Non-coding AT-rich Region Research Articles

First record of the complete mitochondrial genome of Botyodes diniasalis (Walker, 1859) (Lepidoptera: Crambidae)

We performed the first sequencing of the complete mitogenome of Botyodes diniasalis by high-throughput sequencing. A circular DNA molecule of 15,219 bp in size, encoding 2 rRNAs, 22 tRNAs, and 13 PCGs, contains a non-coding AT-rich region. The overall nucleotide composition of the genome is A (39.5%), T (41.3%), C (11.3%), and G (7.8%). Phylogenetic analysis based on mitogenomic data suggest that the species B. diniasalis has a close evolutionary relationship with B. principalis in Margaroniini. The complete mitogenome of B. diniasalis will serve as a valuable resource for future studies on evolution, taxonomy, genetic conservation, and utilization of Botyodes.

Characterization of the complete mitogenome of Trachylophus sinensis (Coleoptera: Cerambycidae: Cerambycinae), the type species of Trachylophus and its phylogenetic implications

• The first complete mitogenome from the genus Trachylophus was determined using next-generation sequencing. • All available mitogenome of Cerambycinae were comparative and analysis to better understand of their mitogenomic evolution patterns. • The phylogenetic relationship of Cerambycinae was explored through all available mitogenome downloaded from GenBank. Complete mitochondrial genomes (mitogenomes) have long been proved as reliable markers for phylogenetic reconstruction among diverse animal groups, especially benefited from recent rapid development of sequencing techniques. However, the mitogenomes of many important clades remain poorly represented, which restricted the understanding of macroscale evolutionary history of these groups. Here, we sequenced and characterized the complete mitogenome of Trachylophus sinensis , a type species of the Trachylophus genus, which also represents the first sequenced mitogenome in this genus. The complete circular mitogenome was 15,746 bp in length, containing 37 typical genes and one noncoding AT-rich control region. The nucleotide composition of the mitogenome was highly A + T biased, accounting for 70.07% of the whole mitogenome with a slightly positive AT skewness (0.106). The 13 Protein coding genes (PCGs) used ATN as their start codons, except nad1 which used TTG. All tRNA genes were predicted with a characteristic cloverleaf secondary structure except trnS1 (AGN) , whose dihydrouridine (DHU) arm was replaced by a simple loop. Phylogenetic analyses recovered Cerambycinae as a monophyletic group with high node supports and the sister relationship between T. sinensis and Nadezhdiella cantori . However, we found that deeper nodes showed not strong support, which may be caused by limited taxa sampling in our study. More mitogenomes should be sequenced representing various taxonomic levels, especially closely related species, which will enhance our understanding of phylogenetic relationships among Cerambycinae.

Characterization of the complete mitochondrial genome and phylogenetic analysis of Cnaphalocrocis patnalis (Bradley 1981) (Lepidoptera: Crambidae)

Cnaphalocrocis patnalis (Bradley 1981) is a major pest that threatens the safety of rice production in the world. In the present study, we determined the complete mitogenome of C. patnalis. This mitogenome was 15,305 bp in length (GenBank accession No. OL449028), which contained two ribosomal RNA genes, 22 transfer RNAs, 13 protein-coding genes (PCGs) and one non-coding AT-rich region with a length of 344 bp. All the 22 tRNA genes displayed a typical clover-leaf structure, except for trnS1. Twelve PCGs were initiated by ATN codons, and COX1 started with TTG. All the PCGs used the typical stop codon ‘TAA’ and ‘TAG.’ Phylogenetic tree demonstrated that C. patnalis belongs to the family Crambidae.

The complete mitochondrial genome of Clepsis pallidana (Lepidoptera: Tortricidae) with phylogenetic implications

The leaf roller, Clepsis pallidana (Fabricius, 1776) (Lepidoptera: Tortricidae), is an important pest of many crops in China. The circular genome is 15,679 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region. The base composition of the whole mitogenome is 41.2% A, 40.1% T, 11.1% C, and 7.7% G, which shows a strong AT bias. Phylogenetic analysis based on 13 PCGs showed that C. pallidana was closely related to Epiphyas postvittana and clustered within Archipini clade, which was consistent with the traditional classification.

