T-rich Region Research Articles

Complete mitochondrial genome of Mycalesis intermedia (Lepidoptera: Nymphalidae)

The Mycalesis intermedia belongs to Nymphalidae in Lepidoptera. We described the complete mitogenome of M. intermedia, which is typical circular duplex molecules and 15,386 bp in length, containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an A + T-rich region with macro-repeat sequences. All the inferred tRNA secondary structures show the common cloverleaf pattern, with the exception of trnS1(AGN) which lacks the DHU arm. The M. intermedia mitochondrial genome has the same gene order with other lepidopterans.

Complete mitochondrial genome of Dioryctria yiai (Lepidoptera: Pyralidae)

The Dioryctria yiai belongs to Pyralidae in Lepidoptera. The complete mitogenome of D. yiai was described in this study, which is typical circular duplex molecules and 15,430 bp in length, containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an A + T-rich region. The gene order is same with other lepidopterans. Except for cox1 started with CGA, all other PCGs started with the standard ATN codons. Most of the PCGs terminated with the stop codon TAA, whereas cox2 has the incomplete stop codon T. The phylogenetic tree showed that D. yiai and other six species belong to Phycitinae, are clustered into a clade.

The complete mitochondrial genome of Hemerobius japonicus (Neuroptera: Hemerobiidae)

The complete mitochondrial genome of Hemerobius japonicus Nakahara, 1915 was sequenced in this study. The complete mitochondrial genome is a typical double-stranded circular molecule of 18,585 bp (GenBank accession number: MN852445), containing 37 typical animal mitochondrial gene and an A + T-rich region. The gene order is identical to that of the putative ancestral arrangement of insects and other lacewings. 13 protein-coding genes (PCGs) possessed common triplet initiation codons ATN except ND1 possessed TTG and mostly terminated with TAN codons except for ND5 and ND4 with a single T residue adjacent to a downstream tRNA gene. All of the 22 tRNAs, ranging from 63 to 72 bp, can be folded into classic clover-leaf secondary structure except for tRNASer(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. The control region is 1416 bp long with an A + T content of 90.3%. In the sampled families of Neuroptera, each family showed a monophyletic cluster and Polystoechotidae + Rapismatidae, Osmylidae + the remaining families, Hemerobiidae + (Chrysopidae + (Polystoechotidae + Rapismatidae)) are recovered in phylogenetic analyses with high supports.

Sequencing and analysis of the complete mitochondrial genome of Habrobracon hebetor (Hymenoptera: Braconidae)

We determined the complete mitochondrial genome sequence of Habrobracon hebetor (Say). The complete mitogenome sequence of H. hebetor was observed to be a circular molecule 15,708 bp long and consists of 13 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes (GenBank accession no. MN842279). This nucleotide composition is biased toward adenine and thymine (85.2% A + T). The A + T-rich region is found between trnM and trnQ, and this entire region was 864 bp long.

The complete mitochondrial genome sequence of the hawk moth, Theretra oldenlandiae (Lepidoptera: Sphingidae)

In this study, we analyzed the complete mitochondrial genome sequence of the hawk moth, Theretra oldenlandiae. The complete mitogenome sequence of T. oldenlandiae was observed to be a circular molecule 15,312 bp long and consisting of 13 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes (GenBank accession number MN885801). The nucleotide composition is biased toward adenine and thymine (80.0% A + T). The A + T-rich region was found between rrnS and trnM, and this entire region was 423 bp long.

Sequencing and characterization of mitochondrial genome of Idaea effusaria (Lepidoptera: Geometridae)

The Idaea effusaria belongs to Geometridae in Lepidoptera. The complete mitogenome of I. effusaria was described in this study, which is typically circular duplex molecules and 16,161 bp in length, containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an A + T-rich region. The gene order is same with other lepidopterans. Except for cox1 started with CGA, all other PCGs started with the standard ATN codons. Most of the PCGs terminated with the stop codon TAA, whereas cox2 has the stop codon CAT. The phylogenetic tree showed that Larentiinae is close to Sterrhinae. The species of Ennominae form a monophyly.

