scholarly journals Complete mitochondrial genome of Whitmania laevis (Annelida, Hirudinea) and comparative analyses within Whitmania mitochondrial genomes

2020 ◽  
Vol 145 (2) ◽  
Author(s):  
Fei Ye ◽  
Ting Liu ◽  
Wenbo Zhu ◽  
Ping You
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Close Relationship

The complete mitochondrial genome of Whitmania laevis is 14,442 bp in length and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The almost-complete mitochondrial genome of Whitmania acranulata, consisting of 13,494 bp, contains 35 genes including 13 PCGs, 20 tRNA genes, and two rRNA genes. COI phylogenetic analyses showed that the samples reported in GenBank and analysed as Hirudo nipponia KC667144, Hirudinaria manillensis KC688268 and Erpobdella octoculata KC688270 are not the named species and they should belong to Whitmania. We compared and analyzed the characteristics of nucleotide composition, codon usage, and secondary structures of 22 tRNAs and two rRNAs from Whitmania taxa. Moreover, we analyzed phylogenetic relationships of Annelida using maximum likelihood (ML) and Bayesian inference (BI) methods, based on 11 mitochondrial genes. Our results reveal that W. laevis has a close relationship with W. pigra.

The mitochondrial genome of Coridius chinensis (Hemiptera: Dinidoridae)

Zootaxa ◽  
2012 ◽  
Vol 3537 (1) ◽  
pp. 29 ◽  
Author(s):  
LI LIU ◽  
HU LI ◽  
FAN SONG ◽  
WEN SONG ◽  
XUN DAI ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Rrna Genes ◽  
Trna Genes ◽  
Structural Domains ◽  
Protein Coding ◽  
Simple Loop ◽  
Transfer Rnas ◽  
Cloverleaf Structure

The nearly complete mitochondrial genome of Coridius chinensis (Dallas) is reported in this study. The mitogenome is a double-stranded circular molecule of more than 14,648 bp in length with an A+T content of 75.1%. It encoded 37 genes as in other insect mtDNAs, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region (unsuccessful sequencing), and the gene order is the same as most other known heteropteran mitogenomes. All of the 22 transfer RNAs can be folded into the typical cloverleaf structure except tRNASer(AGN), which can only form a simple loop at the site of dihydrouridine (DHU) arm as known in other metazoans. The secondary structures of the large and small ribosomal RNAs of C. chinensis are similar to other presented insects. The rrnL consisted of six structural domains and 40 helices, and the rrnS consisted of three structural domains and 26 helices. Nine PCGs are initiated with the standard initiation codons (ATN), while ND6 and ND1 use GTG, and COI and ATP8 use TTG. All PCGs stopped with TAA/TAG termination codons except the COII terminated with a single T residue. Asymmetry in the nucleotide composition between J-strand and N-strand was observed in this mitogenome.

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 Mitochondrial Genome Sequence of Phytophthora sansomeana and Comparative Analysis of Phytophthora Mitochondrial Genomes

2020 ◽  
Author(s):  
Guohong Cai ◽  
Steven R. Scofield
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Proteins ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Circular Molecule

ABSTRACTPhytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthetase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3’ truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.

scholarly journals Complete mitochondrial genome sequence of Bos frontalis (Gayal) from Bangladesh

2020 ◽  
Author(s):  
GK Deb ◽  
R Khatun ◽  
SMJ Hossain ◽  
SS Rahman ◽  
MAB Bhuiyan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Rrna Genes ◽  
Trna Genes ◽  
Closely Related Species ◽  
Protein Coding ◽  
The Family ◽  
Conservation Concern ◽  
Bovine Species

AbstractThe Gayal is a large-sized endangered semi-domesticated bovine species belonging to the family Bovidae, tribe Bovini, group Bovina, genus Bos, and species Bos frontalis. It is also called the Mithan or Mithun. Mitochondrial genome is considered as an important tool for species identification and monitoring the populations of conservation concern and therefore it becomes an obligation to sequence the mitochondrial genome of Bagladeshi gayal. We want to identify some important genes related to a particular trait such as those associated with adaptation, muscle strength, or prolificacy. The data will help explore evolutionary relationships with closely related species. The mitogenome of Bos frontalis is 16,347 bp in length and nucleotide composition is AT-based (60.21%), contains 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region.

