The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications

Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobio elongatus (Yao & Yang, 1977). The mitogenome of M. elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M. elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNASer(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M. elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

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The complete mitochondrial genome of Zicrona caerulea (Linnaeus) (Hemiptera: Pentatomidae: Asopinae) and its phylogenetic implications

Zootaxa ◽

10.11646/zootaxa.4747.3.8 ◽

2020 ◽

Vol 4747 (3) ◽

pp. 547-561

Author(s):

QING ZHAO ◽

GERASIMOS CASSIS ◽

LING ZHAO ◽

YIFAN HE ◽

HUFANG ZHANG ◽

...

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Trna Genes ◽

Stink Bug ◽

Protein Coding ◽

Simple Loop ◽

Phylogenetic Implications ◽

Maximum Likelihood Methods

Zicrona caerulea (Linnaeus, 1758) is a cosmopolitan stink bug species, which belongs to the predatory subfamily Asopinae. In this study, the complete mitochondrial genome of Zicrona caerulea from Shanxi, China was sequenced for the first time, using next generation sequencing. The mitogenome was found to be 15,479 bp in length. It contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region. This research revealed an overall A+T content of 77.14%. All tRNA genes had a clover-leaf structure except for trnS1, which lacks a dihydrouridine (DHU) arm; and for trnV, the DHU arm forms a simple loop. The lengths of rrnS and rrnL were 797 bp and 1,285 bp, respectively. Because of a shortage in tandem repeats, the A+T-rich region was 644 bp in length. Phylogenetic relationships based on these mitogenomes, using Bayesian inference and Maximum likelihood methods, showed that Zicrona caerulea belongs to Asopinae. The monophyly of families of the Pentatomoidea is supported, albeit limited taxon sampling.

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The First Complete Mitochondrial Genome of the Flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the Phylogenetic Relationships within Scorpaeniformes Based on Whole Mitogenomes

Genes ◽

10.3390/genes10070533 ◽

2019 ◽

Vol 10 (7) ◽

pp. 533

Author(s):

Lei Cui ◽

Rongbo Cao ◽

Yuelei Dong ◽

Xingchen Gao ◽

Jingyi Cen ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Tandem Repeats ◽

Complete Mitochondrial Genome ◽

Trna Genes ◽

Protein Coding ◽

Conserved Sequence ◽

Complete Mitogenome ◽

First Time ◽

Rna Genes ◽

Complete Mitochondrial Genomes

Complete mitochondrial genomes (mitogenomes) are important molecular markers for understanding the phylogenetics of various species. Although recent studies on the mitogenomes of the Scorpaeniformes species have been greatly advanced, information regarding molecular studies and the taxonomic localization of Platycephalidae is still sparse. To further analyze the phylogeny of Platycephalidae, we sequenced the complete mitogenome of Cociella crocodilus of the Platycephalidae family within Scorpaeniformes for the first time. The mitogenome was 17,314 bp in length, contained two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two typical noncoding control regions (the control region (CR) and origin of the light strand (OL)). All PCGs used standard initiation codons ATG, apart from cox1. The majority of the tRNA genes could be folded into cloverleaf secondary structures, whereas the secondary structure of tRNASer (AGN) lacked a dihydrouridine (DHU) stem. The CR contained several conserved sequence blocks (CSBs) and eight tandem repeats. In addition, the phylogenetic relationship based on the concatenated nucleotides sequences of 13 PCGs indicated that the Platycephalidae species are relatively basal in the phylogenetic relationships of Scorpaeniformes. Our results may not only advance the origin and the evolution of Scorpaeniformes, but also provide information for the genetic evolution and taxonomy of the teleostean species.

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Characterization of the Complete Mitochondrial Genome of Drabescus ineffectus and Roxasellana stellata (Hemiptera: Cicadellidae: Deltocephalinae: Drabescini) and Their Phylogenetic Implications

Insects ◽

10.3390/insects11080534 ◽

2020 ◽

Vol 11 (8) ◽

pp. 534 ◽

Cited By ~ 1

Author(s):

Deliang Xu ◽

Tinghao Yu ◽

Yalin Zhang

Keyword(s):

Mitochondrial Genome ◽

Stop Codon ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Strong Support ◽

Start Codon ◽

Protein Coding ◽

Simple Loop ◽

Repeat Units ◽

Phylogenetic Implications

To explore the mitogenome characteristics and shed light on the phylogenetic relationships and molecular evolution of Drabescini species, we sequenced and analyzed the complete mitochondrial genome of two species including Drabescus ineffectus and Roxasellana stellata. The complete mitogenomes of D. ineffectus and R. stellata are circular, closed and double-stranded molecules with a total length of 15744 bp and 15361 bp, respectively. These two newly sequenced mitogenomes contain the typical 37 genes. Most protein-coding genes (PCGs) began with the start codon ATN and terminated with the terminal codon TAA or TAG, with an exception of a special initiation codon of ND5, which started with TTG, and an incomplete stop codon T-- was found in the Cytb, COX2, ND1 and ND4. All tRNAs could be folded into the canonical cloverleaf secondary structure except for the trnS1, which lacks the DHU arm and is replaced by a simple loop. The multiple tandem repeat units were found in A + T-control region. The sliding window, Ka/Ks and genetic distance analyses indicated that the ATP8 presents a high variability and fast evolutionary rate compared to other PCGs. Phylogenetic analyses based on three different datasets (PCG123, PCG12R and AA) using both Bayesian inference (BI) and maximum likelihood (ML) methods showed strong support for the monophyly of Drabescini.

