scholarly journals Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Summaya Rahuman ◽  
N. S. Jeena ◽  
P. K. Asokan ◽  
R. Vidya ◽  
P. Vijayagopal
Keyword(s):  
Gene Order ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
Late Triassic ◽  
Protein Coding ◽  
Next Generation Sequencing Technology ◽  
Potential Marker ◽  
Phylogenetic Implications ◽  
Close Relationship ◽  
Complete Mitogenome

Abstract The Indian black clam Villorita cyprinoides (Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data of Villorita. The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome of V. cyprinoides using next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin to Corbicula fluminea. The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs, rrnS and rrnL) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clustered V. cyprinoides and Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship of V. cyprinoides and C. fluminea, analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genus Villorita. Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.

scholarly journals Sequencing of the Complete Mitochondrial Genome of Pingus sinensis (Spirurina: Quimperiidae): Gene Arrangements and Phylogenetic Implications

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1772
Author(s):  
Fanglin Chen ◽  
Hong Zou ◽  
Xiao Jin ◽  
Dong Zhang ◽  
Wenxiang Li ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Coding Regions ◽  
Phylogenetic Implications ◽  
Intergenic Regions ◽  
Complete Mitogenome ◽  
Relationship Of

Despite several decades of intensive research on spirurine nematodes, molecular data on some of the main lineages are still absent, which makes taxonomic classification insufficiently resolved. In the present study, we sequenced the first complete mitogenome for the family Quimperiidae, belonging to P. sinensis (Spirurina: Quimperiidae), a parasite living in the intestines of snakehead (Ophiocephalus argus). The circular mitogenome is 13,874 bp long, and it contains the standard nematode gene set: 22 transfer RNAs, 2 ribosomal RNAs and 12 protein-coding genes. There are also two long non-coding regions (NCR), in addition to only 8 other intergenic regions, ranging in size from 1 to 58 bp. To investigate its phylogenetic position and study the relationships among other available Spirurina, we performed the phylogenetic analysis using Bayesian inference and maximum likelihood approaches by concatenating the nucleotide sequences of all 36 genes on a dataset containing all available mitogenomes of the suborder Spirurina from NCBI and compared with gene order phylogenies using the MLGO program. Both supported the closer relationship of Ascaridoidea to Seuratoidea than to Spiruroidea. Pingus formed a sister-group with the Cucullanus genus. The results provide a new insights into the relationships within Spirurina.

scholarly journals Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Zhang ◽  
Kehua Zhu ◽  
Yifan Liu ◽  
Hua Zhang ◽  
Li Gong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Tandem Duplication ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Muraenesox Cinereus ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

scholarly journals Complete mitochondrial genome of Manis pentadactyla pentadactyla (Mammalia: Pholidota), an endemic subspecies of Chinese pangolin: mitogenome characterisation and phylogenetic implications

2021 ◽  
Vol 9 ◽  
Author(s):  
Nick Sun ◽  
Chi-Chun Huang ◽  
Yu-Wei Tseng ◽  
Tulshi Laxmi Suwal ◽  
Meng-Jou Chi ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Future Research ◽  
Lineage Sorting ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Manis Pentadactyla ◽  
Complete Mitogenome ◽  
Over Exploitation

The Chinese pangolin Manis pentadactyla is critically endangered because of over-exploitation and illegal trafficking and includes three subspecies. However, the taxonomic status of the three subspecies of the Chinese pangolin has not been well resolved, which impedes regional conservation and illegal trade traces. In this study, the complete mitogenome sequence of M. p. pentadactyla, an endemic subspecies of the Chinese pangolin in Taiwan, was determined. The complete mitogenome of M. p. pentadactyla is 16,570 base pairs (bp) in length with 13 protein-coding genes (PCG), 23 transfer RNAs (tRNAs), two ribosomal RNAs and a 1164 bp control region. The overall base composition of the genome showed a slight A + T bias (59.9%), positive AT skew (0.1515) and negative GC skew (-0.3406), which is similar to that of other pangolins. All PCGs started with a typical ATN codon and all tRNAs were typical cloverleaf-shaped secondary structures, except for tRNA-Ser(GCU). Phylogenetic analysis indicated a monophyletic relationship for M. p. pentadactyla and M. p. aurita and was monophyletic for M. p. pentadactyla, but paraphyletic for M. p. aurita. The paraphyly of M. p. aurita resulted from an incomplete lineage sorting. This study enriched the mitogenome database of the Chinese pangolin and the molecular information obtained should be very useful for future research on mitogenome evolution and genetic diversification in M. pentadactyla.