The complete mitochondrial genome of the storage mite pest Tyrophagus fanetzhangorum (Acari: Acaridae)

2020 ◽  
Vol 25 (9) ◽  
pp. 1693-1701
Author(s):  
Xuan Su ◽  
Yu Fang ◽  
Jiao-Yang Xu ◽  
Wei-Xi Fang ◽  
Xue-Bing Zhan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Storage Mite ◽  
Astigmatid Mites

Mitochondrial (mt) genomes of astigmatid mites typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. However, two Tyrophagus mites (Tyrophagus putrescentiae and T. longior) were reported as having lost three tRNAs in their mt genomes. In this study, we sequenced the complete mitochondrial genome of Tyrophagus fanetzhangorum (14,257 bp) and found typical set of mt tRNA genes (22 tRNAs). The gene arrangement of T. fanetzhangorum is consistent with the pattern of possible common ancestor of astigmatid mites. Phylogenetic analyses were conducted using Maximum likelihood (ML) and Bayesian inference (BI) methods. Phylogenetic analysis shows that T. fanetzhangorum is more closely related to T. putrescentiae than to T. longior within the genus Tyrophagus.

scholarly journals The first complete mitochondrial genome of Cheyletus malaccensis (Acari: Cheyletidae): gene rearrangement

2020 ◽  
Vol 25 (8) ◽  
pp. 1433-1443
Author(s):  
Yang-ming Lan ◽  
Shi-qian Feng ◽  
Li-yuan Xia ◽  
Zhi-hong Li ◽  
Yang Cao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mite Species ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Trna Genes ◽  
Protein Coding ◽  
Food Commodities ◽  
Cheyletus Malaccensis

The predatory mite Cheyletus malaccensis (Acari: Cheyletidae), commonly occurring in stores of various food commodities, is an important natural enemy of stored product pests. Disentangling the mt genome sequence of C. malaccensis at molecular level can decrease uncertainties during morphological identification and is useful in reconstructing the phylogeny of Acariformes group. In this study, the complete mitogenome of C. malaccensis was sequenced by the next-generation sequencing. After assembly and annotation, we found the circular 14,732 bp mitogenome of C. malaccensis, containing 13 protein coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Compared with the ancestral mitogenome organization of arthropods, most of tRNA were truncated without D-arm or/and TψC-arm. Rearrangement was found in 12 mitogenome genes. Phylogenetic analyses based on the mitogenome data from other 29 mite species were inferred by Bayesian and maximum likelihood methods, which strongly supported the closer relationship between C. malaccensis and Tetranychidae than other mites. The obtained results represent the first complete mitochondrial genome record for Cheyletidae group. It may help improve molecular phylogenetic relationship and population genetics of the Cheyletidae.

The complete mitochondrial genome of the Formosan black bear (Ursus thibetanus formosanus)

Zootaxa ◽  
2009 ◽  
Vol 1971 (1) ◽  
pp. 50-58 ◽  
Author(s):  
CHI-LI TSAI ◽  
YII-CHENG CHOU ◽  
CHIH-CHIN SHIH ◽  
HSI-CHI CHENG ◽  
CHIEH-CHUNG YANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Pcr Amplification ◽  
Black Bear ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Ursus Thibetanus ◽  
Protein Coding Genes

A complete mitochondrial genome of the Formosan black bear (Ursus thibetanus formosanus) was obtained by PCR amplification and DNA sequencing. The genome spans 17,044 bp that includes 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The base composition of the heavy strain is 31.0% A, 25.6% C, 15.7% G, and 27.7% T. The control region (CR) is located between tRNA-Pro and tRNA-Phe, consists of 1,595 bp, and comprises 9.4% of the whole genome. The DNA sequence shares 98.7%, 96.3%, 91.0%, 91.8%, and 91.7% similarity with those of U. t. thibetanus, U. t. mupinensis, U. americanus, U. arctos, and U. maritimus respectively. Phylogenetic analyses suggest that the Formosan black bear is more closely related to U. t. thibetanus than to U. t. mupinensis.

scholarly journals The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

2018 ◽  
Vol 94 ◽  
Author(s):  
P. Zhang ◽  
R.K. Ran ◽  
A.Y. Abdullahi ◽  
X.L. Shi ◽  
Y. Huang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Squirrel Monkey ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Rrna Genes ◽  
Saimiri Sciureus ◽  
Trna Genes ◽  
Loop Structure ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractDipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

scholarly journals Complete mitochondrial genome of Glomeridesmus spelaeus (Diplopoda), a troglobitic species from Carajás iron-ore caves (Pará, Brazil)

2017 ◽  
Author(s):  
Gisele Lopes Nunes ◽  
Renato Renison Moreira Oliveira ◽  
Eder Soares Pires ◽  
Santelmo Vasconcelos ◽  
Thadeu Pietrobon ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Base Composition ◽  
Iron Ore ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Significant Advance ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Rich Region ◽  
The Public

AbstractWe report the complete mitochondrial genome sequence of Glomeridesmus spelaeus, the first sequenced genome of the order Gomeridesmida. The genome is 14,825 pb in length and encodes 37 mitochondrial (13 PCGs, 2 rRNA genes, 22 tRNA) genes and contains a typical AT-rich region. The base composition of the genome was A (40.1%), T (36.4%), C (15.8%), and G (7.6%), with an AT content of 76.5%. Our results indicated that Glomeridesmus spelaeus only distantly related to the other Diplopoda species with available mitochondrial genomes in the public databases. The publication of the mitogenome of G. spelaeus will contribute to the identification of troglobitic invertebrates, a very significant advance for the conservation of the troglofauna.

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.

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