The complete mitogenomes of Calameuta filiformis (Eversmann, 1847) and Calameuta idolon (Rossi, 1794) (Hymenoptera: Cephidae): The remarkable features of the elongated A+T rich region in Cephini

Korkmaz, Ertan Mahir; Budak, Mahir; Ördek, Merve Nur; Basibuyuk, Hasan H.

doi:10.1016/j.gene.2015.10.050

Cited by 24 publications

(19 citation statements)

References 58 publications

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“…The presence of tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes, and its underlying mechanisms are unclear. These tRNA-like structures may have signaling functions in the process of transcription [32]. When compared with the available 11 CRs of the other stoneflies, four conserved sequence blocks (CSBs) were identified in N. nankinensis (Figure 5).…”

Section: Resultsmentioning

confidence: 99%

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications

Chen

2017

IJMS

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The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer (AGN), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae.

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Section: Resultsmentioning

confidence: 99%

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications

Chen

2017

IJMS

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“…Four complete and three nearly complete mitogenomes of Cephinae have been reported to date (Dowton et al ., ; Korkmaz et al ., , ). Here, the mitogenome characteristics of Cephinae were summarized by combining five new nearly complete mitogenomes representing two tribes: Hartigiini ( J. compressus , H. linearis and S. parreyssi ) and Pachycephini ( P. smyrnensis and P. cruentatus ).…”

Section: Discussionmentioning

confidence: 99%

“…Stein, P. cruentatus (Eversmann), Syrista parreyssi (Spinola) and Characopygus scythicus Dovnar‐Zapolskij. A mitogenome dataset was produced representing three tribes and eight genera of Cephinae by adding seven previously sequenced species (Dowton et al ., ; Korkmaz et al ., , , ). A total of 13 mitogenomes was investigated to explore mitogenome evolution in Cephinae.…”

Section: Introductionmentioning

confidence: 99%

Mitogenome organization and evolutionary history of the subfamily Cephinae (Hymenoptera: Cephidae)

Korkmaz

Doğan

Durel

et al. 2018

Systematic Entomology

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Cephinae represents one of the exclusively endophytophagous sawfly lineages with diverse host plant utilizations, in which most species have great economic importance. However, the evolutionary history of the subfamily has not been thoroughly investigated to date. Here, we characterized the mitogenomes of six species representing five genera of Cephinae. Rearrangements of the tRNA genes were found to be notably common. The rearrangements involve the IQM and TP gene clusters, and the former is a synapomorphy of the subfamily. In spite of the seldom occurrence of gene duplication in arthropods, three tRNA duplication events not known elsewhere in Symphyta were detected in Cephinae. The phylogeny of Cephinae was reconstructed using different datasets generated from mitochondrial genes and two nuclear fragments, EF‐1α and ITS2, under Bayesian inference (BI) and maximum likelihood (ML) approaches by adding the data of previously reported seven species. Five different tree topologies were recovered in which the tree produced from the nP12RNAexc4genes dataset under the BI and ML approaches was highly resolved with high support values. The phylogeny did not support the traditional tribal concept but it suggested two strongly supported clades. Diversification of the subfamily appears to correspond to a great extent to host plant availability and colonization in the Late Cretaceous, Early Eocene and Oligocene, suggesting speciation via host shift. The nonsynonymous substitutions and the most radical changes observed in mitochondrial protein‐coding genes were proposed as evidence for speciation driven by divergent adaptive selection.

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“…Mitochondrial markers are currently one of the most popular molecular markers, particularly in studies of molecular evolution, species identification, and genetic diversity (Yu et al, 2012;Sahoo et al, 2015;Korkmaz et al, 2016). The mitochondrial genome is usually a closed circular molecule, and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus)

Zhu

et al. 2016

Genet. Mol. Res.

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ABSTRACT. In this study, we determined the whole mitochondrial genome profile of the three-spot swimming crab (Portunus sanguinolentus) and elucidated phylogenetic relationships between representative species in the order Decapoda. The mitochondrial genome was 16,024 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Of the 37 genes, 23 were encoded by the heavy strand while 14 were encoded by the light strand. Four types of start codons were identified; ATG initiated nine genes, ATT initiated two genes, and ATC and GTG each started one gene. Nine protein-coding genes ended with a complete TAA or TAG stop codon, and four genes ended with an incomplete T or TA codon. Fourteen non-coding regions were found, which ranged from 1 to 34 bp in length. Nine overlaps were observed, with lengths between 1 and 7 bp. Phylogenetic analysis suggested that P. sanguinolentus is genetically closest to P. trituberculatus and P. pelagicus. Charybdis feriata, C. japonica, and Thalamita crenata formed a single cluster, and were close to the genera Callinectes and Portunus. Therefore, the genera Charybdis and Thalamita should be classified into the subfamily Portuninae.

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The complete mitogenomes of Calameuta filiformis (Eversmann, 1847) and Calameuta idolon (Rossi, 1794) (Hymenoptera: Cephidae): The remarkable features of the elongated A+T rich region in Cephini

Cited by 24 publications

References 58 publications

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications

First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications

Mitogenome organization and evolutionary history of the subfamily Cephinae (Hymenoptera: Cephidae)

Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus)

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