Complete mitochondrial genome sequence of Pareuchiloglanis kamengensis in the Yarlung Zangbo River, Tibet

Pareuchiloglanis kamengensis belongs to the family of Sisoridae, Pareuchiloglanis. It is distributed in the Yarlung Zangbo River, the Irrawaddy River, the Nujiang River, and the Lancang River in southwestern China. In this study, we first published the complete mitochondrial genome sequence of Pareuchiloglanis kamengensis, which was 16,589 bp in length. This genome consists of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a non-coding A + T-rich region. The PCGs start with a traditional ATG except for COX1 and NAD3, which start with GTG and ATA instead, respectively, and end with stop codon TAA, TAG, TA, or a single T base. All tRNA have the typical clover-leaf structure. The phylogenetic tree of the whole mitogenome sequence is constructed by using neighbor-joining (NJ) method and the phylogenetic relationship among the family Sisoridae is further analyzed. We except to provide the theoretical basis for the further study of the phylogenetic relationship, taxonomic status, and conservation and management of genetic resources of Sisoridae catfishes.

Complete mitochondrial genome of Oberea diversipes (Coleoptera, Cerambycidae)

The complete mitochondrial DNA genome of the Oberea diversipes was reported. The genome was a circular molecule of 15,499 base pairs (bp), with 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an estimated 830 bp A + T-rich control region. The total base composition of the mitogenome was A–T bias, with 40.9% for A, 37.0% for T, 13.4% for C, and 8.7% for G. The molecular data presented here would be useful for further study of O. diversipes.

Sequencing and analysis of the complete mitochondrial genome of Mansonia uniformis (Dipera: Culicidae)

In this study, we sequenced and analyzed the complete mitochondrial genome of Mansonia uniformis, and this is the first report on the genus Mansonia. The circular mitogenome is 15,603 bp long and contains 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes, and a A + T-rich control region. Most PCGs start with ATN codons, and end with TAA, except for COX1 starting with TCG codons and COX2 ending with a single thymine stop codon. The phylogenetic tree based on the COX1 gene showed that M. uniformis formed a monophyletic clade, sister to other seven genus from the subfamily Culicinae.

The mitochondrial genome of a social wasp, Vespa simillima simillima (Hymenoptera: Vespidae)

We analyzed the complete mitochondrial genome of a social wasp, Vespa simillima simillima from South Korea prior to a systematic study on Korean Vespidae. The mitogenome is 16,740 bp in length, includes 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a 228 bp short A + T-rich region. The overall base composition is 82.0% AT and 18.0% GC. The maximum-likelihood analysis suggested that V. s. simillima is closely related to V. bicolor, another species of Vespidae.

The first mitochondrial genome from the Sterrhinae (Lepidoptera: Geometridae) and its phylogenetic implications

In this study, the complete mitochondrial genome of a geometrid species, Idaea simplicior (Prout), was sequenced. The I. simplicior mitogenome is a circular, double-stranded molecule, with 15,950 bp in size. The typical 37 mitochondrial genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and an A + T-rich region are included. Gene content and arrangement are highly conserved and typical of Lepidoptera. Interestingly, the I. simplicior mitogenome is rich in microsatellite sequences of (TA)12–18 with a scattered distribution in six intergenic regions. Phylogenetic analyses based on the combined 37 mitochondrial genes show that the Larentiinae and Ennominae are monophyletic. The Sterrhinae, which is represented by the only I. simplicior sequenced in this study, shows a closer relationship with the Larentiinae than Ennominae, which confirms previous morphological studies.

Complete mitochondrial genome of the bamboo-shoot fruit fly, Acrotaeniostola dissimilis (Diptera: Tephritidae) and its phylogenetic relationship within family Tephritidae

Acrotaeniostola dissimilis (Diptera: Tephritidae) is an insect pest of bamboo shoot and distributed in the Yunnan and Sichuan Provinces, Southwest China. Complete mitogenome sequence has been determined in this study. The circular genome is 15384 bp long and contains a standard gene complement, that is, the large and small ribosomal RNA subunits, 22 transfer RNA genes, 13 genes encoding mitochondrial proteins, and a non-coding A + T-rich control region. The phylogeny showed that A. dissimilis in tribe Gastrozonini was a monophyletic branch and clearly separated from both tribe Dacini and tribe Ceratitidini with high bootstrap value supported.

Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications.

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and −0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.

First mitochondrial genome from Yponomeutidae (Lepidoptera, Yponomeutoidea) and the phylogenetic analysis for Lepidoptera.

