Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Chalcophora japonica chinensis Schaufuss, 1879 (Coleoptera: Buprestidae).

ABSTRACT: Chalcophora japonica chinensis Schaufuss, 1879 (Coleoptera: Buprestidae) is a common pine pest in Chongqing, Fujian, Yunnan, and other in China. The mitochondrial genome of C. japonica is 15,759 bp in size. The genome includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The overall GC content of the mitogenome is 32.0%. The results showed that C. japonica was most related to Chrysochroa fulgidissima, Trachys variolaris, and Agrilus mali. The full mitochondrial genome of C. japonica is now available, allowing researchers to better understand the species' genetic evolution and regulatory strategies.

SUBMITTER: Weng M

PROVIDER: S-EPMC9427030 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of Chalcophora japonica chinensis Schaufuss, 1879 (Coleoptera: Buprestidae).

Weng Mingqing M Wang Yue Y Huang Jing J Huang Lulu L Lin Yiqi Y Zheng Qilian Q Wu Yanzhen Y Wu Songqing S

Mitochondrial DNA. Part B, Resources 20220829 8

Chalcophora japonica chinensis Schaufuss, 1879 (Coleoptera: Buprestidae) is a common pine pest in Chongqing, Fujian, Yunnan, and other in China. The mitochondrial genome of C. japonica is 15,759 bp in size. The genome includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The overall GC content of the mitogenome is 32.0%. The results showed that C. japonica was most related to Chrysochroa fulgidissima, Trachys v ...[more]

PMID: 36051368

Similar Datasets

The complete mitochondrial genome of the jewel beetle Trachys variolaris (Coleoptera: Buprestidae).

Project description:The complete mitochondrial genome (mitogenome) of the jewel beetle, Trachys variolaris, was sequenced and described. The mitogenome of T. variolaris is a typical circular DNA molecule with 16,771 bp in length. It contains the typical 37 mitochondrial genes (13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and a long non-coding region called the control region. Twelve protein-coding genes initiate with ATN codons except ND1 uses TTG. Most of the protein-coding genes use TAA or TAG as the stop codon, but COII, COIII, ND4, and ND5 terminate with a single T-- or TA-. The length of the 22 tRNAs ranges from 61 to 70 bp and they all have the clover-leaf structure except for tRNASer(AGN) . The control region is 2155 bp long with the A + T content of 69.4%. The result of our phylogenetic analysis showed that Buprestoidea is monophyletic, and it is the sister group to (Byrrhoidea + Elateroidea).

| S-EPMC7706562 | biostudies-literature

The complete mitochondrial genome of the jewel beetle Coraebus cavifrons (Coleoptera: Buprestidae).

Project description:The complete mitochondrial genome (mitogenome) of the jewel beetle, Coraebus cavifrons, was sequenced and described in the present study. The mitogenome of Coraebus cavifrons is a typical circular DNA molecule of 15,686 bp. All of the 37 mitochondrial genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) were annotated and a putative control region with 1135 bp in length was found between tRNAIle and srRNA. Protein-coding genes all initiate with ATN codons except for COII uses GTG. Most of the protein-coding genes use TAA or TAG as the stop codon, but COII, COIII, and ND5 terminate with a single T. All tRNAs have the clover-leaf structure except for tRNASer(AGN) and the length of them range from 60 to 71 bp. Genome organization and nucleotide composition of the mitogenome were also noted. Our phylogenetic analysis of Elateriformia supported the monophyly of Buprestoidea and the sister relationship between Buprestoidea and (Byrrhoidea + Elateroidea).

| S-EPMC7687635 | biostudies-literature

The complete mitochondrial genome of the pyrophilous jewel beetle Melanophila acuminata (Coleoptera: Buprestidae).

Project description:The complete mitochondrial of genome Melanophila acuminata (DeGeer 1774) is a typical double-stranded circular molecule of 15,853 bp (GenBank accession number: MW287594). All tRNA genes, ranging from 62 to 72 bp, can be folded into typical clover-leaf secondary structure except for tRNA Ser(AGN) . The control region is 1,080 bp long with an A+T content of 87.5%. The phylogeny tree is monophyletic among 19 related species. The Melanophila acuminata cluster was more closely related to Chrysochroa fulgidissima. This mitochondrial genome can be used for further analyses of Buprestidae mitochondrial comparative genomics to improve the understanding of diverse coleopteran species.

| S-EPMC7995886 | biostudies-literature

First Report of Complete Mitochondrial Genome in the Tribes Coomaniellini and Dicercini (Coleoptera: Buprestidae) and Phylogenetic Implications.

Project description:The complete mitochondrial genomes (mitogenomes) of the tribes Coomaniellini and Dicercini were sequenced and described in this study, including Coomaniella copipes (16,196 bp), Coomaniella dentata (16,179 bp), and Dicerca corrugata (16,276 bp). These complete mitogenomes are very similar in length and encoded 37 typical mitochondrial genes, including 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and 13 protein-coding genes (PCGs). Most of PCGs had typical ATN start codons and terminated with TAR. Among these mitogenomes, Leu2 (L2), Ile (I), Ser2 (S2), and Phe (F) were the four most frequently encoded amino acids. Moreover, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) among the available sequenced species of the family Buprestidae using Bayesian inference and Maximum-likelihood methods. The results showed that a Chrysochroninae species interspersed in Buprestinae, and Coomaniellini is more closely related to Dicercini than Melanophilini. Moreover, the clade of Buprestidae was well separated from outgroups and the monophyly of Agrilinae is confirmed again. Our whole mitogenome phylogenetic results support that the genus Dicerca can be transferred from Chrysochroinae to Buprestinae; whether Dicercini can be completely transferred remains to be further verified after enriching samples. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research.

| S-EPMC9222259 | biostudies-literature

The complete mitochondrial genomes of five Agrilinae (Coleoptera, Buprestidae) species and phylogenetic implications.

