The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships

Zhang, Shengdi; Sekerka, Lukáš; Liao, Chengqing; Long, Chengpeng; Xu, Jiasheng; Dai, Xiaohua; Guo, Qianjin

doi:10.3390/insects12111005

Cited by 3 publications

(4 citation statements)

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“…This phenomenon suggested that different selection pressures have been exerted on various functional genes in the mitochondria of Scolytinae during the evolutionary process. Comparable patterns of mitochondrial gene evolution have also been reported in several insect clades, including Psilidae (Diptera; Zhou and Yang, 2022), Cicadellidae (Hemiptera;Xu et al, 2020), Tortricidae (Lepidoptera; Huang et al, 2023), and Chrysomelidae (Coleoptera; Zhang et al, 2021), this suggests that the evolutionary pattern of mitochondrial genes may be relatively conserved among insects.…”

Section: Evolutionary Rate Nucleotide Diversity and Heterogeneity Amo...mentioning

confidence: 71%

“…The largest noncoding region in these mitogenomes of Scolytinae beetles as well as most insects is usually located between 12S rRNA and trnI. It might be identified as the putative control region according to the conserved region aligned with other Coleoptera mitogenomes (Zhang et al, 2021). The length of the control regions of the four mitogenomes vary widely, ranging from 681 bp in E. similis to 1,004 bp in Xylosandrus sp.…”

Section: Protein-coding Genes and Codon Usagementioning

confidence: 99%

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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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Section: Evolutionary Rate Nucleotide Diversity and Heterogeneity Amo...mentioning

confidence: 71%

Section: Protein-coding Genes and Codon Usagementioning

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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“…Intergenic spacers (IGSs) are non-coding regions typically found in metazoan mitochondrial genomes [14]. For example, in some species of beetle, known mitogenomes contain the IGS commonly found at the junction of the trnS2 (UCN) and nad1 genes [8,[15][16][17][18][19][20]. The IGSs have also been found between different genes in the mitogenomes of other beetles, such as between trnW and trnC [8], nad2, and trnW [21], trnI and trnQ [4,22,23], and so on.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Implication of Large Intergenic Spacers: Insights from a Mitogenomic Comparison of Prosopocoilus Stag Beetles (Coleoptera: Lucanidae)

Zhou

Wan

2022

Animals

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To explore the characteristics of mitogenomes and discuss the phylogenetic relationships within the genus Prosopocoilus, the mitogenomes of two species (P. castaneus and P. laterotarsus) were newly sequenced and comparatively analyzed. The arrangement of the mitogenome in these two lucanid beetles was the same as that in the inferred ancestral insect, and the nucleotide composition was highly biased towards A + T as in other lucanids. The evolutionary rates of 13 protein-coding genes (PCGs) suggested that their evolution was based on purifying selection. Notably, we found evidence of the presence of a large IGS between trnI and trnQ genes, whose length varied from 375 bp (in P. castaneus) to 158 bp (in P. laterotarsus). Within the large IGS region, a short sequence (TAAAA) was found to be unique among these two species, providing insights into phylogenomic reconstruction. Phylogenetic analyses were performed using the maximum likelihood (IQ-TREE) and Bayesian (PhyloBayes) methods based on 13 protein-coding genes (PCGs) in nucleotides and amino acids (AA) from published mitogenomes (n = 29). The genus Prosopocoilus was found to constitute a distinct clade with high nodal support. Overall, our findings suggested that analysis of the characteristics of the large IGS (presence or absence, size, and location) in mitogenomes of the genus Prosopocoilus may be informative for the phylogenetic and taxonomic analyses and for evaluation of the genus Prosopocoilus, despite the dense sampling materials needed.

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“…One of the most common DNA barcoding genes used in animals is the mitochondrial cytochrome c oxidase subunit I (COI, cox1 ) (Hebert et al 2003a, b, Ratnasingham & Hebert 2007). The use of COI gene sequences has been widely employed as ‘barcodes’ for multiple invertebrate taxa (Du et al 2021, Meregalli et al 2021, Young et al 2021, Zhang et al 2021, Macher et al 2021) and previous studies have proved the high effectiveness of COI sequences as an identification tool for a great number of species of beetles (Raupach et al 2010, Bergsten et al 2012, Pentinsaari et al 2014b, Zhang et al 2019). The Barcode of Life Data System (BOLD) is an online platform that assemblage molecular, morphological, and distributional data and storages over 11 million records of COI sequences for all eukaryotic life (https://www.boldsystems.org/) (Ratnasingham & Hebert 2007).…”

Section: Introductionmentioning

confidence: 99%

Different Perspectives on the Phylogeny of Mordellidae (Coleoptera) Provided by Two Regions of the mtDNA COI Gene

Sanz-laParra,

García-París,

López-Estrada

2023

Annales Zoologici

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The cytochrome c oxidase subunit I (COI) gene has been used broadly as a DNA barcoding region or and relevant molecular marker for phylogenetic reconstruction. The exact region that has been standardized as a universal barcode is the one amplified by Folmer's primers HCO-LCO. Nevertheless, many other primers have been developed for the amplification of the COI gene, among them the Jerry-Pat primers. This paper aims to analyze the performance of different regions of the COI, in particular those amplified by Folmer's and Jerry-Pat primers, on different taxonomic levels by using specimens from a complex and homogeneous beetle family, Mordellidae Latreille, 1802. To achieve this goal, we used two different datasets: Jerry-Pat matrix included 48 sequences from specimens sampled in the field and 19 sequences from GenBank, whereas Folmer's matrix included 91 sequences from BOLD; representing 24 and 85 species respectively. Our results show different properties of both COI regions regarding GC content (3.7% lower in Jerry-Pat fragment), sequence length, interspecific divergence, evolutionary models, and saturation analyses. We also found that the two studied regions of the COI perform differently, showing notable differences in the topology of the reconstructed trees. Finally, a discussion of the pros and cons of each region is provided. This is a first glance at the molecular data of Mordellidae, where we provided a general picture of the evolutionary history of the family and included new sequences for Mediimorda Méquignon, 1946 and Stenalia Mulsant, 1856.

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The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships

Cited by 3 publications

References 50 publications

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

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

Phylogenetic Implication of Large Intergenic Spacers: Insights from a Mitogenomic Comparison of Prosopocoilus Stag Beetles (Coleoptera: Lucanidae)

Different Perspectives on the Phylogeny of Mordellidae (Coleoptera) Provided by Two Regions of the mtDNA COI Gene

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