Tian-Juan Su

Characterization of the complete mitochondrion genome of diurnal Moth Amata emma (Butler) (Lepidoptera: Erebidae) and its phylogenetic implications.

Mitogenomes can provide information for phylogenetic analyses and evolutionary biology. The complete mitochondrial genome of Amata emma (Lepidoptera: Erebidae) was sequenced and analyzed in the study. The circular genome is 15,463 bp in size, with the gene content, orientation and order identical to other ditrysian insects. The genome composition of the major strand shows highly A+T biased and exhibits negative AT-skew and GC-skew. The initial codons are the canonical putative start codons ATN with the exception of cox1 gene which uses CGA instead. Ten genes share complete termination codons TAA, and three genes use incomplete stop codons TA or T. Additionally, the codon distribution and Relative Synonymous Codon Usage of the 13 PCGs in the A. emma mitogenome are consistent with those in other Noctuid mitogenomes. All tRNA genes have typical cloverleaf secondary structures, except for the trnS1 (AGN) gene, in which the dihydrouridine (DHU) arm is simplified down to a loop. The secondary structures of two rRNA genes broadly conform with the models proposed for these genes of other Lepidopteran insects. Except for the A+T-rich region, there are three major intergenic spacers, spanning at least 10 bp and five overlapping regions. There are obvious differences in the A+T-rich region between A. emma and other Lepidopteran insects reported previously except that the A+T-rich region contains an ‘ATAGA’ -like motif followed by a 19 bp poly-T stretch and a (AT)9 element preceded by the ‘ATTTA’ motif. It neither has a poly-A (in the α strand) upstream trnM nor potential stem-loop structures and just has some simple structures like (AT)nGTAT. The phylogenetic relationships based on nucleotide sequences of 13 PCGs using Bayesian inference and maximum likelihood methods provided a well-supported a broader outline of Lepidoptera and which agree with the traditional morphological classification and recently working, but with a much higher support.

The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of Tachinid flies.

Tachinid flies are natural enemies of many lepidopteran and coleopteran pests of forests, crops, and fruit trees. In order to address the lack of genetic data in this economically important group, we sequenced the complete mitochondrial genome of the Palaearctic tachinid fly Elodia flavipalpis Aldrich, 1933. Usually found in Northern China and Japan, this species is one of the primary natural enemies of the leaf-roller moths (Tortricidae), which are major pests of various fruit trees. The 14,932-bp mitochondrial genome was typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. However, its control region is only 105 bp in length, which is the shortest found so far in flies. In order to estimate dipteran evolutionary relationships, we conducted a phylogenetic analysis of 58 mitochondrial genomes from 23 families. Maximum-likelihood and Bayesian methods supported the monophyly of both Tachinidae and superfamily Oestroidea. Within the subsection Calyptratae, Muscidae was inferred as the sister group to Oestroidea. Within Oestroidea, Calliphoridae and Sarcophagidae formed a sister clade to Oestridae and Tachinidae. Using a Bayesian relaxed clock calibrated with fossil data, we estimated that Tachinidae originated in the middle Eocene.

The complete mitochondrial genome of the rice moth, Corcyra cephalonica

Abstract The complete mitochondrial genome (mitogenome) of the rice moth, Corcyra cephalonica Stainton (Lepidoptera: Pyralidae) was determined as a circular molecular of 15,273 bp in size. The mitogenome composition (37 genes) and gene order are the same as the other lepidopterans. Nucleotide composition of the C. cephalonica mitogenome is highly A+T biased (80.43%) like other insects. Twelve protein-coding genes start with a typical ATN codon, with the exception of coxl gene, which uses CGA as the initial codon. Nine protein-coding genes have the common stop codon TAA, and the nad2, cox1, cox2, and nad4 have single T as the incomplete stop codon. 22 tRNA genes demonstrated cloverleaf secondary structure. The mitogenome has several large intergenic spacer regions, the spacer1 between trnQ gene and nad2 gene, which is common in Lepidoptera. The spacer 3 between trnE and trnF includes microsatellite-like repeat regions (AT)18 and (TTAT)3. The spacer 4 (16 bp) between trnS2 gene and nad1 gene has a motif ATACTAT; another species, Sesamia inferens encodes ATCATAT at the same position, while other lepidopteran insects encode a similar ATACTAA motif. The spacer 6 is A+T rich region, include motif ATAGA and a 20-bp poly(T) stretch and two microsatellite (AT)9, (AT)8 elements.

The complete mitochondrial genome of the Colletes gigas (Hymenoptera: Colletidae: Colletinae)

Abstract The complete mitochondrial genome of the Colletes gigas (Hymenoptera: Colletidae) is determined to be 15,885 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a major non-coding AT-rich region. All PCGs initiate with typical ATN codons and end with the complete termination codon TAA, except for the cob gene, which harbors the stop codon of TAG. Twenty-four intergenic spacers (614 bp in total) and 7 overlapping regions (37 bp in total) are dispersed throughout the whole genome. The non-coding AT-rich region is 539 bp long and contains a tandem repeat region, which has also been reported in other insects. This is the first completely sequenced mitochondrial genome of the family Colletidae.