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.

The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders

Zootaxa ◽  
2017 ◽  
Vol 4329 (6) ◽  
pp. 574
Author(s):  
HYUNG JIK WOO ◽  
ANH D. NGUYEN ◽  
KUEM HEE JANG ◽  
EUN HWA CHOI ◽  
SHI HYUN RYU ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
12S Rrna ◽  
Coding Region ◽  
Protein Coding ◽  
Close Relationship ◽  
Relationship Of ◽  
Rna Genes

The millipede Anaulaciulus koreanus (Verhoeff, 1937), belonging to the family Julidae, is an endemic species of the Korean fauna. In this study, we sequence and annotate the mitochondrial genome of A. koreanus. The complete mitochondrial genome of this species is 14,916 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (16S and 12S rRNA), and a large non-coding region. The genome has a very high A+T content (71.1%), less than of the species Brachycybe lecontii Wood, 1864 (order Platydesmida; 76.6%) and Sphaerotheriidae sp. (order Sphaerotheriida; 71.2%). In comparison with the mitochondrial gene arrangement of eight other millipede species, the whole mitochondrial gene arrangement of A. koreanus is most similar to the nemasomatid species, Antrokoreana gracilipes Verhoeff, 1938, but differs from those of the other diplopod orders. The absence of tRNACys between the ND2 and COI regions is unique to the order Polydesmida, whereas the translocation of tRNATyr to between ND2 and COI is exclusive to the Sphaerotheriida. It is also shown that the translocation of tRNAThr between ND4L and ND1 may be a synapomorphy to support a close relationship of two orders Spirobolida and Spirostreptida. 

scholarly journals Characterizing the Mitogenome of the Endemic Bumblebee Subspecies from the Canary Islands for Conservation Purposes

Sociobiology ◽  
2021 ◽  
Vol 68 (3) ◽  
pp. e5910
Author(s):  
Carlos Ruiz ◽  
Diego Cejas ◽  
Irene Muñoz ◽  
Pilar De la Rua
Keyword(s):  
Canary Islands ◽  
Bombus Terrestris ◽  
Taxonomic Status ◽  
North African ◽  
Protein Coding ◽  
The North ◽  
Close Relationship ◽  
Complete Mitogenome ◽  
Mitochondrial Sequences ◽  
Conservation Plans

The taxonomic status of Bombus terrestris subspecies is complex and has deep implications in the management of commercial bumblebees for crop pollination as well as in the establishment of appropriate conservation plans. Herein, the complete mitogenome of the endemic Canary Islands subspecies Bombus terrestris canariensis is newly sequenced and compared with available mitochondrial sequences in order to shed light into its taxonomic status. The mitochondrial genome was 17,300 bp in length and contained 37 genes, including 13 protein-coding genes (PCGs), two rRNAs, and 22 tRNAs and a partial sequence of the AT rich control region. The phylogenetic analysis of PCGs of the mitogenome was congruent with its subspecific status and a close relationship with the North African subspecies africanus as previously suggested. The sequencing of the mitogenome of B. t. canariensis provides useful genetic information to study the conservation genetics and genetic diversity of these island bumblebee populations.

scholarly journals First report and molecular characterization of the dagger nematode, Xiphinema oxycaudatum (Nematoda, Dorylaimidae) from South Africa

ZooKeys ◽  
2019 ◽  
Vol 894 ◽  
pp. 1-17
Author(s):  
Fisayo Y. Daramola ◽  
Rinus Knoetze ◽  
Antoinette Swart ◽  
Antoinette P. Malan
Keyword(s):  
South Africa ◽  
Mitochondrial Gene ◽  
Soil Health ◽  
Nematode Species ◽  
Plant Viruses ◽  
Parasitic Nematodes ◽  
Western Cape ◽  
Protein Coding ◽  
First Report ◽  
Close Relationship

