Dataset Information

Complete mitochondrial genome of the pine moth Dendrolimus spectabilis (Lepidoptera: Lasiocampidae).

ABSTRACT: We have sequenced the complete mitochondrial genome (mitogenome) of the pine moth Dendrolimus spectabilis Butler (Lepidoptera: Lasiocampidae), which has been a serious pest for the Japanese red pine (Pinus densiflora S. et Z.) in Korea. The 15?409?bp complete mitochondrial genome (mitogenome) of the species consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and the A?+?T-rich region, with an arrangement typical of Ditrysia in Lepidoptera. The 320?bp long A?+?T-rich region of D. spectabilis contains the motif ATAGA near the 5'-end of the srRNA, with a 14?bp-long poly-T stretch - the ATTTA sequence - and a microsatellite-like sequence consisting of (TA)₇, but lacks the poly-A stretch often found immediately upstream of tRNA^Met in other Lepidoptera. A phylogenetic analysis using 13 protein-coding genes from Bombycoidea and Lasiocampoidea has shown that D. spectabilis was placed as a sister to the congeneric species group, D. tabulaeformis?+?D. punctatus.

SUBMITTER: Kim MJ

PROVIDER: S-EPMC7871830 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Complete mitochondrial genome of the pine moth Dendrolimus spectabilis (Lepidoptera: Lasiocampidae).

Kim Min Jee MJ Kim Jong Seok JS Kim Sung-Soo SS Kim Seong Ryul SR Kim Iksoo I

Mitochondrial DNA. Part B, Resources 20160328 1

We have sequenced the complete mitochondrial genome (mitogenome) of the pine moth Dendrolimus spectabilis Butler (Lepidoptera: Lasiocampidae), which has been a serious pest for the Japanese red pine (Pinus densiflora S. et Z.) in Korea. The 15 409 bp complete mitochondrial genome (mitogenome) of the species consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and the A + T-rich region, with an arrangement typical of Ditrysia in Lepidoptera. T ...[more]

PMID: 33644337

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Project description:Dendrolimus houi is one of the most common caterpillars infesting Gymnosperm trees, and widely distributed in several countries in Southeast Asia, and exists soley or coexists with several congeners and some Lasiocampidae species in various forest habitats. However, natural hybrids occasionally occur among some closely related species in the same habitat, and host preference, extreme climate stress, and geographic isolation probably lead to their uncertain taxonomic consensus. The mitochondrial DNA (mtDNA) of D. houi was extracted and sequenced by using high-throughput technology, and the mitogenome composition and characteristics were compared and analyzed of these species, then the phylogenetic relationship was constructed using the maximum likelihood method (ML) and the Bayesian method (BI) based on their 13 protein-coding genes (PCGs) dataset, which were combined and made available to download which were combined and made available to download among global Lasiocampidae species data. Mitogenome of D. houi was 15,373 bp in length, with 37 genes, including 13 PCGs, 22 tRNA genes (tRNAs) and 2 rRNA genes (rRNAs). The positions and sequences of genes were consistent with those of most known Lasiocampidae species. The nucleotide composition was highly A+T biased, accounting for ~80% of the whole mitogenome. All start codons of PCGs belonged to typical start codons ATN except for COI which used CGA, and most stop codons ended with standard TAA or TAG, while COI, COII, ND4 ended with incomplete T. Only tRNASer (AGN) lacked DHU arm, while the remainder formed a typical "clover-shaped" secondary structure. For Lasiocampidae species, their complete mitochondrial genomes ranged from 15,281 to 15,570 bp in length, and all first genes started from trnM in the same direction. And base composition was biased toward A and T. Finally, both two methods (ML and BI) separately revealed that the same phylogenetic relationship of D. spp. as ((((D. punctatus + D. tabulaeformis) + D. spectabilis) + D. superans) + (D. kikuchii of Hunan population + D. houi) as in previous research, but results were different in that D. kikuchii from a Yunnan population was included, indicating that different geographical populations of insects have differentiated. And the phylogenetic relationship among Lasiocampidae species was ((((Dendrolimus) + Kunugia) + Euthrix) + Trabala). This provides a better theoretical basis for Lasiocampidae evolution and classification for future research directions.

Project description:BackgroundKnowledge of animal mitochondrial genomes is very important to understand their molecular evolution as well as for phylogenetic and population genetic studies. The Lepidoptera encompasses more than 160,000 described species and is one of the largest insect orders. To date only nine lepidopteran mitochondrial DNAs have been fully and two others partly sequenced. Furthermore the taxon sampling is very scant. Thus advance of lepidopteran mitogenomics deeply requires new genomes derived from a broad taxon sampling. In present work we describe the mitochondrial genome of the moth Ochrogaster lunifer.ResultsThe mitochondrial genome of O. lunifer is a circular molecule 15593 bp long. It includes the entire set of 37 genes usually present in animal mitochondrial genomes. It contains also 7 intergenic spacers. The gene order of the newly sequenced genome is that typical for Lepidoptera and differs from the insect ancestral type for the placement of trnM. The 77.84% A+T content of its alpha strand is the lowest among known lepidopteran genomes. The mitochondrial genome of O. lunifer exhibits one of the most marked C-skew among available insect Pterygota genomes. The protein-coding genes have typical mitochondrial start codons except for cox1 that present an unusual CGA. The O. lunifer genome exhibits the less biased synonymous codon usage among lepidopterans. Comparative genomics analysis study identified atp6, cox1, cox2 as cox3, cob, nad1, nad2, nad4, and nad5 as potential markers for population genetics/phylogenetics studies. A peculiar feature of O. lunifer mitochondrial genome it that the intergenic spacers are mostly made by repetitive sequences.ConclusionThe mitochondrial genome of O. lunifer is the first representative of superfamily Noctuoidea that account for about 40% of all described Lepidoptera. New genome shares many features with other known lepidopteran genomes. It differs however for its low A+T content and marked C-skew. Compared to other lepidopteran genomes it is less biased in synonymous codon usage. Comparative evolutionary analysis of lepidopteran mitochondrial genomes allowed the identification of previously neglected coding genes as potential phylogenetic markers. Presence of repetitive elements in intergenic spacers of O. lunifer genome supports the role of DNA slippage as possible mechanism to produce spacers during replication.

Dataset Information

Complete mitochondrial genome of the pine moth Dendrolimus spectabilis (Lepidoptera: Lasiocampidae).

Publications

Complete mitochondrial genome of the pine moth <i>Dendrolimus spectabilis</i> (Lepidoptera: Lasiocampidae).

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