scholarly journals The land flatworm Amaga expatria (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10098
Author(s):  
Jean-Lou Justine ◽  
Delphine Gey ◽  
Jessica Thévenot ◽  
Romain Gastineau ◽  
Hugh D. Jones
Keyword(s):  
Citizen Science ◽  
Reproductive Organs ◽  
Start Codon ◽  
Rrna Genes ◽  
Coi Gene ◽  
Trna Genes ◽  
Protein Coding ◽  
Molecular Barcoding ◽  
Complete Mitogenome ◽  
The Caribbean

Background The land flatworm Amaga expatria Jones & Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since. Methods On the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of A. expatria and some information on its prey from contaminating DNA. Results We add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was Obama nungara, a species from South America. An analysis of contaminating DNA in the digestive system suggests that A. expatria preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean.

Comparative analysis the variability of a complete mitochondrial genome of polledness intersexual goat (PIS- -) from China

2015 ◽  
Author(s):  
GuangXin E ◽  
Yong-Fu Huang ◽  
Yong-Ju Zhao ◽  
Ri-Su Na ◽  
Zhong-Quan Zhao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Reproductive Function ◽  
Reproductive Organs ◽  
Rrna Genes ◽  
Capra Hircus ◽  
Trna Genes ◽  
Protein Coding ◽  
Indigenous Breed ◽  
Complete Mitogenome

The polledness intersexual goat (PIS- -) (Capra hircus), deformed individuals, could have malformed reproductive organs and loss of reproductive function. Here, we first determined the complete mitochondrial genome of Chinese native polledness intersexual goat (PIS- -) is 16,640 nt in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region. As in other mammals and intrastrains, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.5%, T: 27.3%, C: 26.1% and G: 13.1%. The complete mitogenome of the Chinese indigenous breed of goat could provide a basic data for further understanding the contribution of mitochondria in the sex-developmental mechanism, tissue and organ cell deformity of polledness intersexual goat via genomic compare.

Complete mitogenome of Psorodonotus venosus (Orthoptera, Tettigoniidae; Tettigoniinae): Short intergenic spacers shorten the total genome

Zootaxa ◽  
2019 ◽  
Vol 4614 (3) ◽  
pp. 498
Author(s):  
UĞUR KARŞI ◽  
BATTAL ÇIPLAK
Keyword(s):  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Data Bases ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Total Length ◽  
Evolutionary Studies ◽  
Complete Mitogenome ◽  
Generation Sequencing

Mitogenomes are popular sources of data in evolutionary studies. By development of next generation sequencing the number of total mitogenome in data bases rapidly increased. However, there is still a limited number of total mitogenome known from species of Tettigoniinae. This paper aims to describe the total mitogenome of Psorodonotus venosus (Orthoptera, Tettigoniidae; Tettigoniinae) obtained by NGS reads. The total mitogenome is 15836-15845 bp and consists of 13 protein coding genes (PCG), 22 tRNA genes, two rRNA genes and an AT rich control region as in other metazozans. The mitogenome is AT skewed with 69.5% AT percentage. The genes are ordered as in pancrustacean. Total length of PCGs is 11229 bp, the start codon for all fits ATN pattern and stop codons are incomplete T-- / TA- and rarely complete TAA. Total length of 22 tRNA genes is 1447 bp and their anticodons are identical to other members of Tettigonioidea. The mitogenome contains 12 overlapping regions constituting 41 bp in total. Of these 12 overlapping regions those between trnW-trnC, atp6-atp8, nad4-nad4L, nad6 –cytb and atp6-cox3 gene pairs seem to be conserved. The total length of seven noncoding intergenic spacers is 46 bp. We concluded that P. venosus is one of the species with short mitogenome amongst Tettigonioidea because of limited number and length of noncoding intergenic spacers. 

scholarly journals The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242541
Author(s):  
Lvpei Du ◽  
Shanya Cai ◽  
Jun Liu ◽  
Ruoyu Liu ◽  
Haibin Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Cold Seep ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
High Support

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

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

ZooKeys ◽  
2021 ◽  
Vol 1061 ◽  
pp. 57-73
Author(s):  
Renyi Zhang ◽  
Qian Tang ◽  
Lei Deng
Keyword(s):  
Complete Mitochondrial Genome ◽  
Genetic Material ◽  
Start Codon ◽  
Trna Genes ◽  
Protein Coding ◽  
Simple Loop ◽  
Stop Codons ◽  
Phylogenetic Implications ◽  
Complete Mitogenome ◽  
Rna Genes

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.

scholarly journals Mitogenomes of nine Asian skipper genera and their phylogenetic position (Lepidoptera: Hesperiidae: Pyrginae)

2021 ◽  
Author(s):  
Jintian Xiao ◽  
Jiaqi Liu ◽  
Lu yao Ma ◽  
Hideyuki Chiba ◽  
Xiangyu Hao ◽  
...  
Keyword(s):  
Stop Codon ◽  
Phylogenetic Signal ◽  
Start Codon ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Protein Coding ◽  
The Status ◽  
The One ◽  
Complete Mitochondrial Genomes

