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

Guo, Qiuhong; Liu, Liyuan; Huang, Weidong; Sang, Wen; Chen, Xiaosheng; Wang, Xingmin

doi:10.1016/j.aspen.2022.101977

Cited by 6 publications

(6 citation statements)

References 45 publications

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“…The Ka/Ks ratios of all the 13 PCGs calculated by KaKs_Calculator v2.0 were below 1, which suggests the existence of purifying selection in the two species ( Figure 3 A). The results of Ka/Ks calculation were similar to a recent mitogenomic work [ 47 ], which used DnaSP for the calculation. The gene-wide BUSTED analysis based on the likelihood-ratio test found no evidence of episodic diversifying selection in the PCGs.…”

Section: Resultssupporting

confidence: 82%

Complete Mitochondrial Genomes and Phylogenetic Positions of Two Longicorn Beetles, Anoplophora glabripennis and Demonax pseudonotabilis (Coleoptera: Cerambycidae)

Liu²,

Wu³

et al. 2022

Genes

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Anoplophora glabripennis (Motschulsky, 1854) and Demonax pseudonotabilis Gressitt & Rondon, 1970 are two commonly found longicorn beetles from China. However, the lack of sufficient molecular data hinders the understanding of their evolution and phylogenetic relationships with other species of Cerambycidae. This study sequenced and assembled the complete mitochondrial genomes of the two species using the next-generation sequencing method. The mitogenomes of A. glabripennis and D. pseudonotabilis are 15,622 bp and 15,527 bp in length, respectively. The mitochondrial gene content and gene order of A. glabripennis and D. pseudonotabilis are highly conserved with other sequenced longicorn beetles. The calculation of nonsynonymous (Ka) and synonymous (Ks) substitution rates in PCGs indicated the existence of purifying selection in the two longicorn beetles. The phylogenetic analysis was conducted using the protein-coding gene sequences from available mitogenomes of Cerambycidae. The two species sequenced in this study are, respectively, grouped with their relatives from the same subfamily. The monophyly of Cerambycinae, Dorcasominae, Lamiinae, and Necydalinae was well-supported, whereas Lepturinae, Prioninae, and Spondylidinae were recovered as paraphyletic.

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Section: Resultssupporting

confidence: 82%

Complete Mitochondrial Genomes and Phylogenetic Positions of Two Longicorn Beetles, Anoplophora glabripennis and Demonax pseudonotabilis (Coleoptera: Cerambycidae)

Liu²,

Wu³

et al. 2022

Genes

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“…The size of each tRNA gene for these newly determined mitogenomes was hardly different, ranging from 57 to 72 bp (Supplementary Table 2). In all four mitogenomes of Scolytinae, 21 tRNAs displayed the classic clover-leaf secondary structure, whereas trnS1 lacks the dihydrouridine (DHU) arm and forms a simple loop, which was common in other metazoan mitogenomes (Guo et al, 2022a;Huang et al, 2023). The AT content of the tRNA genes was slightly higher than that of the PCGs, and the combined tRNA genes exhibited positive AT skew and negative GC skew (Supplementary Table 3).…”

Section: Protein-coding Genes and Codon Usagementioning

confidence: 99%

“…Compared to the individual mitochondrial genes, the complete mitogenome could provide not only more genetic information but also a series of evolutionary characters, such as RNA secondary structures, gene arrangements, and models of control of replication (San et al, 2006;Cameron, 2014). With the development of DNA sequencing technology, much more mitochondrial genomes of insect species have been sequenced (Guo et al, 2022a;Huang et al, 2023). However, available data on the mitogenomes of bark and ambrosia beetles remain limited.…”

Section: Introductionmentioning

confidence: 99%

Characterization, comparative analyses, and phylogenetic implications of mitochondrial genomes among bark and ambrosia beetles (Coleoptera: Curculionidae, Scolytinae)

