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.

The complete mitochondrial genomes of four Baikal molluscs from the endemic family Baicaliidae (Caenogastropoda: Truncatelloida)

2020 ◽  
Vol 86 (3) ◽  
pp. 201-209
Author(s):  
T E Peretolchina ◽  
T Ya Sitnikova ◽  
D Yu Sherbakov
Keyword(s):  
Lake Baikal ◽  
Ribosomal Rna ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Canonical Base ◽  
Complete Mitochondrial Genomes

Abstract Here, we present the complete mitochondrial (mt) genomes of four members of the Baicaliidae Fisher, 1885, a truncatelloidean family that is endemic to Lake Baikal (East Siberia). The mt genomes are those of Korotnewia korotnevi (15,171 bp), Godlewskia godlewskii (15,224 bp), Baicalia turriformis (15,127) and Maackia herderiana (15,154 bp). All these mt genomes contain 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. We detected non-canonical base pairs in some of the tRNA genes and variable numbers of non-coding spacers; some tRNAs do not have a TψC loop. We found gene order to be highly conserved in these Lake Baikal species and similar to the majority of caenogastropod mt genomes available on GenBank. A position of the putative control region is delimited to the non-coding region between trnF and the cox3 gene. It contains the ‘GAA(A)nT’ motif at the 3′ end and is similar to the replication origin found in most Caenogastropoda studied to date. We also compared the evolutionary rates of different genes to evaluate their use in different kinds of population or phylogenetic studies of this group of gastropods.

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 plastome of real yellow wood (Podocarpus latifolius): gene organization and comparison with related species

Holzforschung ◽  
2019 ◽  
Vol 73 (6) ◽  
pp. 525-536
Author(s):  
Josphat K. Saina ◽  
Zhi-Zhong Li ◽  
Andrew W. Gichira ◽  
Sheila Avoga ◽  
Qing-Feng Wang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Evolutionary History ◽  
Gene Organization ◽  
Mononucleotide Repeat ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Circular Molecule ◽  
Rna Genes ◽  
Simple Sequence

AbstractPodocarpus latifolius[(Thunb.) R.Br.exMirb.], also known as real yellow wood, is a large evergreen tree with exceptionally high-quality wood. It is a member of the Podocarpaceae family, which includes many species widely grown for wood pulp as well as timber for construction. Despite its importance, studies focusing on its genetic characterization and molecular biology are limited. Therefore, this study reports the complete plastome ofP. latifolius, which is a circular molecule of 134 020 base pairs (bp) in length, lacking a quadripartite structure. TheP. latifoliusplastome encodes 117 unique genes, consisting of 82 protein-coding genes, 31 transfer RNA genes and four ribosomal RNA genes. The analysis showed that the Podocarpaceae plastomes have experienced some intron and gene losses, inversions, and inverted repeat (IR) loss resulting in a diverse plastome organization at the species and genus levels. Therefore, to understand the extent of these genomic rearrangements, more sampling of the Podocarpaceae plastomes is necessary. A total of 149 editing sites were predicted in 28 genes, all of which were C to U conversions. Moreover, a total of 164 simple sequence repeats (SSRs) were identified in theP. latifoliusplastome, the majority being mononucleotide repeat motifs with A/T sequence predominance. Overall, the data obtained in this study will be useful for population genetics, evolutionary history and phylogenetic studies of the species in this genus.

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.

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.

The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)

2015 ◽  
Vol 63 (2) ◽  
pp. 111 ◽  
Author(s):  
Anna J. MacDonald ◽  
Theresa Knopp ◽  
Mitzy Pepper ◽  
J. Scott Keogh ◽  
Stephen D. Sarre
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Rrna Genes ◽  
Trna Genes ◽  
Base Pairs ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Typical Vertebrate

The Pygopodidae comprise an enigmatic group of legless lizards endemic to the Australo-Papuan region. Here we present the first complete mitochondrial genome for a member of this family, Aprasia parapulchella, from Australia. The mitochondrial genome of A. parapulchella is 16 528 base pairs long and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and the control region, conforming to the typical vertebrate gene order. The overall mitochondrial nucleotide composition is 31.7% A, 24.5% T, 30.5% C and 13.2% G. This corresponds to a total A+T content of 56.3%, which is similar to that of other squamate lizard genomes.

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.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genomes of Two Tiny Necrophagous Phorid Flies, Metopina sagittata and Puliciphora borinquenensis (Diptera: Phoridae)

2021 ◽  
Author(s):  
Shu-Tong Dai ◽  
Dian-Xing Feng ◽  
Da-Peng Sun
Keyword(s):  
Mitochondrial Genome ◽  
Species Identification ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

Abstract The mitochondrial genome is frequently used for species identification and phylogenetic studies. In this study, we first sequenced and annotated the complete mitochondrial genomes of two phorid species that are forensically important in buried or enclosed environments: Metopina sagittata (Liu) and Puliciphora borinquenensis (Wheeler). The complete mitochondrial genome sequences of M. sagittata and P. borinquenensis were 15,640 bp with an A+T content of 75.97% and 15,429 bp with an A+T content of 75.38%, respectively. Their circular genomes both contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region located between rrnS and trnI which was 808 bp for M. sagittata and 746 bp for P. borinquenensis. All the PCGs of both species started with ATN codons except for cox1 which used TTG codon. In addition to the common stop codon TAA and TAG, the incomplete stop codon T was used in two PCGs (cox1 and nad4) of M. sagittata and five PCGs (cox1, cox2, cox3, nad5, and nad4) of P. borinquenensis. There were 3 and 10 mismatched base pairs in the tRNA secondary structures from M. sagittata and P. borinquenensis, respectively. Both maximum likelihood and Bayesian inference analyses indicated that Platypezidae and Phoridae are sister taxa. M. sagittata is closely related to P. borinquenensis within the subfamily Metopininae. This work enhances the databases of Phoridae genomes and contributes to the further study of species identification and phylogenetics of this family.

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.

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