scholarly journals The complete mitochondrial genome of endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and Phylogeny

2019 ◽  
Author(s):  
Shantanu Kundu ◽  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Kailash Chandra
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
De Novo ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Genomic Feature ◽  
Trna Genes ◽  
Nadh Dehydrogenase Subunit ◽  
Sister Relationship ◽  
Protein Coding

AbstractAssam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The genomic feature of P. sylhetensis mitogenome is still anonymous to the scientific community. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. This de novo assembly encodes 13 Protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5) with GTG. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine (trnS1) with lack of conventional DHU arm and loop. Both, Bayesian and Maximum-likelihood topologies showed distinct clustering of all the Testudines species with their respective taxonomic ranks and congruent with the previous phylogenetic hypotheses (Pangshura and Batagur sister taxa). Nevertheless, the mitogenomic phylogeny with other amniotes corroborated the sister relationship of Testudines with Archosaurians (Birds and Crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated that, most of the Testudines species showed plesiomorphy with typical vertebrate GO.

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 Indian tent turtle, Pangshura tentoria and comparative mitochondriomics

2018 ◽  
Author(s):  
Shantanu Kundu ◽  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Iftikar Rahaman ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
Tandem Repeats ◽  
Synonymous Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Bootstrap Support ◽  
Nadh Dehydrogenase Subunit ◽  
Strong Negative Selection

Complete mitochondrial genomes of Indian tent turtle, Pangshura tentoria was sequenced and annotated as 16,657 bp in length. This first assembly was encoded by 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs) as similar to the typical vertebrate mitochondrial gene arrangement. The complete mitogenome has a base composition of A (33.30%), G (13.54%), C (27%), and T (26.13%). Most of the genes were encoded on major strand, except for the eight tRNAs and one PCG (nad6). Almost all PCGs were starting with an ATG initiation codon, except for cytochrome oxidase subunit 1 (cox1) with ‘GTG’ and NADH dehydrogenase subunit 5 (nad5) with ‘ATA’. The typical termination codons, ‘TAA’ and ‘AGA’ has been observed in NADH dehydrogenase subunit 4l (nad4l) and NADH dehydrogenase subunit 6 (nad6) respectively; and others were used incomplete stop codons. The Relative Synonymous Codon Usage (RSCU) analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine in P. tentoria. Codon distribution per thousand codon (CDsPT) values for all the amino acids showed the maximum values were present for Leucine in all geoemydid turtles. Further, the PCGs showed non-synonymous (Ka)/synonymous (Ks) values were <1 that indicated a strong negative selection among the studied species. The tRNAs were folded into classic clover-leaf secondary structures, except for trnS (GCT), lacking of the conventional DHU arm or stem. Further, the 10 tRNAs showed G-T mismatches and forming weak bonds. In the control region (CR) of P. tentoria, a single tandem repeat of eight base pairs (TTCTCTTT) was resulted with two copy numbers. The comparative study of CR with other geoemydid turtles revealed the numbers of tandem repeats were frequent in the 3´ end and structural characteristic were species-specific. The Maximum Likelihood (ML) phylogeny showed 32 geoemydid turtles were clustered distinctly with high bootstrap support and congruent with the previous phylogenetic hypothesis. Further, the representative mitogenome sequences of other family/suborder were depicted discrete clades in the ML tree. The study argued the complete mitochondrial genome sequence of P. tentoria and comparative mitochondriomics of geoemydid turtles would be useful for further phylogenetic reconciliation and evolutionary research.

scholarly journals Complete mitochondrial genome of Indian tent turtle, Pangshura tentoria and comparative mitochondriomics

2018 ◽  
Author(s):  
Shantanu Kundu ◽  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Iftikar Rahaman ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
Tandem Repeats ◽  
Synonymous Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Bootstrap Support ◽  
Nadh Dehydrogenase Subunit ◽  
Strong Negative Selection

Complete mitochondrial genomes of Indian tent turtle, Pangshura tentoria was sequenced and annotated as 16,657 bp in length. This first assembly was encoded by 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs) as similar to the typical vertebrate mitochondrial gene arrangement. The complete mitogenome has a base composition of A (33.30%), G (13.54%), C (27%), and T (26.13%). Most of the genes were encoded on major strand, except for the eight tRNAs and one PCG (nad6). Almost all PCGs were starting with an ATG initiation codon, except for cytochrome oxidase subunit 1 (cox1) with ‘GTG’ and NADH dehydrogenase subunit 5 (nad5) with ‘ATA’. The typical termination codons, ‘TAA’ and ‘AGA’ has been observed in NADH dehydrogenase subunit 4l (nad4l) and NADH dehydrogenase subunit 6 (nad6) respectively; and others were used incomplete stop codons. The Relative Synonymous Codon Usage (RSCU) analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine in P. tentoria. Codon distribution per thousand codon (CDsPT) values for all the amino acids showed the maximum values were present for Leucine in all geoemydid turtles. Further, the PCGs showed non-synonymous (Ka)/synonymous (Ks) values were <1 that indicated a strong negative selection among the studied species. The tRNAs were folded into classic clover-leaf secondary structures, except for trnS (GCT), lacking of the conventional DHU arm or stem. Further, the 10 tRNAs showed G-T mismatches and forming weak bonds. In the control region (CR) of P. tentoria, a single tandem repeat of eight base pairs (TTCTCTTT) was resulted with two copy numbers. The comparative study of CR with other geoemydid turtles revealed the numbers of tandem repeats were frequent in the 3´ end and structural characteristic were species-specific. The Maximum Likelihood (ML) phylogeny showed 32 geoemydid turtles were clustered distinctly with high bootstrap support and congruent with the previous phylogenetic hypothesis. Further, the representative mitogenome sequences of other family/suborder were depicted discrete clades in the ML tree. The study argued the complete mitochondrial genome sequence of P. tentoria and comparative mitochondriomics of geoemydid turtles would be useful for further phylogenetic reconciliation and evolutionary research.