et al. 2023

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Bark and ambrosia beetles of Scolytinae are well-known forest pests which can cause significant economic losses to trees and timber. Comparative analyses of structural characteristics of mitochondrial genomes (mitogenomes) and phylogenetic analyses could significantly improve our understanding of mitogenomic evolution and evolutionary history of this important group. Here, we have assembled new mitogenome data of four taxa (Euwallacea interjectus, E. fornicatus, E. similis, and Xylosandrus sp.) and presented a comparative analysis with available mitogenomes of Scolytinae. Phylogenetic analyses of Scolytinae were also conducted with different methods and datasets. The four mitogenomes are 15,419–16,265 bp in length and contain 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a control region, except for E. similis wherein the trnI is not detected. All PCGs initiate with either standard start codon of ATN or nonstandard GTG/TTG. TAA codon is used for termination more than TAG and incomplete T. The analysis of nonsynonymous/synonymous mutation ratio (Ka/Ks) of PCGs suggests the highest and lowest evolutionary rates are within nad4 and cox1, respectively. The heterogeneity analyses of different mitogenomic datasets show excluding the third-codon positions from the datasets largely reduce their heterogeneity. Our phylogenetic analyses derived from mitogenome data provide new evidence toward the revision of the distinguishing characteristics of related genera in this subfamily and highly supported most of nodes at deeper and shallow level. The present study highlights the utility of mitogenome data for resolving the phylogenetic framework of bark and ambrosia beetles, although more taxa sampling is needed to elucidate the complicated relationships of Scolytinae.

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“…The 23 genes, including 9 PCGs and 14 tRNAs, are located on the major strand (J-strand), and the other 14 genes (4 PCGs, 8 tRNAs and 2 rRNAs) are located on the minor strand (N-strand). The gene arrangement and orientation are similar to the typical mitogenomes of Coleoptera (Guo et al, 2022(Guo et al, , 2023. The gene overlapping regions between atp8 and atp6, and nad4 and nad4l, a 7 bp motif of "ATGATAA" and "TTATCAT" were determined in all four newly sequenced mitogenomes.…”

Section: Mitogenome Organization and Base Compositionmentioning

confidence: 59%

“…Mitochondrial genome (mitogenome) is a broadly applied organelle genome in exploring the evolution, phylogeny, and biogeography of insects (Du et al, 2019;Guo et al, 2022Guo et al, , 2023Huang et al, 2023), which contains complete genetic information from molecular sequence to gene structure. The typical mitogenome of insect is a 14-20 kb circular molecule, containing 37 genes (13 protein coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and a control region on a single chromosome (Cameron, 2014).…”

Section: Introductionmentioning

confidence: 99%

Comparative and phylogenetic analyses of mitochondrial genomes in Elateridae (Coleoptera: Elateroidea)

Huang,

Zhu,

Wen

et al. 2023

Arch Insect Biochem Physiol

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The click‐beetles (Elateridae) are a species‐rich beetle family that is easily recognizable. They are distributed in all zoogeographical regions with over 11,000 species. Comparative studies of the structural characteristics of mitochondrial genomes (mitogenomes), as well as phylogenetic relationships of click‐beetles, can improve our understanding of mitogenomic evolution. In this study, we determined four mitogenomes from Elateridae by next‐generation sequencing. The four mitogenomes were 16,005 to 16,930 bp in length with 37 typical genes and a control region (A + T‐rich region). Combined with previously reported elaterid mitogenomes, all PCGs initiate with either the standard start codon of ATN or TTG. According to the nonsynonymous/synonymous mutation ratio (Ka/Ks) of all PCGs, the highest and the lowest evolutionary rates were found for atp8 and cox1, respectively. Among the control regions of the four mitogenomes, several different patterns and numbers of tandem repeats were identified, which was the primary cause of the length variation in control regions. Phylogenetic analyses were conducted based on 13 protein‐coding genes and two ribosomal RNA genes from 33 species of Elateridae and two outgroups. The Bayesian inference and maximum likelihood trees had an identical topological structure. The monophyly of Cardiophorinae, Agrypninae and Elaterinae was recovered with high support in all topologies, and the Tetralobinae was placed as the earliest branch in the Elateridae. Expanding the availability of mitogenomic and genomic data from a broader range of click‐beetles could provide more clarity on the disputed relationships among subfamilies within Elateridae.

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

Cited by 6 publications

References 45 publications

Complete Mitochondrial Genomes and Phylogenetic Positions of Two Longicorn Beetles, Anoplophora glabripennis and Demonax pseudonotabilis (Coleoptera: Cerambycidae)

Complete Mitochondrial Genomes and Phylogenetic Positions of Two Longicorn Beetles, Anoplophora glabripennis and Demonax pseudonotabilis (Coleoptera: Cerambycidae)

Characterization, comparative analyses, and phylogenetic implications of mitochondrial genomes among bark and ambrosia beetles (Coleoptera: Curculionidae, Scolytinae)

Comparative and phylogenetic analyses of mitochondrial genomes in Elateridae (Coleoptera: Elateroidea)

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