Project description:Five complete mitochondrial genomes of five species from the subfamily Agrilinae were sequenced and annotated, including Coraebusdiminutus Gebhardt, 1928 (15,499 bp), Coraebuscloueti Théry, 1893 (15,514 bp), Meliboeussinae Obenberger, 1935 (16,108 bp), Agrilussichuanus Jendek, 2011 (16,521 bp), and Sambusfemoralis Kerremans, 1892 (15,367 bp). These mitogenomes ranged from 15,367 to 16,521 bp in length and encoded 37 typical mitochondrial genes: 13 protein-coding genes (13 PCGs), 2 ribosomal RNA genes (2 rRNAs), 22 transfer RNA genes (22 tRNAs), and a control region (CR). Most of PCGs had typical ATN start codons and terminated with TAR or an incomplete stop codon T-. Among these five mitogenomes, Leu2, Ile, Phe, Ser2, Gly, Met, and Val were the seven most frequently encoded amino acids. Interestingly, in A.sichuanus, a 774 bp insertion was present at trnW and trnC junction, which is unusual in Buprestidae. Additionally, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) using Bayesian inference and maximum-likelihood methods. The results showed that the clade of Buprestidae was well separated from outgroups and all Agrilinae species formed to a single highly supported clade. The tribe Coraebini was polyphyletic, as the genus Meliboeus (Coraebini) clustered with the genus Trachys (Tracheini). The rRNA genes had important impact for the tree topology of Agrilinae. Compared to the tribes Tracheini and Agrilini, the tribe Coraebini is a younger group.

| S-EPMC9007928 | biostudies-literature

Complete mitochondrial genome of a leaf-mining beetle, Agonita chinensis Weise (Coleoptera: Chrysomelidae).

Project description:The complete circular mitochondrial genome of Agonita chinensis was 16,395 bp in length, which contained two ribosomal RNA genes, 22 transfer RNAs, 13 protein-coding genes (PCGs) and one non-coding AT-rich region with the length of 2001 bp. All of the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of tRNASer (TCT). Twelve PCGs were initiated by ATN codons, except that nad1 started with TTG. Only four PCGs used the typical stop codon 'TAA' and 'TGA', while nine PCGs terminated with incomplete stop codons (TA or T). Phylogenetic analysis based on 13 PCGs of Chrysomelidae mitogenomes showed that A. chinensis was closely related to Cassida viridis.

| S-EPMC7800852 | biostudies-literature

First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications.

Project description:Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.

| S-EPMC9860506 | biostudies-literature

Three Mitochondrial Genomes of Chrysochroinae (Coleoptera, Buprestidae) and Phylogenetic Analyses.

Project description:Three mitochondrial genomes of Chrysochroinae (Buprestidae) were sequenced and analyzed. The mitogenomes of the genera Catoxantha and Nipponobuprestis are first reportedand Chrysochroa opulenta is a first record for China. The complete mitogenomes of Catoxantha luodiana, Nipponobuprestis guangxiensis and Chrysochroa opulenta exhibit striking similarities in their lengths and composition. Specifically, their lengths are 15,594 bp, 15,775 bp and 15,587 bp, respectively. Each of these genomes encodes 37 typical mitochondrial genes. The overwhelming majority of protein-coding genes (PCGs) have the typical ATN (ATT, ATA, ATG or ATC) as the start codon and terminate with TAR (TAA or TAG) as the stop codon or an incomplete stop codon T-. Among the three mitogenomes, Leu2, Ser2 and Phe were the most frequently encoded amino acids. In the PCGs, the Ka/Ks ratio of cox1 is the lowest, whereas atp6 has the highest value. This suggests that cox1 can be used as a molecular barcode for species delimitation and phylogeny in Chrysochroinae. The phylogenetic results showed that C. luodiana and two Chrysochroa species formed a clade. Based on the topology of the phylogenetic tree, the genus Catoxantha should be reassigned as a subgenus of Chrysochroa.

| S-EPMC11506987 | biostudies-literature

Complete mitochondrial genome of the Loligo chinensis.

Project description:In this study, we determined the complete mitochondrial genome of Loligo chinensis. The genome was 17,353 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The overall base composition of L. chinensis is A 38.62%, C 19.40%, T32.37% and G 9.61%, with a highly A + T bias of 70.99%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. Here, we describe a phylogenetic analysis of 11 species Cephalopoda based on the complete mitochondrial genome; the result showed that the Loligo edulis is most closely related to L. chinensis. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Cephalopoda.

| S-EPMC7800812 | biostudies-literature

Complete mitochondrial genome of the Loligo japonica.

Project description:In this study, we determined the complete mitochondrial genome of Loligo japonica. The genome was 17,232 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The overall base composition of L. japonica is A 39.60%, C 18.22%, T33.38% and G 8.80%, with a highly A + T bias of 72.98%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. Here, we describe a phylogenetic analysis of 11 species Cephalopoda based on the complete mitochondrial genome, and the result showed that the Loligo Beka and Loligo uyii are most closely related to L. japonica. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Cephalopoda.

| S-EPMC7800932 | biostudies-literature