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The complete mitochondrial genome of a tessaratomid bug, Eusthenes cupreus (Hemiptera: Heteroptera: Pentatomomorpha: Tessaratomidae)

Zootaxa ◽

10.11646/zootaxa.3620.2.4 ◽

2013 ◽

Vol 3620 (2) ◽

pp. 260-272 ◽

Cited By ~ 8

Author(s):

WEN SONG ◽

HU LI ◽

FAN SONG ◽

LI LIU ◽

PEI WANG ◽

...

Keyword(s):

Mitochondrial Genome ◽

Control Region ◽

Complete Mitochondrial Genome ◽

Repetitive Sequences ◽

Rrna Genes ◽

Gene Arrangement ◽

Trna Genes ◽

Protein Coding ◽

Simple Loop ◽

Complete Mitogenome

The 16, 299 bp long mitochondrial genome (mitogenome) of a tessaratomid bug, Eusthenes cupreus (Westwood), is reported and analyzed. The mitogenome represents the first sequenced complete mitogenome of the heteropteran family Tessaratomidae. The mitogenome of E. cuopreus is a typical circular DNA molecule with a total AT content of 74.1%, and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The gene arrangement is identical with the most common type in insects. Most PCGs start with the typical ATN codon, except that the initiation codon for COI is TTG. All tRNAs possess the typical clover-leaf structure, except tRNASer (AGN), in which the dihydrouridine (DHU) arm forms a simple loop. Six domains with 45 helices and three domains with 27 helices are predicted in the secondary structures of rrnL and rrnS, respectively. The control region is located between rrnS and tRNAIle, including some short microsatellite repeat sequences. In addition, three different repetitive sequences are found in the control region and the tRNAIle-tRNAGln-tRNAMet-ND2 gene cluster. One of the unusual features of this mitogenome is the presence of one tRNAGln-like sequence in the control region. This extra tRNAGln-like sequence is 73 bp long, and the anticodon arm is identical to that of the regular tRNAGln.

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Complete Mitogenomes of Euploea mulciber (Nymphalidae: Danainae) and Libythea celtis (Nymphalidae: Libytheinae) and Their Phylogenetic Implications

ISRN Genomics ◽

10.1155/2013/491636 ◽

2013 ◽

Vol 2013 ◽

pp. 1-14 ◽

Cited By ~ 26

Author(s):

Jiasheng Hao ◽

Minǵe Sun ◽

Qinghui Shi ◽

Xiaoyan Sun ◽

Lili Shao ◽

...

Keyword(s):

Complete Mitochondrial Genome ◽

Coi Gene ◽

Trna Genes ◽

Butterfly Species ◽

Genome Sequences ◽

Protein Coding ◽

Simple Loop ◽

Protein Coding Genes ◽

Lepidopteran Species ◽

Phylogenetic Implications

The complete mitochondrial genome sequences of the two butterfly species Euploea mulciber (Lepidoptera: Nymphalidae: Danainae) and Libythea celtis (Lepidoptera: Nymphalidae: Libytheinae) were determined in this study, comprising 15,166 bp and 15,164 bp, respectively. The orientation and the gene order of the two mitogenomes are identical to those of most of the other lepidopteran species. All protein-coding genes of Euploea mulciber and Libythea celtis mitogenomes start with a typical ATN codon with the exception of COI gene which uses CGA as its initial codon. All tRNA genes possess the typical cloverleaf secondary structure except for tRNASer (AGN), which has a simple loop with the absence of the DHU stem. There are short microsatellite-like repeat regions, but no conspicuous macrorepeats scattered throughout the A + T-rich regions. Phylogenetic analysis among the available butterfly species suggests that Libythea celtis (Libytheinae) is closely related to Calinaga davidis (Calinaginae), indicating that the subfamily Libytheinae may not represent a basal lineage of the Nymphalidae as previously suggested, and that Euploea mulciber stands at the base of the nymphalid tree as a sister to all other nymphalids.

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Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications

Genes ◽

10.3390/genes10120992 ◽

2019 ◽

Vol 10 (12) ◽

pp. 992

Author(s):

Lifang Xiao ◽

Shengdi Zhang ◽

Chengpeng Long ◽

Qingyun Guo ◽

Jiasheng Xu ◽

...

Keyword(s):

Tandem Repeats ◽

Synonymous Codon ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Common Finding ◽

Trna Genes ◽

Rich Region ◽

Stop Codons ◽

Phylogenetic Implications ◽

Complete Mitogenome

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and −0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.