Complete mitochondrial genome of Ricania shantungensis Chou & Lu, 1977 (Hemiptera: Ricaniidae)

Ricania shantungensis Chou & Lu, 1977 (Hemiptera: Ricaniidae), is an invasive pest that attacks forest as well as agricultural trees. We sequenced the 15,358 bp long complete mitochondrial genome (mitogenome) of this species; it consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one major non-coding AT-rich region. The orientation and gene order of the R. shantungensis mitogenome are identical to that of the ancestral type found in majority of the insects. Bayesian inference (BI) phylogeny placed the R. shantungensis examined in our study, together with Ricania spp. in a group with the highest nodal support, forming the family Ricaniidae to which R. shantungensis belongs.

The complete mitochondrial genome of Neomyia cornicina (Diptera: Muscidae)

Neomyia cornicina (Fabricius, 1781) (Diptera: Muscidae) is considered to be an important dung-degrading species in Japan. In this study, we report the first mitochondrial genome (mitogenome) of N. cornicina. The complete mitogenome of N. cornicina was 17,254 bp in length (GenBank accession No. MW592695), containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding AT-rich region. Its nucleotide composition was A (41.0%), G (8.4%), C (11.8%), and T (38.8%). Phylogenetic analysis indicated that N. cornicina is closely related to the species of Eudasyphora canadiana. This mitogenome contributes useful information for further understanding of the phylogenetic relationship and species identification within Muscidae species.

Complete mitochondrial genome of nipa palm hispid beetle Octodonta nipae Maulik (Coleoptera: Chrysomelidae: Cassidinae)

Octodonta nipae (Maulik 1921) is a dangerous forestry quarantine pest, which mainly harms palms. In the present study, we determined complete mitogenome of O. nipae. This mitogenome was 15,397 bp in length (GenBank Accession no. MW802252), which contained 2 ribosomal RNA genes, 22 transfer RNAs, 13 protein-coding genes (PCGs) and one non-coding AT-rich region with the length of 883 bp. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of tRNAPhe, tRNALeu, tRNAAsn, tRNAPro and tRNAThr. Twelve PCGs were initiated by ATN codons, and NAD1 started with TTG. Ten PCGs used the typical stop codon ‘TAA’ and ‘TGA’, while three PCGs (COX2, COX3, NAD4) used the incomplete stop codons ‘TA’ or ‘T’. Phylogenetic tree demonstrated that O. nipae belongs to the family Chrysomelidae and closer to the superfamily Cassidinae.

The complete mitochondrial genome of Ips calligraphus (Germar 1824) (Coleoptera: Curculionidae: Scolytinae)

The complete mitogenome of Ips calligraphus was sequenced, the length was 19,144 bp which consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a major non-coding AT-rich region (GenBank accession no. MW589547). All of 13 protein-coding genes (PCGs) started with ATN. 12 PCGs used the typical stop codon ‘TAA,’ while ATP8 terminated with stop codon ‘TAG.’ Phylogenetic analyses were performed using mitochondrial PCGs for the I. calligraphus and other 18 species within the Scolytinae. The I. calligraphus was clustered together with the other two Ips species in tribe Ipini which were closely related to Xyleborini and Dryocoetini.

The complete mitochondrial DNA genome of a cone snail, Conus betulinus (Neogastropoda: Conidae), from the South China sea

The complete mitochondrial genome of the tubular cone snail Conus betulinus is presented in this study. The C. betulinus mitochondrial genome was 16,240 bp with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding AT-rich region (D-loop). The overall base composition was estimated to be 25.67% for A, 38.26% for T, 21.38% for G, and 14.69% for C, with a high A + T content of 63.93%. Phylogenetic analyses based on 13 PCGs showed the close relationship of vermivorous C. betulinus with the common ancestor of molluscivorous Conus textile and Conus gloriamaris, providing a basis for further studies on the phylogenetics of cone snails according to their dietary type.

Complete mitochondrial genome of the Small-Branded Swift: Pelopidas mathias (Lepidoptera, Hesperiidae)

We report the complete mitochondrial genome of the Small-Branded Swift: Pelopidas mathias, which is an important pest of rice. The total length of the circular double-stranded mitogenome is 15,524 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and a non-coding AT-rich region with the nucleotide base composition of 40.07% A, 40.83% T, 11.59% C, and 7.51% G, showing a relatively strong AT bias. The gene order and organization are consistent with typical Lepidoptera species. This work will provide molecular data support for the study of the phylogeny and evolution in the family Hesperiidae.

