scholarly journals The complete mitochondrial genome and phylogeny of the green chromide, Etroplus suratensis (Bloch, 1790) from Vembanad Lake, Kerala, south India

2019 ◽  
Vol 66 (3) ◽  
Author(s):  
Wilson Sebastian ◽  
Sandhya Sukumaran ◽  
Gopalakrishnan A
Keyword(s):  
Complete Mitochondrial Genome ◽  
12S Rrna ◽  
Trna Genes ◽  
Sri Lankan ◽  
Protein Coding ◽  
Cichlid Species ◽  
Etroplus Suratensis ◽  
D Loop ◽  
Complete Mitogenome ◽  
Coding Control

The green chromide Etroplus suratensis (Bloch, 1790), is a cichlid species which forms an economically valuable food fish and a preferred candidate for brackishwater aquaculture in India. The complete mitogenome of E. suratensis collected from Vembanad Lake, Kerala, India has been characterised in the present study. The entire mitogenome was PCR amplified as contiguous, overlapping segments and sequenced. The assembled mitogenome of E. suratensis is 16456 bp circle, contained the 37 mitochondrial structural genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, 13 protein-coding genes and 1 non-coding control region/D-loop, with the gene order identical to vertebrates. In the phylogenetic analysis, E. suratensis is clustered with other Indo-Sri Lankan taxa. Among cichlids, the groups from South America and Africa are monophyletic in origin. The mitogenomic information generated in this study will be valuable for further studies on evolution, taxonomy, conservation, environmental adaptation and selective breeding of this species having aquaculture, ornamental and evolutionary importance.

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 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.

An additional record of Fejervarya manoharani Garg and Biju from the Western Ghats with a description of its complete mitochondrial genome

Zootaxa ◽  
2017 ◽  
Vol 4277 (4) ◽  
pp. 491 ◽  
Author(s):  
S. KUMAR KIRAN ◽  
V. S. ANOOP ◽  
K. C. SIVAKUMAR ◽  
RAGHUNATHAN DINESH ◽  
J. P. MANO ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Gene Organization ◽  
Morphological Data ◽  
12S Rrna ◽  
Trna Genes ◽  
Protein Coding ◽  
Its Gene ◽  
Nd5 Gene

An additional sighting of newly described frog species, Fejervarya manoharani Garg and Biju, outside of the type locality along with their morphological data is reported herewith. We are also providing the whole DNA sequence of the mitochondrial genome with its gene organization as additional data to distinguish this species from its congeners. The mitogenome of F. manoharani was 17,654 bp in length. It contains 38 genes including two rRNAs, 23 tRNAs, 13 protein-coding genes and a control region. Similar to other dicroglossid frogs, a tandem duplication of tRNAMet was found. The ND5 gene was located at the 3' end of the control region like in three other Fejervarya species for which mitogenomic data are available. A rearrangement of four tRNA genes, namely Leucine, Threonine, Proline, and Phenylalanine, between ND5 and 12S rRNA, differing from other Fejervarya species, was also observed. 

scholarly journals Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Dong Liu ◽  
Yuanyuan Zhang ◽  
Ming Zhang ◽  
Jinquan Yang ◽  
Wenqiao Tang
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Morphological Evolution ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
12S Rrna ◽  
Trna Genes ◽  
Protein Coding ◽  
Jaw Apparatus ◽  
Intergenic Regions

Abstract Background The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species. Results We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments. Conclusions This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

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

Genes ◽  
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.

The symbiotic mites of some Appalachian Xystodesmidae (Diplopoda:Polydesmida) and the complete mitochondrial genome sequence of the mite Stylochyrus rarior (Berlese) (Acari:Mesostigmata:Ologamasidae)

2009 ◽  
Vol 23 (5) ◽  
pp. 445 ◽  
Author(s):  
Lynn Swafford ◽  
Jason E. Bond
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mite Species ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Rrna Gene ◽  
Protein Coding ◽  
Coding Regions ◽  
The Family ◽  
Coding Control

