Lepidopteran Mitogenomes Research Articles

Complete Mitochondrial Genome ofHelicoverpa zea(Lepidoptera: Noctuidae) and Expression Profiles of Mitochondrial-Encoded Genes in Early and Late Embryos

The mitochondrial genome (mitogenome) of the bollworm, Helicoverpa zea (Boddie), was assembled using paired-end nucleotide sequence reads generated with a next-generation sequencing platform. Assembly resulted in a mitogenome of 15,348 bp with greater than 17,000-fold average coverage. Organization of the H. zea mitogenome (gene order and orientation) was identical to other known lepidopteran mitogenome sequences. Compared with Helicoverpa armigera (Hübner) mitogenome, there were a few differences in the lengths of gaps between genes, but the lengths of nucleotide overlaps were essentially conserved between the two species. Nucleotide composition of the H. zea mitochondrial genome was very similar to those of the related species H. armigera and Helicoverpa punctigera Wallengren. Mapping of RNA-Seq reads obtained from 2-h eggs and 48-h embryos to protein coding genes (PCG) revealed that all H. zea PCGs were processed as single mature gene transcripts except for the bicistronic atp8 + atp6 transcript. A tRNA-like sequence predicted to form a hammer-head-like secondary structure that may play a role in transcription start and mitogenome replication was identified within the control region of the H. zea mitogenome. Similar structures were also found within the control regions of several other lepidopteran species. Expression analysis revealed significant differences in levels of expression of PCGs within each developmental stage, but the pattern of variation was similar in both developmental stages analyzed in this study. Mapping of RNA-Seq reads to PCG transcripts also identified transcription termination and polyadenylation sites that differed from the sites described in other lepidopteran species.

Characterization of the complete mitochondrial genome of tea tussock moth, Euproctis pseudoconspersa (Lepidoptera: Lymantriidae) and its phylogenetic implications

In present work, we described the mitochondrial genome (mitogenome) of the tea tussock moth Euproctis pseudoconspersa (Lepidoptera: Lymantriidae). The complete mitogenome of E. pseudoconspersa is a circular genome 15,461bp in size. It contains 37 genes and an A+T-rich region usually presented in lepidopteran mitogenomes, which genes share a lot of features with other known lepidopteran mitogenomes. Nucleotide composition of A+T in this mitogenome is 79.92%, and the AT skew is slightly positive. Both codon distribution and relative synonymous codon usage of the 13 protein-coding genes (PCGs) are consistent with those published lepidopteran sequences. All tRNA genes have typical cloverleaf secondary structures, except for the tRNASer(AGN), in which the dihydrouridine (DHU) arm is simplified down to a loop. The A+T-rich region of E. pseudoconspersa mitogenome possess the motif ‘ATAGA’ and poly-T stretch as the formerly identified conserved elements of Lepidoptera mitogenomes. The phylogenetic relationships were reconstructed by using maximum likelihood (ML) and Bayesian inference (BI) methods based on nucleotide sequences of 13 PCGs of 38 moths. The results were very consistent with the traditional relationships within Noctuoidea from morphological data, and showed that Lymantriidae is more closely related to Erebidae than to Noctuidae.

The Complete Mitochondrial Genome of the Beet Webworm, Spoladea recurvalis (Lepidoptera: Crambidae) and Its Phylogenetic Implications.

The complete mitochondrial genome (mitogenome) of the beet webworm, Spoladea recurvalis has been sequenced. The circular genome is 15,273 bp in size, encoding 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes and containing a control region with gene order and orientation identical to that of other ditrysian lepidopteran mitogenomes. The nucleotide composition of the mitogenome shows a high A+T content of 80.9%, and the AT skewness is slightly negative (-0.023). All PCGs start with the typical ATN codons, except for COX1, which may start with the CGA codon. Nine of 13 PCGs have the common stop codon TAA; however, COX1, COX2 and ND5 utilize the T nucleotide and ND4 utilizes TA nucleotides as incomplete termination codons. All tRNAs genes are folded into the typical cloverleaf structure of mitochondrial tRNAs, except for the tRNASer(AGY) gene, in which the DHU arm fails to form a stable stem-loop structure. A total of 157 bp intergenic spacers are scattered in 17 regions. The overlapping sequences are 42 bp in total and found in eight different locations. The 329 bp AT-rich region is comprised of non-repetitive sequences, including the motif ATAG, which is followed by a 14 bp poly-T stretch, a (AT11 microsatellite-like repeat, which is adjacent to the motif ATTTA, and a 9 bp poly-A, which is immediately upstream from the tRNAMet gene. Phylogenetic analysis, based on 13 PCGs and 13 PCGs+2 rRNAs using Bayesian inference and Maximum likelihood methods, show that the classification position of Pyraloidea is inconsistent with the traditional classification. Hesperioidea is placed within the Papilionoidea rather than as a sister group to it. The Pyraloidea is placed within the Macrolepidoptera with other superfamilies instead of the Papilionoidea.

