Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera

Abstract

BackgroundInsect 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.ResultsWe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4102-y) contains supplementary material, which is available to authorized users.

Characteristics of the complete mitochondrial genome ofSuhpalacsa longialata(Neuroptera, Ascalaphidae) and its phylogenetic implications

“…3 ). The absence of this arm in tRNA Ser(AGN) is a typical feature of many insect mtDNAs ( Wolstenholme, 1992 ; Salvato et al, 2008 ; Sheffield et al, 2008 ; Negrisolo, Babbucci & Patarnello, 2011 ; Yan et al, 2014 ; Du et al, 2017 ; Zhang, Song & Zhou, 2008 ), and is usually demonstrated to be functional ( Hanada et al, 2001 ; Stewart & Beckenbach, 2003 ). We also found that the tRNA Phe and tRNA Leu (CUN) lack the TψC loops.…”

“…Consequently, the particular gene arrangement becomes a significant marker to delimit taxonomic boundaries. Furthermore, the mitogenome has been increasingly used to reconstruct phylogenetic relationships because of its simple genetic structure, maternal inheritance, and high evolutionary rate properties ( Boyce, Zwick & Aquadro, 1989 ; Sheffield et al, 2008 ; Jia & Higgs, 2008 ; Du et al, 2017 ).…”

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

“…In fact, this pattern is located in a single region of the Trigonopterus mitogenome, (3 end of cob -trnS2 -spacer -3 end of nad1, since the latter is coded on the minus strand), and hence length variation and presence of a non-coding spacer could be related to a single evolutionary event. In fact, this intergenic spacer, including TACTA motifs, between cob-trnS2 and nad1 genes of Trigonopterus was also described in other Cryptorhynchinae (Liu et al, 2016), Cerambycidae (Kim et al, 2009;Wang et al, 2019;Liu et al, 2018), other beetles families (Du et al, 2017;Kim et al, 2009;Liu et al, 2018), and is extremely long in Bruchinae (Sayadi et al, 2017). This spacer was probably formed by slipped-strand mispairing and duplication/random loss, and the conserved motif could be a binding site of a transcription termination peptide (Du et al, 2017;Wang et al, 2019) and references therein).…”

The Complete Mitochondrial Genome of The American Palm Cixiid, Haplaxius Crudus (Hemiptera: Cixiidae)

“…This is not uncommon among insects as the Adoxophyes mitochondrial genome has 26 non-coding intergenic regions [37]. In this insect, the control region is less likely to be variable than coding regions of the mitochondrial genome due to the high AT content that consequently limits the usefulness as a diagnostic marker [43]. The unique TA-dinucleotides and TTAtrinucleotides repeats within the H. crudus mitochondrial genome sequence are similar to microsatellite sequence divergence and showed potential to be species identi cation markers which do not appear in the closely related Hemipteran species, however further analysis is required to interpret the e cacy of microsatellites at these loci.…”

“…The ingroup taxa A. aurantii (MN397939.1) and N. lugens (NC021748.1) are monophyletic with H. crudus (MT385107). Mitochondrial genomes may provide a better approach to resolving intractable phylogenetic relationships than single gene analyses, however, comprehensive phylogenetic analysis is required to recover strong support for the de nitive relationships between insects in the order Auchenorrhyncha [43][44][45]. Considering the diversity of the family Cixiidae and the limitation of the present molecular information, more conclusive phylogenetic results will be achievable as bioinformation/genomic data becomes increasingly available.…”