Characteristics of the complete mitochondrial genome of Suhpalacsalongialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

10.7287/peerj.preprints.27183v2 ◽

2018 ◽

Author(s):

Xin-Yan Gao ◽

Yin-Yin Cai ◽

Dan-Na Yu ◽

Kenneth B. Storey ◽

Jia-Yong Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Nucleotide Composition ◽

The Other ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Duplicated Genes ◽

Sister Clade ◽

Phylogenetic Implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsalongialata (Neuroptera, Ascalaphidae). The total length of the S.longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr(CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S.longialata mitogenome was as follows: A=41.0%, T=33.8%, C=15.5%, G=9.7%. Both BI and ML analyse strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

10.7287/peerj.preprints.27183 ◽

2018 ◽

Author(s):

Xin-Yan Gao ◽

Yin-Yin Cai ◽

Dan-Na Yu ◽

Kenneth B. Storey ◽

Jia-Yong Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Nucleotide Composition ◽

The Other ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Duplicated Genes ◽

Sister Clade ◽

Phylogenetic Implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsalongialata (Neuroptera, Ascalaphidae). The total length of the S.longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr(CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S.longialata mitogenome was as follows: A=41.0%, T=33.8%, C=15.5%, G=9.7%. Both BI and ML analyse strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

PeerJ ◽

10.7717/peerj.5914 ◽

2018 ◽

Vol 6 ◽

pp. e5914 ◽

Cited By ~ 4

Author(s):

Xin-Yan Gao ◽

Yin-Yin Cai ◽

Dan-Na Yu ◽

Kenneth B. Storey ◽

Jia-Yong Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Nucleotide Composition ◽

The Other ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Duplicated Genes ◽

Sister Clade ◽

Phylogenetic Implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae). The total length of the S. longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr (CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S. longialata mitogenome was as follows: A = 41.0%, T = 33.8%, C = 15.5%, G = 9.7%. Both Bayesian inference and ML analyses strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

The complete mitochondrial genome of the flat bug Aradacanthia heissi (Hemiptera: Aradidae)

Zootaxa ◽

10.11646/zootaxa.3238.1.2 ◽

2012 ◽

Vol 3238 (1) ◽

pp. 23 ◽

Cited By ~ 12

Author(s):

AIMIN SHI ◽

HU LI ◽

XIAOSHUAN BAI ◽

XUN DAI ◽

JIAN CHANG ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Gene Arrangement ◽

Entire Genome ◽

Protein Coding ◽

Simple Loop ◽

Secondary Structure Models ◽

Mt Genome

The 15528 bp long complete mitochondrial genome (mt-genome) of a flat bug, Aradacanthia heissi Bai, Zhang & Cai,was determined. The entire genome contains typical 37 genes with an A+T content of 74.7%. The gene arrangement dif-fers from that of Drosophila yakuba Burla which is considered the representative ground pattern for insect mt-genomes,as the results of inversion of tRNAIle - tRNAGln and tRNACys - tRNATrp . All protein-coding genes (PCGs) use standard initia-tion codons (methionine and isoleucine), except COI which starts with TTG. Three of the 13 PCGs harbor the incompletetermination codon. Meanwhile, opposite CG-skew tendency occurs on the nucleotide composition and codon usage andthis tendency is also reflected on the J-strand and N-strand of PCGs. All tRNAs can fold into classic clover-leaf structure,whereas the dihydrouridine (DHU) arm of tRNASer(AGN) forms a simple loop. Secondary structure models of the ribosomalRNA genes of A. heissi are predicted and similar to those proposed for other insects. The control region is located betweensrRNA and tRNAGln with 81.5% A+T content, which was the most A+T-rich region of the mt-genome and four 68 bp tan-dem repeat units were found in this region. Phylogenetic analyses of available species of Pentatomomorpha showed Ara-doidea and the Trichophora are sister groups that bolstered the mainstream hypothesis, and provide the evidence for the feasibility of mt-genome data to resolve relationships at the subfamily level in Aradidae.

Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

Genes ◽

10.3390/genes10080563 ◽

2019 ◽

Vol 10 (8) ◽

pp. 563 ◽

Cited By ~ 2

Author(s):

Hu Li

Keyword(s):

Mitochondrial Genome ◽

Stop Codon ◽

Complete Mitochondrial Genome ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Future Studies ◽

Protein Coding Genes ◽

Phylogenetic Implications ◽

Paraphyletic Group ◽

Complete Mitochondrial Genomes

In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.

Complete mitochondrial genome of Whitmania laevis (Annelida, Hirudinea) and comparative analyses within Whitmania mitochondrial genomes

Belgian Journal of Zoology ◽

10.26496/bjz.2015.52 ◽

2020 ◽

Vol 145 (2) ◽

Author(s):

Fei Ye ◽

Ting Liu ◽

Wenbo Zhu ◽

Ping You

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Close Relationship

The complete mitochondrial genome of Whitmania laevis is 14,442 bp in length and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The almost-complete mitochondrial genome of Whitmania acranulata, consisting of 13,494 bp, contains 35 genes including 13 PCGs, 20 tRNA genes, and two rRNA genes. COI phylogenetic analyses showed that the samples reported in GenBank and analysed as Hirudo nipponia KC667144, Hirudinaria manillensis KC688268 and Erpobdella octoculata KC688270 are not the named species and they should belong to Whitmania. We compared and analyzed the characteristics of nucleotide composition, codon usage, and secondary structures of 22 tRNAs and two rRNAs from Whitmania taxa. Moreover, we analyzed phylogenetic relationships of Annelida using maximum likelihood (ML) and Bayesian inference (BI) methods, based on 11 mitochondrial genes. Our results reveal that W. laevis has a close relationship with W. pigra.