The complete mitochondrial genome of Melanargia asiatica (Lepidoptera: Nymphalidae: Satyrinae)

Abstract We sequenced the complete mitochondrial genome of Melanargia asiatica (Lepidoptera: Nymphalidae: Satyrinae). The entire closed circular molecule is 15,142 bp long, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a AT-rich region. All protein-coding genes (PCGs) initiate with the typical start codons ATN, with the exception of cox1, which uses CGA instead. Nine PCGs use the conventional stop codons (TAA) and the other four genes (cox1, cox2, nad4 and nad5) use a single T as the stop codon. All tRNA genes display typical secondary cloverleaf structures, except for trnS1 (AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop, as observed in all other lepidopterans. The AT-rich region is 319 bp in length and contains some features characteristic of lepidopterans, such as the ATAGA motif followed by a 19-bp poly-T stretch and a microsatellite-like repeat of (TA)6T(TA) preceded by the ATTTA motif.

Sequencing and characterization of the Megachile sculpturalis (Hymenoptera: Megachilidae) mitochondrial genome.

Abstract The mitochondrial genome (mitogenome) of Megachile sculpturalis (Hymenoptera: Megachilidae) has been reported in this study. This is the first sequenced mitogenome from the family Megachilidae. The sequenced region of this mitochondrial genome is determined to be 16 581 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a partial sequence of the AT-rich region, and the AT-rich region contains several characteristic repeated sequences. Additionally, we conducted a phylogenetic analysis using all the mitochondrial genomes of Apoidea that are available in Genbank. Bayesian method supported the monophyly of both Apidae and Colletidae. And Megachilidae was inferred as the sister group of Apidae.

The complete mitochondrial genome of Carposina sasakii (Lepidoptera: Carposinidae).

Abstract The peach fruit moth, Carposina sasakii belongs to Carposinidae in Lepidoptera. In this paper, we described the complete mitogenome of C. sasakii. It is 15,611 bp in length, including 13 PCGs, 2 rRNAs, 22 tRNAs and a major noncoding A + T-rich region, which revealed the typical gene content found in other metazoan mitogenomes. The overall base composition is 42.0% A, 39.5% T, 7.75% G and 10.75% C. The A + T-rich region is located between rrnS and trnM. There is a motif ATAGA in downstream of rrnS followed by a 19 bp Poly-T stretch. The Poly-A is not found in upstream of trnM, and the position of Poly-A is replaced by a stem-loop structure. There are eight mononucleotide repeat sequences (Tn/An) with the length of 7 bp-19bp, three dinucleotide repeat sequences (TA)n/(AT)n, and a longer repeat sequence (AATATATA)5 in A + T-rich region. The mononucleotide repeat sequences occur repeatedly in A + T-rich reigion of C. sasakii, which is special in insects sequenced of Lepidoptera.

The complete mitochondrial genome of Acleris fimbriana (Lepidoptera: Tortricidae)

Abstract The yellow tortrix, Acleris fimbriana belongs to Tortricidae in Lepidoptera. We described the complete mitogenome of A. fimbriana, which is typical circular duplex molecules and 15,933 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 A. fimbriana mitochondrial genome has the same gene order with other lepidopterans.

Phylogenetic analysis of the mitochondrial genomes in bees (Hymenoptera: Apoidea: Anthophila)

In this study, the first complete mitogenome of Andrenidae, namely Andrena camellia, is newly sequenced. It includes 13 protein-coding (PCG) genes, 22 transfer RNA (rRNA) genes, two ribosomal RNA (tRNA) genes, and a control region. Among PCGs, high conservation is observed in cytochrome oxidase genes with cox1 exhibits the highest conservation. Conversely, NADH dehydrogenase and ATPase subunit genes are more variable with atp8 presents the maximal variation. Comparison of the gene order indicates complex rearrangement in bees. Most of the rearranged events are located in the tRNA clusters of trnI-trnQ-trnM, trnW-trnC-trnY, and trnA-trnR-trnN-trnS1-trnE-trnF. Furthermore, we present the most comprehensive mitochondrial phylogeny of bee families. The monophyly of each family and the long-tongued bees is highly supported. However, short-tongued bees are inferred as paraphyletic relative to the sister relationship between Melittidae and other bee families. Furthermore, to improve the resolution of phylogeny, various datasets and analytical approaches are performed. It is indicated that datasets including third codons of PCGs facilitate to produce identical topology and higher nodal support. The tRNA genes that have typical cloverleaf secondary structures also exhibit similar positive effects. However, rRNAs present poor sequence alignment and distinct substitution saturation, which result in negative effects on both tree topology and nodal support. In addition, Gblocks treatment can increase the congruence of topologies, but has opposite effects on nodal support between the two inference methods of maximum likelihood and Bayesian inference.

Sequencing and characterization of mitochondrial genome of Eurytoma sp. (Hymenoptera: Eurytomidae)

Abstract The mitochondrial genome (mitogenome) of Eurytoma sp. (Hymenoptera: Eurytomidae: Eurytominae) was determined in this study. The sequenced region is 14,946 bp with an A + T content of 82.65%, including 13 protein-coding genes, 2 ribosomal RNAs, 18 transfer RNAs, and a partial sequence of AT-rich region. All PCGs begin with typical ATN codons and use standard canonical TAA as their termination codons, except for atp6 gene, which stops with an incomplete codon T. A comparison of all the sequenced hymenopteran mitogenomes revealed that Eurytoma sp. has dramatic gene rearrangements, some of which is peculiar to Chalcidoidea. What’s more, Maximum likelihood (ML) analysis highly supported the monophyly of both Chalcidoidea and Apocrita.