The complete mitochondrial genome of Gynaephora alpherakii (Lepidoptera: Lymantriidae)

The complete mitochondrial genome (mitogenome) of Gynaephora alpherakii (Lepidoptera: Lymantriidae) has been sequenced and annotated in this study. This mitogenome is 15,755 bp in length with an A + T content of 81.44%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of other lepidopteran species. All protein-coding genes (PCGs) start with a typical ATN codon, with the exception of cox1 which uses CGA as the initial codon. All of the 22 transfer RNA genes present the typical clover leaf secondary structure. The A + T-rich region is located between rrnS and trnM with a length of 449 bp, and contains a 19 bp poly-T stretch as found in other lepidopteran mitogenomes. This is the third completely sequenced mitogenome from the family Lymantriidae of Lepidoptera.

The complete mitochondrial genome of Parnassius imperator (Lepidoptera: Papilionidae: Parnassiinae)

The complete mitochondrial genome (mitogenome) of Parnassius imperator (Lepidoptera: Parnassiinae) is a circular molecule of 15,424 bp in length, containing 37 typical insect mitochondrial genes and one non-coding A + T-rich region. Its gene order and arrangement are identical to the common type found in most lepidopteran mitogenomes. All protein-coding genes (PCGs) start with a typical ATN initiation codon, except for the cox1, which is initiated by the CGA codon as observed in other lepidopteran species. Some PCGs use standard TAA, while others use TAG (nad1) or incomplete codon T (cox1 and cox2), as their termination codons. 15 intergenic spacers (175 bp in total) and 10 overlapping sequences (29 bp in total) are dispersed throughout the whole genome. The 491 bp long A+ T-rich region contains some conserved structures similar to those found in other lepidopteran mitogenomes, such as the motif ATAGA followed by an 18-bp poly-T stretch, a microsatellite-like (AT)6 element preceded by the ATTTA motif. In addition, a 36 bp sequence stretch potential to form stem-loop structures is also found in the A+ T-rich region.

The complete mitochondrial genome of the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae)

The complete mitochondrial genome (mitogenome) of Plutella xylostella (Lepidoptera: Plutellidae) was determined (GenBank accession No. KM023645). The length of this mitogenome is 16,014 bp with 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and an A + T-rich region. It presents the typical gene organization and order for completely sequenced lepidopteran mitogenomes. The nucleotide composition of the genome is highly A + T biased, accounting for 81.48%, with a slightly positive AT skewness (0.005). All PCGs are initiated by typical ATN codons, except for the gene cox1, which uses CGA as its start codon. Some PCGs harbor TA (nad5) or incomplete termination codon T (cox1, cox2, nad2 and nad4), while others use TAA as their termination codons. The A + T-rich region is located between rrnS and trnM with a length of 888 bp.

Characterization of the mitochondrial genome of the threatened alpine butterfly, Parnassius nomion (Lepidoptera: Papilionidae)

The sequenced mitochondrial genome of the threatened alpine butterfly Parnassius nomion includes 13 protein-coding genes (ND1-6, COI-III, ATP6, ATP8, ND4, ND4L, CTYB), 2 ribosomal RNAs (12 S and 16 S), 22 transfer RNAs, which is 14,547 bp in length. Its gene order and orientation are identical to the common type found in most of other completely sequenced lepidopteran mitogenomes. All protein-coding genes are initiated by ATN codons, except for COI, which uses CGA as its start codon. Eleven PCGs use the standard TAA as their termination codon, and COI, COII use the incomplete termination codon T.

The complete mitochondrial genome of the Daimio tethys (Lepidoptera: Hesperoidea: Hesperiidae)

The complete mitochondrial genome of Daimio tethys (Hesperoidea: Hesperiidae) is a circular molecule of 15,341 bp in length, containing 37 typical animal mitochondrial genes: 13 protein coding genes (ATP6, ATP8, COI-III, ND1-6, ND4L, Cytb), 2 rRNA genes, 22 tRNA genes and a non-coding AT-rich region. Its gene order and content are identical to all other available butterfly mitogenomes. All PCGs initiate with typical ATN codons, except for COI, which is initiated by the CGA codon as observed in other butterfly species. Ten PCGs use complete termination codons TAA or TAG, whereas the COI, COII and ND5 genes end with a single T. A total of 179 bp of intergenic spacers are interspersed in 11 regions, ranging in size from 1 to 82 bp. The AT-rich region is 415 bp long and contains some conserved structures characteristic of the lepidopteran mitogenomes, including the motif ATAGA followed by a 17 bp poly-T stretch and a microsatellite-like (AT)8 element preceded by the ATTA motif.