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The First Conserved Mitochondrial Genome of Polygraphus Poligraphus (Coleoptera: Curculionidae) and Its Phylogenetic Implications

10.21203/rs.3.rs-923616/v1 ◽

2021 ◽

Author(s):

Xianmei Song ◽

Yuchen Zhao ◽

Peng Zhao ◽

Yinxiang Ma ◽

Ming Bai ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Trees ◽

Molecular Taxonomy ◽

Start Codon ◽

Trna Genes ◽

Data Set ◽

Protein Coding ◽

Phylogenetic Implications ◽

Picea Asperata ◽

Rna Genes

Abstract Background: Polygraphus poligraphus L., the four-eyed spruce bark beetle, belongs to the Curculionidae (Coleoptera), which mainly harms Picea asperata Mast and Pinus armandii Franch tree trunks. So far, there is no mitochondrial genome reported for P. poligraphus.Results: In this study, we sequenced and annotated the nearly complete mitogenome of P. poligraphus for the first time and predicted the secondary structures of its tRNAs. The results showed that the mitogenome of P. poligraphus was 15,302 bp (partial genome) in length with A + T content of 69.65% due to large-scale duplication. The nearly complete mitochondrial genome of P. Poligraphus contained a set of 36 genes typical of the insect mitogenome, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 21 transfer RNA genes (tRNAs) but lacked tRNA-Ile, as for the typical insect mitogenome. The results of nucleotide skew statistics showed that the AT-skews and GC-skew of P. poligraphus were positive and negative, respectively, which were similar to other Scolytinae insects. All PCGs were initiated with the standard start codon ATN. All tRNA genes had the typical cloverleaf structure, except for the trnS1, which lacked a dihydroxyuridine (DHU) arm. Furthermore, we reconstructed phylogenetic trees of P. poligraphus based on the data set of the mitogenome’s protein-coding gene sequences using the Bayesian inference (BI) method. Phylogenetic analysis indicated that the P. poligraphus mitogenome clustered with Gnathotrichus materiarius and Pityophthorus pubescens mitogenomes in a monophyletic manner. The phylogeny of these three genera of Scolytinae is presented as Polygraphus + (Gnathotrichus + Pityophthorus). Conclusions: The results presented herein will provide a reference for further molecular taxonomy, evolution and phylogenetic research of P. poligraphus. However, additional mitogenome samples are still needed to more satisfactorily resolve the phylogeny of the Scolytinae.

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The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

Scientific Reports ◽

10.1038/s41598-019-57065-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Vikas Kumar ◽

Kaomud Tyagi ◽

Rajasree Chakraborty ◽

Priya Prasad ◽

Shantanu Kundu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Start Codon ◽

Gene Arrangement ◽

Sister Relationship ◽

Protein Coding ◽

Relationship Of ◽

Rna Genes ◽

Boundary Mapping ◽

Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

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Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽

10.3390/genes12081185 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1185

Author(s):

Wenqian Wang ◽

Huan Zhang ◽

Jérôme Constant ◽

Charles R. Bartlett ◽

Daozheng Qin

Keyword(s):

Control Region ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Start Codon ◽

Rrna Genes ◽

Rich Region ◽

Protein Coding ◽

Phylogenetic Implications ◽

Rna Genes ◽

Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

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The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae

Zootaxa ◽

10.11646/zootaxa.4363.4.3 ◽

2017 ◽

Vol 4363 (4) ◽

pp. 506

Author(s):

HUAXUAN LIU ◽

LIYUN YAN ◽

GUOFANG JIANG

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Ribosomal Rna ◽

Complete Mitochondrial Genome ◽

Taxonomic Status ◽

Polymerase Chain Reaction Method ◽

Ribosomal Rna Genes ◽

Start Codon ◽

Trna Genes ◽

Rna Genes

In this study, we reported the complete mitochondrial genome (mitogenome) of Sinopodisma pieli by polymerase chain reaction method for the first time, the type species of the genus Sinopodisma. Its mitogenome was a circular DNA molecule of 15,625 bp in length, with 76.0% A+T, and contained 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes and one A+T control region. The overall base composition of the S. pieli mitogenome was 42.8% for A, 33.2% for T, 13.5% for C, and 10.5% for G, respectively. All 13 mitochondrial PCGs shared the start codon ATN. Twelve of the PCGs ended with termination codon TAA and TAG, while cytochrome coxidase subunit 1 (COI) utilized an incomplete T as terminator codon. All tRNA genes could be folded into the typical cloverleaf secondary structure, except trnS(AGN) lacking of dihydrouridine arm. The sizes of the large and small ribosomal RNA genes were 1379 bp and 794 bp, respectively. The A+T rich region was 798 bp in length and contained 88.5% AT content. A phylogenetic analysis based on 13 PCGs by using Bayesian inference (BI) and maximum likelihood (ML) revealed that Sinopodisma is not monophyletic group. We think that the name and taxonomic status of S. tsinlingensis are right, and it should not be moved into the genus Pedopodisma. These data will provide important information for a better understanding of the population genetics and species identification for Sinopodisma.

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