Plant-parasitic nematodes of the genus Xiphinema Cobb, 1913 comprise a complex group of nematode species, some of which are important vectors of plant viruses. During a field survey to determine the soil health of an abandoned honeybush (Cyclopia genistoides) monoculture, a high density of the dagger nematode, Xiphinema oxycaudatum Lamberti & Bleve-Zacheo, 1979 (Nematoda, Dorylaimidae), was observed in soil around the roots of honeybush plants in an abandoned farmland at Bereaville, an old mission station in the Western Cape province of South Africa. Soil samples were taken from the rhizosphere of plants and nematodes were extracted from the soil using a modified extraction tray method. Specimen of the dagger nematodes were processed for scanning electron microscopy, morphological and molecular analysis. Molecular profiling of the nematode species was done in order to give an accurate diagnosis and to effectively discriminate the nematode from other species within the Xiphinema americanum group. Phylogenetic analysis based on the D2D3 expansion segment of the 28S gene supported a close relationship of species within the americanum group, however, the protein-coding cytochrome oxidase (coxI) of the mitochondrial gene provided a useful tool for distinguishing the nematode from other species within the group. This study represents the first report of X. oxycaudatum from South Africa.

scholarly journals Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11086
Author(s):  
Xianyi Wang ◽  
Jiajia Wang ◽  
Ren-Huai Dai
Keyword(s):  
Phylogenetic Tree ◽  
Control Region ◽  
Strong Support ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Nucleotide Composition ◽  
Protein Coding ◽  
Approval Ratings ◽  
Phylogenetic Implications ◽  
Paraphyletic Group

Similar morphological characteristics and limited molecular data of Olidiana resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus Olidiana, we sequenced and annotated five Olidiana complete mitochondrial genomes (mitogenomes). Our results show that Olidiana mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Their nucleotide composition, codon usage, features of control region, and tRNA secondary structures are similar to other members of Cicadellidae. We constructed the phylogenetic tree of Cicadellidae using the maximum likelihood (ML) and Bayesian inference (BI) methods based on all valid mitogenome sequences. The most topological structure of the obtained phylogenetic tree is consistent. Our results support the monophyletic relationships among 10 subfamilies within Cicadellidae and confirm Iassinae and Coelidiinae to be sister groups with high approval ratings. Interestingly, Olidiana was inferred as a paraphyletic group with strong support via both ML and BI analyses. These complete mitogenomes of five Olidiana species could be useful in further studies for species diagnosis, evolution, and phylogeny research within Cicadellidae.

Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'

2002 ◽  
Vol 16 (3) ◽  
pp. 345 ◽  
Author(s):  
M. Dowton ◽  
L. R. Castro ◽  
A. D. Austin
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Gene Rearrangement ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Genome Organisation ◽  
Rearrangement Mechanism ◽  
Molecular Characters

Mitochondrial gene rearrangements are the latest tool in the arsenal of phylogeneticists for investigating historical relationships. They are complex molecular characters that may provide more reliable evidence of ancestry than comparative molecular data. Here we review the phylogenetic utility of mitochondrial gene rearrangements, and find that despite isolated incidences of convergence, derived gene order appears highly congruent with phylogenies produced from other sources of data. We calculate that the chance of two mitochondrial genomes sharing the same derived genome organisation is only 1/2664, but caution that this ignores the possibility that the (as yet uncharacterised) gene rearrangement mechanism may greatly increase the chance of convergence. Broader taxonomic surveys of mitochondrial genome organisation will lead to a more realistic indication of the historical incidence of convergence in genome organisation.

scholarly journals The Complete Mitogenome of Pyrrhocoris tibialis (Hemiptera: Pyrrhocoridae) and Phylogenetic Implications

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 820 ◽  
Author(s):  
Qi-Lin Zhang ◽  
Run-Qiu Feng ◽  
Min Li ◽  
Zhong-Long Guo ◽  
Li-Jun Zhang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Nucleotide Composition ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Transcription Termination Factor ◽  
Phylogenetic Implications ◽  
Homogeneous Models ◽  
Complete Mitogenome ◽  
A Site ◽  
Rna Genes

We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of the mitochondrial transcription termination factor were well conserved in Pyrrhocoroidea. Different protein-coding genes have been subject to different evolutionary rates correlated with the G + C content. The size of control regions (CRs) was highly variable among mitogenomes of three sequenced Pyrrhocoroidea species, with the P. tibialis CR being the largest. All the transfer RNA genes found in Pyrrhocoroidea had the typical clover leaf secondary structure, except for trnS1 (AGN), which lacked the dihydrouridine arm and possessed an unusual anticodon stem (9 bp vs. the normal 5 bp). A total of three different phylogenetic relationships among the five super-families of Pentatomomorpha were obtained using three analytical methods (MrBayes and RAxML under site-homogeneous models and PhyloBayes under a site-heterogeneous CAT + GTR model) and two mitogenomic datasets (nucleotides and amino acids). The tree topology test using seven methods statistically supported a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))) as the best topology, as recognized by both RAxML and MrBayes based on the two datasets.

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