Characterization of the mitochondrial genome of the cabbage webworm, Hellula undalis (Lepidoptera: Pyralidae)

The sequenced mitochondrial genome of the cabbage webworm Hellula undalis includes 13 protein-coding genes (PCGs) (nad1-6, cox1-3, atp6, atp8, nad4L and cob), two ribosomal RNAs (12S and 16S) and 19 transfer RNAs, which is 14,678 bp in length. Its gene order and orientation are identical to the common types found in most of the other completely sequenced lepidopteran mitogenomes. Thirteen PCGs start with a typical ATN codon, while cox1 uses CGA as its start codon. Some PCGs use the standard TAA as their termination codon, while others use the incomplete termination codon T (cox1, cox2 and nad4).

The complete mitochondrial genome of Triphysa phryne (Lepidoptera: Nymphalidae: Satyrinae)

The complete mitochondrial genome (mitogenome) sequence of Triphysa phryne (Lepidoptera: Nymphalidae: Satyrinae) was determined in this study. The mitogenome is 15,143 bp in length, containing 37 typical animal mitochondrial genes: 13 putative protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene content and order are identical to those of other lepidopteran mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, except for COI gene which uses CGA as its start codon. Nine PCGs terminate in the common stop TAA, whereas the COI, COII, ND5 and ND4 genes end with single T. All tRNA genes showed typical secondary cloverleaf structures except for the tRNASer(AGN), which has a simple loop with the absence of its DHU stem. The 316 bp AT-rich region contains several features common to the other lepidopterans, such as the motif ATAGA followed by an 19-bp poly-T stretch and two microsatellite-like (TA)8(AT) and (TA)4 elements preceded by the ATTTA motif.

The complete mitochondrial genome of Parage aegeria (Insecta: Lepidoptera: Papilionidae)

Pararge aegeria is a palearctic butterfly used as a model organism in ecology, behavior, evolution and development, with significant geographically-correlated morphological variation and two close relatives in Macaronesia. In this study, I have determined the complete mitogenome sequence of P. aegeria. The genome is 15,240 bp long, and has the typical gene organization of other lepidopteran mitogenomes. Salient features include the IMQ order of tRNA genes, a sizable (52 bp) spacer between trnQ and nad2, a CGA start codon in cox1 and the ATAGA(T)19 motif in the control region. Interestingly, this region also contains four copies of the imperfect palindrome TAAATATWTATAWATATTTA.

The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae)

The mitochondrial genome (mitogenome) of Parara guttata (Hesperiidae: Hesperiinae) is a circular molecule of 15,441 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most lepidopteran mitogenomes. All PCGs start with a typical ATN codon except for COI and ND1 which use CGA and GTG as their start codons, respectively. Some PCGs harbor TAG (ND1) or incomplete termination codon T (COI, COII, ND5, ND4), while others use standard TAA as their termination codons. The 411-bp long AT-rich region contains a conserved motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)5 element preceded by the ATTTA motif.

鳞翅目昆虫比较线粒体基因组学研究进展

Lepidopteran insects have a marked impact on human society, whether functioning as major pests of agriculture and forestry, pollinators, or a primary producer of silk. Insect mitochondrial genome (mitogenome) has a relatively conserved gene content and gene order, so it has been widely used in molecular phylogeny and evolution. To date, complete mitogenomes have been sequenced for a total of 63 species of Lepidoptera. Among the sequenced mitogenomes, however, only 58 are reference sequences available in GenBank. Here, a comparative analysis of all the mitogenome reference sequences revealed some basic features of lepidopteran mitogenomes. Furthermore, the phylogenetic relationships within Lepidoptera based on the complete mitogenome sequences proved to be similar to that based on traditional morphological characters. This work paves the way for better understanding of the evolution of lepidopteran insects, and suggests that comparative mitogenomic analysis has great potential for resolving phylogenetic relationships among the major groups of insects at the dawn of the postgenomic era.