The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae)

Psyche A Journal of Entomology ◽

10.1155/2021/6625462 ◽

2021 ◽

Vol 2021 ◽

pp. 1-8

Author(s):

Lidia Komondy ◽

Jose Huguet-Tapia ◽

Marina S. Ascunce ◽

Ericka E. Helmick ◽

Erica M. Goss ◽

...

Keyword(s):

Mitochondrial Genome ◽

Internal Control ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Economic Losses ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Protein Coding Genes ◽

Lethal Yellowing ◽

Primer Sets

Haplaxius crudus Van Duzee is a pest of various economically important palms due to its ability to transmit lethal yellowing, a fatal phytoplasma infection. It is also the putative vector of lethal bronzing in Florida, another lethal phytoplasma disease causing significant economic losses. To date, no mitochondrial genomes for species in the family Cixiidae are sequenced. In this study, the complete mitochondrial genome of H. crudus was sequenced, assembled, and annotated from PacBio Sequel II long sequencing reads using the University of Florida’s HiPerGator. The mitogenome of H. crudus is 15,848 bp long and encodes 37 mitochondrial genes (including 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs) in addition to a putative noncoding internal control region. The nucleotide composition of H. crudus is asymmetric with a bias toward A/T (44.8 %A, 13.4 %C, 8.5 %G, and 33.3 %T). Protein-coding genes (PCGs) possess the standard invertebrate mitochondrial start codons with few exceptions while the gene content and order of the H. crudus mitogenome is highly similar to most completely sequenced insect mitochondrial genomes. Phylogenetic analysis based on the entire mitogenome shows H. crudus resolving closely to Delphacidae, the accepted sister taxon of Cixiidae. These data provide a useful resource for developing novel primer sets that could aid in either phylogenetic studies or population genetic studies. As more full mitogenomes become available in the future for other planthopper species, more robust phylogenies can be constructed, giving more accurate perspectives on the evolutionary relationships within this fascinating and economically important group of insects.

The complete mitochondrial genome of Pentatoma rufipes (Hemiptera, Pentatomidae) and its phylogenetic implications

ZooKeys ◽

10.3897/zookeys.1042.62302 ◽

2021 ◽

Vol 1042 ◽

pp. 51-72

Author(s):

Ling Zhao ◽

Jiufeng Wei ◽

Wanqing Zhao ◽

Chao Chen ◽

Xiaoyun Gao ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Trees ◽

Complete Mitochondrial Genome ◽

Genome Structure ◽

Nucleotide Composition ◽

Genome Database ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenetic Implications ◽

Rna Genes

Pentatoma rufipes (Linnaeus, 1758) is an important agroforestry pest widely distributed in the Palaearctic region. In this study, we sequence and annotate the complete mitochondrial genome of P. rufipes and reconstruct the phylogenetic trees for Pentatomoidea using existing data for eight families published in the National Center for Biotechnology Information database. The mitogenome of P. rufipes is 15,887-bp-long, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region, with an A+T content of 77.7%. The genome structure, gene order, nucleotide composition, and codon usage of the mitogenome of P. rufipes were consistent with those of typical Hemiptera insects. Among the protein-coding genes of Pentatomoidea, the evolutionary rate of ATP8 was the fastest, and COX1 was found to be the most conservative gene in the superfamily. Substitution saturation assessment indicated that neither transition nor transversion substitutions were saturated in the analyzed datasets. Phylogenetic analysis using the Bayesian inference method showed that P. rufipes belonged to Pentatomidae. The node support values based on the dataset concatenated from protein-coding and RNA genes were the highest. Our results enrich the mitochondrial genome database of Pentatomoidea and provide a reference for further studies of phylogenetic systematics.

The Complete Mitochondrial Genome of Meloidogyne graminicola (Tylenchina): A Unique Gene Arrangement and Its Phylogenetic Implications

PLoS ONE ◽

10.1371/journal.pone.0098558 ◽

2014 ◽

Vol 9 (6) ◽

pp. e98558 ◽

Cited By ~ 11

Author(s):

Longhua Sun ◽

Kan Zhuo ◽

Borong Lin ◽

Honghong Wang ◽

Jinling Liao

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Meloidogyne Graminicola ◽

Unique Gene ◽

Phylogenetic Implications

Novel gene rearrangement in the mitochondrial genome of Siliqua minima (Bivalvia, Adapedonta) and phylogenetic implications for Imparidentia

PLoS ONE ◽

10.1371/journal.pone.0249446 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0249446

Author(s):

Jiantong Feng ◽

Yahong Guo ◽

Chengrui Yan ◽

Yingying Ye ◽

Xiaojun Yan ◽

...

Keyword(s):

Mitochondrial Genome ◽

Gene Rearrangement ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Protein Coding ◽

Sinonovacula Constricta ◽

Phylogenetic Implications ◽

The Family ◽

Phylogenetic Resolution ◽

Rna Genes

Siliqua minima (Gmelin, 1791) is an important economic shellfish species belonging to the family Pharidae. To date, the complete mitochondrial genome of only one species in this family (Sinonovacula constricta) has been sequenced. Research on the Pharidae family is very limited; to improve the evolution of this bivalve family, we sequenced the complete mitochondrial genome of S. minima by next-generation sequencing. The genome is 17,064 bp in length, consisting of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). From the rearrangement analysis of bivalves, we found that the gene sequences of bivalves greatly variable among species, and with closer genetic relationship, the more consistent of the gene arrangement is higher among the species. Moreover, according to the gene arrangement of seven species from Adapedonta, we found that gene rearrangement among families is particularly obvious, while the gene order within families is relatively conservative. The phylogenetic analysis between species of the superorder Imparidentia using 12 conserved PCGs. The S. minima mitogenome was provided and will improve the phylogenetic resolution of Pharidae species.