scholarly journals The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Priya Prasad ◽  
Shantanu Kundu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Start Codon ◽  
Gene Arrangement ◽  
Sister Relationship ◽  
Protein Coding ◽  
Relationship Of ◽  
Rna Genes ◽  
Boundary Mapping ◽  
Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

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.

The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

2022 ◽  
Author(s):  
Tianhong Wang ◽  
Zihao Wang ◽  
Ruwei Bai ◽  
Zhijun Yu ◽  
Jingze Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Haemaphysalis Qinghaiensis ◽  
Mitogenome Sequence ◽  
Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

The complete mitochondrial genome of Zicrona caerulea (Linnaeus) (Hemiptera: Pentatomidae: Asopinae) and its phylogenetic implications

Zootaxa ◽  
2020 ◽  
Vol 4747 (3) ◽  
pp. 547-561
Author(s):  
QING ZHAO ◽  
GERASIMOS CASSIS ◽  
LING ZHAO ◽  
YIFAN HE ◽  
HUFANG ZHANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Stink Bug ◽  
Protein Coding ◽  
Simple Loop ◽  
Phylogenetic Implications ◽  
Maximum Likelihood Methods

Zicrona caerulea (Linnaeus, 1758) is a cosmopolitan stink bug species, which belongs to the predatory subfamily Asopinae. In this study, the complete mitochondrial genome of Zicrona caerulea from Shanxi, China was sequenced for the first time, using next generation sequencing. The mitogenome was found to be 15,479 bp in length. It contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region. This research revealed an overall A+T content of 77.14%. All tRNA genes had a clover-leaf structure except for trnS1, which lacks a dihydrouridine (DHU) arm; and for trnV, the DHU arm forms a simple loop. The lengths of rrnS and rrnL were 797 bp and 1,285 bp, respectively. Because of a shortage in tandem repeats, the A+T-rich region was 644 bp in length. Phylogenetic relationships based on these mitogenomes, using Bayesian inference and Maximum likelihood methods, showed that Zicrona caerulea belongs to Asopinae. The monophyly of families of the Pentatomoidea is supported, albeit limited taxon sampling. 

The mitochondrial genome of Leuctra sp. (Plecoptera: Leuctridae) and its performance in phylogenetic analyses

Zootaxa ◽  
2019 ◽  
Vol 4671 (4) ◽  
pp. 571-580 ◽  
Author(s):  
YUE SHEN ◽  
YU-ZHOU DU
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Likelihood Methods ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Rna Genes ◽  
Drosophila Yakuba

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae). 

scholarly journals Comparative Mitochondrial Genome Analysis of Eligma narcissus and other Lepidopteran Insects Reveals Conserved Mitochondrial Genome Organization and Phylogenetic Relationships

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Li-Shang Dai ◽  
Bao-Jian Zhu ◽  
Yue Zhao ◽  
Cong-Fen Zhang ◽  
Chao-Liang Liu
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Relationships ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Lepidopteran Insects ◽  
Usage Analysis ◽  
Mitochondrial Trna Genes ◽  
Cloverleaf Structure

Abstract In this study, we sequenced the complete mitochondrial genome of Eligma narcissus and compared it with 18 other lepidopteran species. The mitochondrial genome (mitogenome) was a circular molecule of 15,376 bp containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an adenine (A) + thymine (T) − rich region. The positive AT skew (0.007) indicated the occurrence of more As than Ts. The arrangement of 13 PCGs was similar to that of other sequenced lepidopterans. All PCGs were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which was initiated by the CGA sequence, as observed in other lepidopterans. The results of the codon usage analysis indicated that Asn, Ile, Leu, Tyr and Phe were the five most frequent amino acids. All tRNA genes were shown to be folded into the expected typical cloverleaf structure observed for mitochondrial tRNA genes. Phylogenetic relationships were analyzed based on the nucleotide sequences of 13 PCGs from other insect mitogenomes, which confirmed that E. narcissus is a member of the Noctuidae superfamily.

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