Mitochondrial Genomes of Blister Beetles (Coleoptera, Meloidae) and Two Large Intergenic Spacers in Hycleus Genera

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2017 Sep 7

PMID 28874137

Citations 31

Authors

Chao Du

Lifang Zhang

Ting Lu

Jingnan Ma

Chenjuan Zeng

Bisong Yue

Xiuyue Zhang

Affiliations

Soon will be listed here.

Abstract

Background: Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of Meloidae.

Results: We determined complete or nearly complete mitogenomes of seven meloid species. The circular genomes encode 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and two ribosomal RNAs (rRNAs), and contain a control region, with gene arrangement identical to the ancestral type for insects. The evolutionary rates of all PCGs indicate that their evolution is based on purifying selection. The comparison of tRNA secondary structures indicates diverse substitution patterns in Meloidae. Remarkably, all mitogenomes of the three studied Hycleus species contain two large intergenic spacers (IGSs). IGS1 is located between trnW and trnC, including a 9 bp consensus motif. IGS2 is located between trnS2 (UCN) and nad1, containing discontinuous repeats of a pentanucleotide motif and two 18-bp repeat units in both ends. To date, IGS2 is found only in genera Hycleus across all published Coleopteran mitogenomes. The duplication/random loss model and slipped-strand mispairing are proposed as evolutionary mechanisms for the two IGSs (IGS1, IGS2). The phylogenetic analyses using MrBayes, RAxML, and PhyloBayes methods based on nucleotide and amino acid datasets of 13 PCGs from all published mitogenomes of Tenebrionoids, consistently recover the monophylies of Meloidae and Tenebrionidae. Within Meloidae, the genus Lytta clusters with Epicauta rather than with Mylabris. Although data collected thus far could not resolve the phylogenetic relationships within Meloidae, this study will assist in future mapping of the Meloidae phylogeny.

Conclusions: This study presents mitogenomes of seven meloid beetles. New mitogenomes retain the genomic architecture of the Coleopteran ancestor, but contain two IGSs in the three studied Hycleus species. Comparative analyses of two IGSs suggest that their evolutionary mechanisms are duplication/random loss model and slipped-strand mispairing.

Citing Articles

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The complete mitochondrial genome of Pallas, 1773 (Coleoptera: Meloidae).

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The first complete mitochondrial genome of (Coleoptera: Meloidae) and its phylogenetic analysis.

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Comparative mitogenome research revealed the phylogenetics and evolution of the superfamily Tenebrionoidea (Coleoptera: Polyphage).

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PMID: 38932962 PMC: 11199344. DOI: 10.1002/ece3.11520.

References

Babbucci M, Basso A, Scupola A, Patarnello T, Negrisolo E . Is it an ant or a butterfly? Convergent evolution in the mitochondrial gene order of Hymenoptera and Lepidoptera. Genome Biol Evol. 2014; 6(12):3326-43. PMC: 4466343. DOI: 10.1093/gbe/evu265. View

Boore J . Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii. Mol Biol Evol. 2001; 18(7):1413-6. DOI: 10.1093/oxfordjournals.molbev.a003925. View

Salvato P, Simonato M, Battisti A, Negrisolo E . The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Genomics. 2008; 9:331. PMC: 2488359. DOI: 10.1186/1471-2164-9-331. View

Stewart J, Beckenbach A . Phylogenetic and genomic analysis of the complete mitochondrial DNA sequence of the spotted asparagus beetle Crioceris duodecimpunctata. Mol Phylogenet Evol. 2003; 26(3):513-26. DOI: 10.1016/s1055-7903(02)00421-9. View

Cameron S, Johnson K, Whiting M . The mitochondrial genome of the screamer louse Bothriometopus (phthiraptera: ischnocera): effects of extensive gene rearrangements on the evolution of the genome. J Mol Evol. 2007; 65(5):589-604. DOI: 10.1007/s00239-007-9042-8. View

Sheffield N, Song H, Cameron S, Whiting M . A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol Biol Evol. 2008; 25(11):2499-509. PMC: 2568038. DOI: 10.1093/molbev/msn198. View

Ronquist F, Teslenko M, van der Mark P, Ayres D, Darling A, Hohna S . MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012; 61(3):539-42. PMC: 3329765. DOI: 10.1093/sysbio/sys029. View

Shao R, Barker S . The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol Biol Evol. 2003; 20(3):362-70. DOI: 10.1093/molbev/msg045. View

Hua J, Li M, Dong P, Cui Y, Xie Q, Bu W . Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera). BMC Genomics. 2008; 9:610. PMC: 2651891. DOI: 10.1186/1471-2164-9-610. View

10.

Wei S, Tang P, Zheng L, Shi M, Chen X . The complete mitochondrial genome of Evania appendigaster (Hymenoptera: Evaniidae) has low A+T content and a long intergenic spacer between atp8 and atp6. Mol Biol Rep. 2009; 37(4):1931-42. PMC: 2831182. DOI: 10.1007/s11033-009-9640-1. View

11.

Hanada T, Suzuki T, Yokogawa T, Sprinzl M, Watanabe K . Translation ability of mitochondrial tRNAsSer with unusual secondary structures in an in vitro translation system of bovine mitochondria. Genes Cells. 2001; 6(12):1019-30. DOI: 10.1046/j.1365-2443.2001.00491.x. View

12.

Wang G . Medical uses of mylabris in ancient China and recent studies. J Ethnopharmacol. 1989; 26(2):147-62. DOI: 10.1016/0378-8741(89)90062-7. View

13.

Lanfear R, Calcott B, Ho S, Guindon S . Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 2012; 29(6):1695-701. DOI: 10.1093/molbev/mss020. View

14.

Andujar C, Arribas P, Linard B, Kundrata R, Bocak L, Vogler A . The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles. Mitochondrial DNA A DNA Mapp Seq Anal. 2016; 28(2):156-158. DOI: 10.3109/19401736.2015.1115488. View

15.

Fenn J, Cameron S, Whiting M . The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability. Insect Mol Biol. 2007; 16(2):239-52. DOI: 10.1111/j.1365-2583.2006.00721.x. View

16.

Wei S, Li Q, Achterberg K, Chen X . Two mitochondrial genomes from the families Bethylidae and Mutillidae: independent rearrangement of protein-coding genes and higher-level phylogeny of the Hymenoptera. Mol Phylogenet Evol. 2014; 77:1-10. DOI: 10.1016/j.ympev.2014.03.023. View

17.

Cheng X, Zhang L, Yu D, Storey K, Zhang J . The complete mitochondrial genomes of four cockroaches (Insecta: Blattodea) and phylogenetic analyses within cockroaches. Gene. 2016; 586(1):115-22. DOI: 10.1016/j.gene.2016.03.057. View

18.

Shao R, Campbell N, SCHMIDT E, Barker S . Increased rate of gene rearrangement in the mitochondrial genomes of three orders of hemipteroid insects. Mol Biol Evol. 2001; 18(9):1828-32. DOI: 10.1093/oxfordjournals.molbev.a003970. View

19.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View

20.

Timmermans M, Barton C, Haran J, Ahrens D, Culverwell C, Ollikainen A . Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics. Genome Biol Evol. 2015; 8(1):161-75. PMC: 4758238. DOI: 10.1093/gbe/evv241. View