahanpaa, J., Kaila, L., Jari, P., Kakko, A., Kakko, I., Karhu, A., Karjalainen, S., Kjaerandsen, J., Koskinen, J., Laasonen, E.M., Laasonen, L., Laine, E., Lampila, P., Levesque-Beaudin, V., Lu, L., Lahteenaro, M., Majuri, P., Malmberg, S., Manjunath, R., Martikainen, P., Mattila, J., McKeown, J., Metsala, P., Miklasevskaja, M., Miller, M., Miskie, R., Muinonen, A., Veli, M., Naik, S., Nikolova, N., Nupponen, K., Ovaskainen, O., Osterblad, I., Paasivirta, L., Pajunen, T., Parkko, P., Paukkunen, J., Penttinen, R., Perez, K., Pohjoismaki, J., Prosser, S., Raekunnas, M., Rahulan, M., Rannisto, M., Ratnasingham, S., Raukko, P., Rinne, A., Rintala, T., Miranda Romo, S., Salmela, J., Salokannel, J., Savolainen, R., Schulman, L., Sihvonen, P., Soliman, D., Sones, J., Steinke, C., Stahls, G., Tabell, J., Tiusanen, M., Varkonyi, G., Vesterinen, E.J., Viitanen, E., Vikberg, V., Viitasaari, M., Vilen, J., Warne, C., Wei, C., Winqvist, K., Zakharov, E. & Mutanen, M. (2022) A molecular-based identification resource for the arthropods of Finland. Molecular Ecology Resources, 22 (2), 803–822. https://doi.org/10.1111/1755-0998.13510
Sharp, P.M. & Li, W.-H. (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution, 24 (1), 28–38. https://doi.org/10.1007/BF02099948
Semenov, A. (1891) Diagnoses Coleopterorum novorum ex Asia Centrali et Orientali. Horae Societatis Entomologicae Rossicae, 25, 262–382.
Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30 (9), 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Švácha, P. (1994) Bionomics, behaviour and immature stages of Pelecotoma fennica(Paykull) (Coleoptera: Rhipiphoridae). Journal of Natural History, 28 (3), 585–618. https://doi.org/10.1080/00222939400770271
Talavera, G. & Vila, R. (2011) What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny. BMC Ecology and Evolution, 11, 315. https://doi.org/10.1186/1471-2148-11-315
Tang, M., Tan, M.H., Meng, G.L., Yang, S.Z., Su, X., Liu, S.L., Song, W.H., Li, Y.Y., Wu, Q., Zhang, A.B. & Zhou, X. (2014) Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Research, 42 (22), e166–e166. https://doi.org/10.1093/nar/gku917
Vaidya, G., Lohman, D.J. & Meier, R. (2011) SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics, 27 (2), 171–180. https://doi.org/10.1111/j.1096-0031.2010.00329.x
Van Oystaeyen, A., van Zweden, J. S., Huyghe, H., Drijfhout, F., Bonckaert, W. & Wenseleers, T. (2015) Chemical strategies of the beetle Metoecus paradoxus, social parasite of the wasp Vespula vulgaris. Journal of Chemical Ecology, 41 (12), 1137–1147. https://doi.org/10.1007/s10886-015-0652-0
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
Xiao, L.F., Zhang, S.D., Long, C.P., Guo, Q.Y., Xu, J.S., Dai, X.H. & Wang, J.G. (2019) Complete mitogenome of a Leaf-Mining buprestid beetle, Trachys auricollis, and its phylogenetic implications. Genes, 10 (12), 992. https://doi.org/10.3390/genes10120992
Yu, X.L., Tan, W., Zhang, H.Y., Jiang, W.L., Gao, H., Wang, W.X., Liu, Y.X., Wang, Y. & Tian, X.X. (2019) Characterization of the complete mitochondrial genome of Harpalus sinicus and its implications for phylogenetic analyses. Genes, 10 (9), 724. https://doi.org/10.3390/genes10090724
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, K.J., Zhu, W.C., Rong, X., Zhang, Y.K., Ding, X.L., Liu, J., Chen, D.S., Du, Y. & Hong, X.Y. (2013) The complete mitochondrial genomes of two rice planthoppers, Nilaparvata lugens and Laodelphax striatellus: conserved genome rearrangement in Delphacidae and discovery of new characteristics of atp8 and tRNA genes. BMC Genomics, 14 (1), 417. https://doi.org/10.1186/1471-2164-14-417
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献
|
|