Characterization of complete mitochondrial genome of Polyura narcaeus (Lepidoptera: Nymphalidae: Charaxinae)

The complete mitochondrial genome of Polyura narcaeus (Hewitson, 1854) (Lepidoptera: Nymphalidae: Charaxinae) was sequenced in the study. The circular genome is 15,319 bp in size and includes 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. The base composition of the whole mitogenome is 39.15% A, 42.08% T, 11.18% C and 7.59% G, showing a strong AT bias. The characteristics of encoding PCGs, rRNAs and tRNAs, as well as the non-coding intergenic spacers and overlapping sequences are nearly the same with other known butterflies. The AT-rich region also contains several features characteristic of the typical butterflies. Phylogenetic analysis distinctly showed that the family Nymphalidae was a monophyletic group, and that the newly determined Polyura narcaeus of this study was firstly sister to Polyura nepenthes, then they were clustered with Polyura arja.

The complete mitochondrial genome of the freshwater crab Bottapotamon lingchuanense Türkay and Dai 1997 (Decapoda: Brachyura: Potamoidea)

We report the complete mitochondrial genome of Bottapotamon lingchuanense for the first time, which is found to be 17,612 base pairs in length, and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA), and 1 non-coding AT-rich region known as the D-loop. In addition, the mitogenome has 17 intergenic regions ranging from 1 to 1512 bp in length. The mitochondrial genome of B. lingchuanense is the first mitochondrial genome under the genus Bottapotamon, providing DNA data for species identification, enriching the species diversity of Brachyura. The maximum-likelihood (ML) tree and Bayesian inference (BI) tree based on the 13 PCGs of mitochondrial genome of Brachyura species showed similar topologies with high confidence, and the analysis results were consistent with the current mainstream classification system. The results indicating that B. lingchuanense is closely related to Neilupotamon sinense, Sinopotamon, and Tenuilapotamon, and it is likely to be derived from them.

The complete mitochondrial genome of Sarcophaga scopariiformis (Diptera: Sarcophagidae)

Sarcophaga scopariiformis (Diptera: Sarcophagidae), a potential vector of pathogens as well as one of the important flesh fly specie in forensic entomology. We have firstly sequenced and assembled the whole mitogenome of S. scopariiformis in this study. The circular mitogenome is 15,325 bp in length, consisting of A (39.3%), G (9.4%), T (36.8%), and C (14.5%). It showed in a typical mitochondrial genome similar to other sarcophagids species, which is composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and a non-coding AT-rich region. Moreover, the phylogenetic analysis based on 13 PCGs has been conducted. The topological structure of the phylogenetic tree clearly indicated that S. scopariiformis was more closed to the species of Sarcophaga peregrina in genetic distance, compared to the other sarcophagids species. This study provided a useful data reference for genetic structure and phylogenetic analysis of Sarcophagidae.

The complete mitochondrial genome and phylogenetic analysis of the Arabian Honeybee Apis mellifera jemenitica (Insecta: Hymenoptera: Apidae) from Saudi Arabia

Fourteen mitochondrial genomes from workers of the Arabian Honeybee Apis mellifera jemenitica were determined. Genomes range from 16,352 to 16,445 bp. Each consists of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one control region. The mitogenome sequences revealed 753 Variable sites in total, distributed within protein-coding loci (199), ribosomal RNAs genes (117), transfere RNAs genes (48), and non-coding AT-rich region's (389). Phylogenetic analysis with Neighbor-Joining method suggested three evolutionary groups for these mitogenomes, closely related to A. m. jemenitica, A. m. lamarckii, A. m. syriaca, and A. m. scutellata.

The complete mitochondrial genome of the freshwater crab Sinolapotamon patellifer (Decapoda: Brachyura: Potamoidea)

We report the complete mitochondrial genome of Sinolapotamon patellifer for the first time, which is found to be 16,547 base pairs in length, and contains 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA), and one non-coding AT-rich region known as the D-loop. In addition, the mitogenome has 17 intergenic regions ranging from 1 to 1512 bp in length. The mitochondrial genome of S. patellifer is the first mitochondrial genome under the genus Sinolapamon, providing DNA data for species identification, enriching the species diversity of Brachyura, and providing a basis for further studies on population genetics and phylogenetics.