In this study, complete mitochondrial genomes of nine species representing three tribes in the subfamily Pyrginae sensu lato were newly sequenced. The mitogenomes are closed double-stranded circular molecules, with the length ranging from 15,232 bp to 15,559 bp, which all encode 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. The orientation and gene order of these nine mitogenomes are identical to the inferred ancestral arrangement of insects. All PCGs exhibit the typical start codon ATN except for cox1 (using CGA) and cox2 (using TTG) in Mooreana trichoneura. Most of the PCGs terminate with a TAA stop codon, while cox1, cox2, nad4, and nad5 end with the incomplete codon single T. For the different datasets, we found that the one comprising all 37 genes of mitogenome produced the highest nodal support, indicating that the inclusion of RNAs improves the phylogenetic signal. This study re-confirmed the status of Capila, Pseudocoladenia and Sarangesa, namely Capila belongs to the tribe Tagiadini, and Pseudocoladenia and Sarangesa to the tribe Celaenorrhini. Diagnostic characters distinguishing the two tribes, the length of the forewing cell and labial palpi, are no longer significant. Two population of Pseudocoladenia dan fabia from China and Myanmar and P. dan dhyana from Thailand are confirmed conspecific.

scholarly journals The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)

2016 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel A. Moreira ◽  
Paulo A. Buckup ◽  
Marcelo R. Britto ◽  
Maithê G. P. Magalhães ◽  
Paula C. C. de Andrade ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Southeastern Brazil ◽  
Trna Genes ◽  
Protein Coding ◽  
Atpase Subunit ◽  
C Subunit ◽  
D Loop ◽  
Mitochondrial Transcripts ◽  
Complete Mitogenome

ABSTRACT The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL). Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI) demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.

scholarly journals Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽  
2021 ◽  
Vol 1070 ◽  
pp. 13-30
Author(s):  
Wanqing Zhao ◽  
Dajun Liu ◽  
Qian Jia ◽  
Xin Wu ◽  
Hufang Zhang
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Purifying Selection ◽  
Sister Group ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

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

Zootaxa ◽  
2013 ◽  
Vol 3620 (2) ◽  
pp. 260-272 ◽  
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.

Mitogenome of Anterastes babadaghi (Orthoptera: Tettigoniinae; Platycleidini): Frequent conserved overlapping regions within Tettigoniinae

Zootaxa ◽  
2019 ◽  
Vol 4651 (1) ◽  
pp. 173-190
Author(s):  
UĞUR KARŞI ◽  
BATTAL ÇIPLAK
Keyword(s):  
Control Region ◽  
Start Codon ◽  
Gene Location ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Stop Codons ◽  
Protein Coding Genes ◽  
Generation Sequencing

Development of next generation sequencing rapidly increased the number of total mitogenome in data bases. However, the documented number of total mitogenome from species of Tettigoniinae is still limited and a comparison at subfamily level has not been made sufficiently. This paper aims to describe total mitogenome of A. babadaghi (Orthoptera, Tettigoniidae) by comparing to the known mitogenomes of other Tettigoniinae. The total mitogenome of A. babadaghi is 15882–15883 bp, AT skewed with 70.2% AT percentage, and consists of 13 protein coding genes (PCG), 22 tRNA genes, two rRNA genes and an AT rich control region. The genes are ordered as in pancrustacean. The comparative description of mitogenomes in Tettigoniinae showed that total length varies between 15766-16788 bp, the start codon for protein coding genes almost always fits to the ATN pattern, the stop codons are incomplete T-- / TA- and rarely complete TAA, intergenic spacers (IGS) and overlapping regions (OR) in species of the subfamily are similar in number, location, length and nucleotide sequence. We arrived to following conclusion from comparative data: (i) A. babadaghi has a typical orthopteran mitogenome by general features; (ii) this generalisation seems valid for Tettigoniinae as gene content, gene location, gene order, average AT content, anticodons and secondary structure of the tRNA genes, the start and stop codons of the protein coding genes, and several IGSs/ORs are similar to other orthopteran and hexapopods, (iii) variation range in total mitogenome length is narrow in Tettigoniinae and mainly determined by the lengths of control region and total IGSs, (iv) mitogenome of the subfamily exhibits conserved patterns especially in overlapping regions, but conserved features are mostly plesiomorphic. 

scholarly journals The First Complete Mitochondrial Genome of Lachninae Species and Comparative Genomics Provide New Insights into the Evolution of Gene Rearrangement and the Repeat Region

Insects ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 55
Author(s):  
Hui Zhang ◽  
Qian Liu ◽  
Congcong Lu ◽  
Jun Deng ◽  
Xiaolei Huang
Keyword(s):  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Repeat Region ◽  
Protein Coding ◽  
Research Fields ◽  
Tandem Repeat Region ◽  
Complete Mitogenome ◽  
Evolutionary Lineages ◽  
Complete Mitochondrial Genomes

Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.

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