The complete mitochondrial genome (mitogenome) of Yponomeuta montanatus is sequenced and compared with other published yponomeutoid mitogenomes. The mitogenome is circular, 15,349 bp long, and includes the typical metazoan mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and an A + T-rich region. All 13 protein-coding genes use a typical start codon ATN, the one exception being cox1, which uses CGA across yponomeutoid mitogenomes. Comparative analyses further show that the secondary structures of tRNAs are conserved, including loss of the Dihydorouidine (DHU) arm in trnS1 (AGN), but remarkable nucleotide variation has occurred mainly in the DHU arms and pseudouridine (TψC) loops. A + T-rich regions exhibit substantial length variation among yponomeutoid mitogenomes, and conserved sequence blocks are recognized but some of them are not present in all species. Multiple phylogenetic analyses confirm the position of Y. montanatus in Yponomeutoidea. However, the superfamily-level relationships in the Macroheterocera clade in Lepidoptera recovered herein show considerable difference with that recovered in previous mitogenomic studies, raising the necessity of extensive phylogenetic investigation when more mitogenomes become available for this clade.

The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae.

Cerambycidae is one of the most diversified groups within Coleoptera and includes nearly 35,000 known species. The relationships at the subfamily level within Cerambycidae have not been convincingly demonstrated and the gene rearrangement of mitochondrial genomes in Cerambycidae remains unclear due to the low numbers of sequenced mitogenomes. In the present study, we determined five complete mitogenomes of Cerambycidae and investigated the phylogenetic relationship among the subfamilies of Cerambycidae based on mitogenomes. The mitogenomic arrangement of all five species was identical to the ancestral Cerambycidae type without gene rearrangement. Remarkably, however, two large intergenic spacers were detected in the mitogenome of Pterolophia sp. ZJY-2019. The origins of these intergenic spacers could be explained by the slipped-strand mispairing and duplication/random loss models. A conserved motif was found between trnS2 and nad1 gene, which was proposed to be a binding site of a transcription termination peptide. Also, tandem repeat units were identified in the A + T-rich region of all five mitogenomes. The monophyly of Lamiinae and Prioninae was strongly supported by both MrBayes and RAxML analyses based on nucleotide datasets, whereas the Cerambycinae and Lepturinae were recovered as non-monophyletic.

Characterization of the complete mitochondrial genomes of two species of the genus Aphaena Guérin-Méneville (Hemiptera: Fulgoridae) and its phylogenetic implications

The complete mitochondrial genomes (mitogenomes) of Aphaena (Callidepsa) amabilis and Aphaena (Aphaena) discolor nigrotibiata were sequenced. The mitogenomes of these two species are 16,237 bp and 16,116 bp in length with an A + T content of 77.9% and 77.0%, respectively. Each contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). All PCGs initiate with the standard start codon of ATN and terminate with the complete stop codon of TAA or TAG except for atp6, where nad1 ends with an incomplete T codon. All tRNAs have the typical clover-leaf structure except for trnS1 and trnV which have a reduced DHU arm. Moreover, these two mitogenomes have trnL2, trnR and trnT with an unpaired base in the acceptor stem. The putative A + T-rich region includes multiple types of tandem repeat regions. These phylogenetic analyses are reconstructed based on 13 protein-coding genes of 25 auchenorrhynchan mitogenomes, with both maximum likelihood and Bayesian analyses yielding robust identical phylogenetic trees. These results support a monophyletic Auchenorrhyncha and the relationship (Pyrops + (Lycorma + Aphaena)) within Fulgoridae.

Complete mitochondrial genome of two Thitarodes species (Lepidoptera, Hepialidae), the host moths of Ophiocordyceps sinensis and phylogenetic implications

Thitarodes (Lepidoptera, Hepialidae) is the only genus that hosts to the Ophiocordyceps sinensis, a traditional Chinese medicine considered as a powerful medicinal supplement. In this study, the complete mitochondrial genomes (mitogenomes) of two species, T. damxungensis and T. pui, have been sequenced, which are 15,928 bp and 15,362 bp in size respectively, and both contain 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and an AT-rich region. Like other hepialoids, the gene arrangement of the mitogenomes of T. damxungensis and T. pui is identical to the ancestral arrangement but differs from those of other lepidopteran species on account of the different arrangements of trnM, trnI, and trnQ. The size of AT-rich region is 545 bp in T. damxungensis and 1030 bp in T. pui. Tandem repetition in the AT-rich region is responsible for the length difference of the A + T-rich region in both species. In Hepialidae, the phylogenetic study based on the dataset of the sequences that combined the protein-coding genes and RNA genes suggested that the species T. yunnanensis should still belong to the genus Thitarodes rather than Ahamns, which is different from the results based on the traditional phylogeny.