Characterization of the complete mitochondrial genome of Diaphania pyloalis (Lepidoptera: Pyralididae)

The complete mitochondrial genome (mitogenome) of Diaphania pyloalis (Lepidoptera: Pyralididae) was determined to be 15,298bp and has the typical gene organization of mitogenomes from lepidopteran insects. It consists of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A+T-rich region. The A+T content of this mitogenome is 80.83% and the AT skew is slightly positive. All PCGs are initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which is initiated by CGA. Only the cox2 gene has an incomplete stop codon consisting of just a T. All the tRNA genes display a typical clover-leaf structure of mitochondrial tRNA. The A+T-rich region of the mitogenome is 332bp in length, including several common features found in lepidopteran mitogenomes. Phylogenetic analysis showed that the D. pyloalis is close to Pyralididae.

The complete mitochondrial genome of the mountainous duskywing, Erynnis montanus (Lepidoptera: Hesperiidae): a new gene arrangement in Lepidoptera

The mountainous duskywing, Erynnis montanus, belongs to a lepidopteran family Hesperiidae. The 15,530-bp long complete mitochondrial genome (mitogenome) of the species has the typical gene content of animals (13 protein-coding genes, two rRNA genes, 22 tRNA genes and one major non-coding A+T-rich region). As typical in lepidopteran mitogenome E. montanus mitogenome also contained a high A/T content in the whole genome (81.7%) and the CGA (arginine) as the start codon for the COI gene. Unlike other lepidopteran species, including two sequenced skippers, the E. montanus mitogenome has a unique arrangement tRNASer–tRNAAsn, instead of the tRNAAsn–tRNASer found unanimously in other lepidopteran species, providing a new gene arrangement in Lepidoptera. Such rearrangement probably was likely caused by duplication of gene block tRNASer–tRNAAsn and subsequent random loss of tRNAAsn in the first copy and tRNASer in the second copy, resulting in the arrangement tRNASer–tRNAAsn.

The complete mitochondrial genome of Gynaephora menyuanensis (Lepidoptera: Lymantriidae) from the Qinghai-Tibetan Plateau

We sequenced and annotated the complete mitochondrial genome (mitogenome) of Gynaephora menyuanensis (Lepidoptera: Lymantriidae), which is a major pest in alpine meadows and endemic to the Qinghai-Tibetan Plateau. This mitogenome is 15,770 bp in length with an A+T content of 81.48%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of other lepidopteran species. All protein-coding genes (PCGs) start with a typical ATN codon, with the exception of cox1, which begins with CGA. Eleven PCGs stop with termination codon TAA, whereas cox2 and nad4 have single T as the incomplete stop codon. All of the 22 transfer RNA genes present the typical clover leaf secondary structure. The A+T-rich region is located between rrnS and trnM with a length of 449 bp, and contains a 19 bp poly-T stretch as found in other lepidopteran mitogenomes. This is the second completely sequenced mitogenome from the family Lymantriidae of Lepidoptera, providing important molecular information to phylogenetic and population genetic researches.

The Complete Mitochondrial Genome of the Wild Type of Antheraea pernyi (Lepidoptera: Saturniidae)

Abstract Antheraea pernyi (Guérin-Méneville) (Lepidoptera: Saturniidae), a well-known economically important insect, was domesticated from its wild type. In this study, the complete mitochondrial genome (mitogenome) of the wild type of A. pernyi was determined and compared for nucleotide variation with its domesticated type. The mitogenome of the wild type of A. pernyi is 15,537 bp in size, thus 29 bp smaller than that of the domesticated type. The gene content, order, and orientation of the complete mitogenome of the wild type are identical to those of the domesticated type, as are those of the other completely sequenced lepidopteran mitogenomes. A striking difference between the two mitogenomes was found in the A+T-rich region because of the numbers of tandem repeat units. The wild type has five tandem repeat units, whereas the domesticated type has six. Comparative analysis of the two mitogenomes revealed a relatively lower level of sequence divergence (1.70%). Within the two mitogenomes, there are no significant differences in nucleotide substitution rate for the 13 protein-coding genes except for the nad4L gene, which is different from those differences observed between the domesticated silkmoth Bombyx mori (L.) (Lepidoptera: Bombycidae) and its wild-type ancestor Chinese B. mandarina Moore. The divergence time between the two Antheraea mitochondrias was estimated to be between 0.74 ± 0.13 and 0.97 ± 0.17 million years ago, based on the genes cox1+cox2 sequences. To our knowledge, this is the first report on sequence variation of the complete mitogenomes between the domesticated insect and its wild-type ancestor, within a single species.