Millipedes of the family Xystodesmidae (Polydesmida) are often host to several symbiotic mite species, but very little work has been done to identify these acarines or to understand their relationship to the millipedes. In an attempt to better understand these associations, mites found on xystodesmid millipedes, a group for which a species phylogeny has been proposed, were collected in the Appalachian Mountains of Kentucky, Virginia, Tennessee and North Carolina. Mites in the genera Stylochyrus Canestrini & Canestrini, 1882 (Mesostigmata: Ologamasidae) and Schwiebea Oudemans, 1916 (Sarcoptiformes: Acaridae) were prevalent among millipedes in the genera Apheloria Chamberlin, 1921, Appalachioria Marek & Bond, 2006, Boraria Chamberlin, 1943, Brachoria Chamberlin, 1939, Dixioria Chamberlin, 1947, Nannaria Chamberlin, 1918, Pleuroloma Rafinesque, 1820, Prionogonus Shelley, 1982, Rudiloria Causey, 1955 and Sigmoria Chamberlin, 1939. Of the mite taxa collected, the species Stylochyrus rarior (Berlese, 1916) was found on the greatest number of sampled millipede taxa. To enhance future coevolutionary studies of xystodesmid millipedes and their mite symbionts, the complete mitochondrial genome of S. rarior associated with the millipede genus Apheloria (Polydesmida: Xystodesmidae) was sequenced. The genome is 14 899 nucleotides in length, has all the typical genes of an arthropod mitochondrion, differs in gene arrangement from that of the ancestral arthropod, and has a gene order that is unique among mites and ticks. The major difference in S. rarior is the placement of the protein-coding gene nad1, which is positioned between the rRNA gene 12S and the protein-coding gene nad2 (tRNA genes and non-coding regions excluded). There are also two non-coding control regions within this mitochondrial genome.

scholarly journals The phylogeny of the Anderson’s White-bellied Rat (Niviventer andersoni) based on complete mitochondrial genomes provides insight into its evolutionary history

2021 ◽  
Author(s):  
Shujing Liu ◽  
Lili Fu ◽  
Jihua Zhou ◽  
Jizhou Lv ◽  
Zhongyang Tan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Gene Tree ◽  
Sister Group ◽  
Protein Coding ◽  
Mitogenome Sequence ◽  
D Loop ◽  
Coding Control ◽  
Rna Genes

Anderson’s White-bellied Rat, Niviventer andersoni (Thomas, 1911) (Muridae, Niviventer) is an species endemic to China. In the present study, we have sequenced the first complete mitochondrial genome of N. andersoni using next-generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and one non-coding control region (D-Loop). Phylogenetic analyses of the nucleotide sequences of all 13 PCGs, PCGs minus ND6 and the entire mitogenome sequence except for the D-loop, produce nearly identical, well-resolved topologies. Our results support that N. andersoni clustered with N. excelsior and form a sister group with N. confucianus, and they statistically reject the hypothesis from one cytochrome b (cytb) gene tree that N. confucianus is sister to N. fulvescens. Our research may be helpful to further reconsideration of clearer taxonomy and improve our understanding of mitogenomic evolution in the genus Niviventer.

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.

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.

A complete mitogenome from Orconectes (Procericambarus) cf. ozarkae (Williams)

2016 ◽  
Vol 22 (1) ◽  
pp. 95-98 ◽  
Author(s):  
Paul R. Cabe
Keyword(s):  
Ribosomal Rna ◽  
Dna Sequences ◽  
Complete Mitochondrial Genome ◽  
Trna Genes ◽  
Sequence Information ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Complete Mitogenome ◽  
Mitochondrial Sequences

Abstract Mitochondrial DNA sequences have been used extensively for studies of phylogeny, biogeography, and systematics in a vast array of taxa. In crayfish, the most widely used mitochondrial sequences are from the genes 16S ribosomal RNA, 12S ribosomal RNA, and cytochrome oxidase I. Other regions might perform well for certain questions, and entire mtDNA genome sequences might be very useful for phylogenetic studies, but these uses are curtailed by lack of sequence information. The complete mitochondrial genome from an individual of Orconectes cf. ozarkae (Williams) was sequenced, assembled, and annotated. The circular genome was 15,815 base pairs in length, and included the complement of 37 genes expected for metazoans, two ribosomal RNA genes, thirteen protein coding genes, and 22 tRNA genes. The gene order is equivalent to other species of crayfish from the family Cambaridae.

Sign in / Sign up

Export Citation Format

Share Document