The first two complete mitochondrial genome of Dacus bivittatus and Dacus ciliatus (Diptera: Tephritidae) by next-generation sequencing and implications for the higher phylogeny of Tephritidae

Dacus bivittatus and Dacus ciliatus are destructive pests of Cucurbitaceae crops including cucumber, zucchini and melons. Recent molecular phylogenetic studies conflicted with morphological taxonomy regarding relationships between Bactrocera, Dacus and Zeugodacus. In this study, we sequenced the complete mitochondrial genomes of the above species which are representatives of two subgenera of Dacus (Dacus and Didacus) not previously sequenced and reconstructed the phylogeny of Tephritidae. The mitochondrial genomes of D. bivittatus and D. ciliatus were 15,833 bp and 15,808 bp in length, respectively. The 37 genes, including 13 protein-coding genes (PCGs), 2 rRNA genes and 22 tRNA genes, with a long non-coding region (A + T-rich control region) were in the same arrangement as the ancestral insect mitochondrial genome. Phylogenetic analysis showed that Dacus has a closer relationship of Zeugodacus rather than Bactrocera. Our phylogenetic results further support the recent proposals that Zeugodacus should be considered as a genus not a subgenus of Bactrocera. Whole mitochondrial genomes of D. bivittatus and D. ciliatus could be useful in further studies for species diagnosis, evolution and phylogeny research within Tephritidae.

Complete mitochondrial genome of Dacus conopsoides (Insecta: Tephritidae) with tRNA gene duplication and molecular phylogeny of Dacini tribe

To date there is only a single report on the complete mitochondrial genome of the Dacus fruit flies. We report here the whole mitogenome of Dacus conopsoides with first report of tRNA gene duplication in tephritid fruit flies determined using next-generation sequencing and discuss the molecular phylogeny of Dacini tribe. It had a total length of 15,852 bp, comprising 13 protein coding genes, 2 rRNA genes, 23 tRNA genes, and a non-coding region (A + T-rich control region). The 65-bp trnF gene was duplicated, and the 68-bp trnE gene was partially duplicated resulting in a 31-bp pseudogene. The cloverleaf structure for trnN , trnH , and trnF lacked the TΨC-loop, while trnS lacked the D-stem. The start codons for the protein coding genes included 6 ATG, 3 ATC, 2 ATA, and 1 each of ATT and TCG. Seven PCGs had TAA stop codon, two had TAG and four had incomplete T stop codon. Molecular phylogeny based on 15 mt-genes (13 PCGs +2 rRNA genes) and 30 taxa of Tephritidae indicated D. conopsoides forming a monophyletic sister group with D. longicornis supported by high bootstrap value. The lineage containing also the monophyletic genus Zeugodacus . The Dacini and Ceratitidini tribes of the subfamily Dacinae were monophyletic but the subfamilies Dacinae and Trypetinae were paraphyletic. A broader taxa sampling of the Tephritidae is needed to better elucidate the phylogenetics and systematics of the tribes and subfamilies of tephritid fruit flies. • Whole mitogenome of D. conopsoides was sequenced. • The mitogenome has 13 PCGs, 2 rRNA genes, 23 tRNA genes and a non-coding region. • First report of tRNA gene duplication in tephritid fruit flies of Dacini tribe. • D. conopsoides formed a monophyletic sister group with D. longicornis .

Complete mitochondrial genome of the silver stripped skipper, Leptalina unicolor (Lepidoptera: Hesperiidae)

The silver stripped skipper, Leptalina unicolor Bremer and Grey, 1853 (Lepidoptera: Hesperiidae), is listed as endangered insect in South Korea. We sequenced the whole genome (15,854 bp) of L. unicolor species using Next-Generation Sequencing method and the subsequent gap-filling method. This genome included a set of typical genes and one major non-coding A + T-rich region, with an arrangement identical to that observed in most lepidopteran genomes. Twelve protein-coding genes (PCGs) had the typical ATN start codon, whereas COI had the atypical CGA codon that is frequently found in the start region of the lepidopteran COI. The 757-bp long A + T-rich region was the second largest among completely sequenced Hesperiidae, which ranged from 234 to 793 bp. Phylogenetic reconstruction was performed by maximum-likelihood method using the concatenated sequences of 13 PCGs and two rRNAs of available species of Hesperiidae, including that of L. unicolor (a total of 28 species). The resulting phylogeny provided strong support for monophyletic Heteropterinae in which L. unicolor belongs, with the highest nodal support and a sister relationship between current L. unicolor and co-subfamilial species Carterocephalus silvicola with a bootstrap value of 91%.