The complete mitochondrial genome of the butterfly Apatura metis (Lepidoptera: Nymphalidae)

As an important pest in the Slender Leaved Willow (Salix alba), Apatura metis is called Freyer's purple emperor, and its mitochondrial genome is 15,236 bp long. The encoded genes for 22 tRNA genes, two ribosomal RNA (rrnL and rrnS) genes, and 13 protein-coding genes (PCGs), and a control region in the A. metis mitochondria are highly homologous to other lepidopteran species. The mitochondrial genome of A. metis is biased toward a high A + T content (A + T = 80.5%). All protein-coding genes, except for COI begins with the CGA codon as observed in other lepidopterans, start with a typical ATN initiation codon. All tRNAs show the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA(Ser(AGN)) forms a simple loop. The A. metis A + T-rich region contains some conserved structures including a structure combining the motif 'ATAGA' and 19 bp poly (T) stretch, which is similar to those found in other lepidopteran mitogenomes. The phylogenetic analyses of lepidopterans based on mitogenomes sequences demonstrate that each of the six superfamilies is monophyletic, and the relationship among them is (((Noctuoidea + (Geometroidea + Bombycoidea)) + Pyraloidea) + Papilionoidea) + Tortricoidea. In Papilionoidea group, our conclusion argues that ((Lycaenidae + Pieridae) + Nymphalidae) + Papilionidae.

Complete sequence of the mitochondrial genome of the Japanese buff-tip moth, Phalera flavescens (Lepidoptera: Notodontidae)

We sequenced the complete mitochondrial genome of Phalera flavescens. The mitogenome is 15,659 bp in length, including 13 protein-coding genes (atp6, atp8, cox1-3, nad1-6, nad4L, cob), two ribosomal RNAs (rrnS and rrnL), 22 transfer RNAs and an AT-rich region, a putative control region (D-loop). Gene order and orientation were found to be identical to those of other completely sequenced lepidopteran mitogenomes. All 13 protein-coding genes start with the common codon ATN, except for the cox1 gene, which uses CGA as the initial codon. Nine of the 13 protein-coding genes stop with codon TAA, while the cox1, cox2, nad5, and nad4 genes stop with the single nucleotide T. All tRNA genes can be folded into canonical cloverleaf secondary structure, except for trnS1, which loses the ''DHU'' arm. Six overlapping sequences totaling 20 bp (1-8 bp for each sequence) and 16 intergenic spacer sequences, totaling 276 bp (1-58 bp for each sequence) are scattered throughout the genome; the largest intergenic spacer is located between the trnQ and nad2 genes. A microsatellite-like structure (AT)(6)ACC(AT)(6) and 16-bp poly-T elements preceded by the ATTTA motif are present in the D-loop region. Additionally, unexpectedly, an extra 190-bp insertion, with unknown function, was found in the small subunit rRNA gene (rrnS); this gene is the longest known (1020 bp) among all of the Lepidoptera.

Complete mitochondrial genome of the laced fritillary Argyreus hyperbius (Lepidoptera: Nymphalidae).

We investigated the complete mitochondrial genome (mitogenome) of Argyreus hyperbius. The 15156 bp long genome harbored the gene content (13 protein coding genes, 22 tRNA genes, 2 rRNA genes and an A+T-rich region) and the gene arrangement was identical to all known lepidopteran mitogenomes. Mitogenome sequence nucleotide organization and codon usage analyses showed that the genome had a strong A+T bias, accounting for A+T content of 80.8%, with a small negative AT skew (-0.019). Eleven intergenic spacers totaling 96 bp, and 14 overlapping regions totaling 34 bp were scattered throughout the whole genome. As has been observed in other lepidopteran species, 12 of the 13 protein-coding genes (PCGs) were initiated by ATN codons, while the COI gene was tentatively designated by the CGA codon. A total of 11 PCGs harbored the complete termination codon TAA, while the COI and COII genes ended at a single T residue. All of the 22 tRNA genes showed typical clover structures except that the tRNA(Ser(AGN)) lacks the dihydrouridine (DHU) stem which is replaced by a simple loop. The intergenic spacer sequence between the tRNA(Ser(AGN)) and ND1 also contained the ATACTAA motif, which is conserved in all other lepidopterans as well. Additionally, the 349 bp A+T-rich region was not comprised of large tandem repetitive sequences, but harbored a few structures common to other lepidopteran insects, such as the motif ATAGA followed by a 20 bp poly-T stretch, a microsatellite-like (AT)(9) element preceded by the ATTTA motif, and a 5 bp poly-A site present immediately upstream of tRNA(Met). The mitochondrial genomic sequence features found in this study not only contribute to genetic diversity information of the group, but also are useful in future studies of the endangered nymphalid butterfly in population genetic dynamics, species conservation, phylogeography and evolution.