A complete mitochondrial DNA genome of whitefly species (Hemiptera: Aleyrodidae) from Litchi chinensis

A novel complete mitochondrial genome (mitogenome) of whitefly species, collected from Litchi chinensis at Fujian province of China (hereafter whitefly_Litchi chinensis _China) (GenBank accession number: MH999477), was described in this study. The mitogenome of whitefly_Litchi chinensis _China is 15,360 bp in length and contains 13 protein-coding genes, 21 transfer RNAs, 2 ribosomal RNAs and a non-coding AT-rich region (D-loop). The arrangement of mitochondrial genes of whitefly_Litchi chinensis_China are identical with Aleurochiton aceris, but remarkably different from the mitogenomes of the other whitefly genus. Most protein-coding genes (PCGs) start with ATN, except for nad2, cox2 and atp6 genes starting with TTG, GTG, and TTG, respectively; 10 of the 13 PCGs use the typical stop codon TAN, whereas cox1, and cox2 stop with a single T. Phylogenetic analyses based on 13 PCGs support the close relationship of the sample with Aleurochiton aceris, which would provide us further insights on the taxonomy and phylogeny of Aleyrodidae.

The complete mitochondrial genome of the firefly, Diaphanes citrinus (Olivier), (coleoptera: Lampyridae)

We report the complete mitochondrial genome of firefly, Diaphanes citrinus (Olivier). The circular genome of 18,594 bp and has a base composition of A (41.26%), C (11.64%), G (10.18%), T (36.92%). Similar to other Metazoa, our sequence contains 13 protein-coding genes, 21 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region. We sequenced the mitochondrial genome of fireflies to analyze phylogenetic relationships and deduce the evolution of their flashing signals.

Complete mitochondrial genome sequence of Bekko Tombo Libellula angelina Selys, 1883 (Odonata: Libellulidae)

The dragonfly Libellula angelina Selys, 1883 (Odonata: Libellulidae) has been listed as a critically endangered species by the International Union for Conservation of Nature (IUCN) and is also an endangered insect in South Korea. We sequenced the whole genome (15,233 bp) of L. angelina species, which included a set of typical genes and one major non-coding AT-rich region with an arrangement identical to that observed in most insect genomes. The A + T-rich region harbored one identical repeat composed of 65 bp and two tRNA-like structures (trnF and trnK-like sequences) with proper anticodon and clover-leaf structures. Phylogenetic reconstruction using the concatenated sequences of 13 protein-coding genes (PCGs) and two rRNAs of the representative odonate mitogenomes utilizing both Bayesian inference and maximum-likelihood methods revealed a strong support for the monophyletic Zygoptera and a moderate to high support for the monophyletic Anisoptera suborders. Unlike that in conventional phylogenetic analysis, a relatively strong sister relationship was revealed between the suborders of Anisozygoptera and Zygoptera.

Characterization of the complete mitochondrial genome of Minois dryas (Lepidoptera: Nymphalidae: Satyrinae) with phylogenetic analysis

The complete mitochondrial genome (mitogenome) of Minois dryas (Lepidoptera: Nymphalidae: Satyrinae) is determined to be 15,195 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding AT-rich region. The mitogenome includes a cox1 gene with an atypical CGA(R) start codon and five genes (cox1, cox2, nad5, nad4, nad1) exhibiting incomplete stop codons. The 385-bp AT-rich region contains the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)6 element preceded by the ATTTA motif. The phylogenetic analysis indicated that M. dryas is formed a monophyletic group with other Satyrinae species.

The complete mitochondrial genome of Hydrotaea dentipes (Diptera: Muscidae)

Hydrotaea dentipes (Diptera: Muscidae) is one of the forensically important fly species and distributed worldwide. We describe the complete mitochondrial genome of the H. dentipes for the first time. It is a circular molecule of 16,070 bp in size, consisting of A (40.10%), G (9.20%), T (38.50%), and C (12.30%). The order and structure of the genes are similar to other Muscidae species. The mitochondrial genome (mitogenome) is composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and a non-coding AT-rich region. Most PCGs used the canonical putative codon to start and stop.