The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae): Comparative analysis

Chakraborty, Rajasree; Tyagi, Kaomud; Kundu, Shantanu; Rahaman, Iftikar; Singha, Devkant; Chandra, Kailash; Patnaik, Srinivas; Kumar, Vikas

doi:10.1371/journal.pone.0199404

Cited by 24 publications

(20 citation statements)

References 51 publications

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“…These pairwise tests of the Ks and Ka substitutions were evidence of the adaptive evolution in vertebrates and other species (Montoya‐Burgos, ; Yang & Nielsen, ). It was stated that, the Ka/Ks > 1 evidenced for positive selection, Ka/Ks = 1 for neutrality, and Ka/Ks < 1 for negative selection (Chakraborty et al, ). To explore evolutionary rates, Ka/Ks substitutions were calculated for P. tentoria and other Geoemydid species mitogenomes.…”

Section: Resultsmentioning

confidence: 99%

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

Kundu

Kumar

Tyagi

et al. 2019

Ecology and Evolution

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The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next‐generation sequencing. This denovo assembly encodes 37 genes: 13 protein‐coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with “GTG” and NADH dehydrogenase subunit 5 with “ATA.” The termination codons, “TAA” and “AGA” were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3′ end of CR. Further, two copies of a unique tandem repeat “TTCTCTTT” were identified in P. tentoria. The Bayesian and maximum‐likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in‐depth phylogenetic and evolutionary relationships.

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Section: Resultsmentioning

confidence: 99%

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

Kundu

Kumar

Tyagi

et al. 2019

Ecology and Evolution

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“…Ltd. Bangalore, India (http://www.genotypic.co.in/) had carried out the sequencing. The sequencing and assembly protocol was followed by our previous study 20,21 . The whole genome library of genomic DNA was sequenced using Illumina Hiseq.…”

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confidence: 99%

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

Kumar

Tyagi

Chakraborty

et al. 2020

Sci Rep

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Rajasree chakraborty, priya prasad, Shantanu Kundu, inderjeet tyagi & Kailash chandra the 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. The order Araneae is classified into two infra-orders Mesothelae (primitive spiders) and Opisthothelae (modern spiders). The infra-order Opisthothelae is further classified into two suborders Mygalomorphae and Araneomorphae with 117 families. The family Theraphosidae belongs to suborder Mygalomorphae of infra-order Opisthothelae with 992 species. Out of 992 species, 52 species are known from India 1. The members of family Theraphosidae are commonly known as tarantulas or giant spiders for their huge body size. These giant spiders play an important role in controlling the insects 2 and also predators on vertebrates and invertebrates 3. The venom of these tarantulas is the main source of pharmacological research 3. The Pet trade of tarantulas across the globe is in great demand due to their body size, attractiveness, longitivity and for economic point of view 4. So far, 13 species in three genera (Poecilotheria, Thrigmopoeus and Lyrognathus) from India have been reported in the pet trade 4. The species Lyrognathus crotalus is endemic to India restricted to northeast region and frequently traded. The correct identification of these tarantulas is the basic need due to their economical and medicinal values and involvement in the pet trade. However, identification of species in the absence of well-preserved specimens is not possible through morphology ...

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“…Analysis of mtDnA genomes. The mtDNA genetic diversity of HA-Tajiks (including haplotype numbers, nucleotide and haplotype diversity, Tajima's D, and Fu's Fs) was calculated by DnaSP6.0 28 . The genetic distances between the HA-Tajiks and the reference populations based on the mtDNA genomes were analyzed by PCA based on the haplogroup distributions in different populations after normalized transformation 29 .…”

Section: Resultsmentioning

confidence: 99%

Mitochondrial DNA genomes revealed different patterns of high-altitude adaptation in high-altitude Tajiks compared with Tibetans and Sherpas

Chen

Gong

Liu

et al. 2020

Sci Rep

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High-altitude Tajiks (HA-Tajiks), Tibetans and Sherpas are three groups of high-altitude native people in China. The differences in the mtDNA genome between the three populations and the role of the mtDNA genome in the high-altitude adaptation of HA-Tajiks were seldom investigated. In this study, 80 HA-Tajiks were enrolled, and their whole mtDNA genomes were sequenced. The haplogroup of each subject was determined by comparison to the revised Cambridge Reference Sequence (rCRS). Ten additional populations from East Asia and Central Asia, including Tibetans and Sherpas, were selected as references. The top haplogroup was U, followed by H, T and J. Principle component analysis and genetic distance analysis indicated that HA-Tajiks showed a close relationship with Wakhi Tajiks, pamiri tajiks and Sarikoli tajiks, indicating that they should be considered one nation scattered around the Pamirs. The difference in the mtDNA genome between HA-Tajiks and Sherpas was significantly greater than that between HA-Tajiks and Tibetans. Among the 13 genes related to the OXPHOS pathway encoded by the mtDNA genome, HA-Tajiks showed more significant differences in ND3 and CYTB compared to Tibetans. Compared to Sherpas, HA-Tajiks showed more significant differences in ND1, ND2, COX1, ATP8, ATP6, ND3, ND4L, ND4, ND5 and CYTB. The associated functional changes and underlying molecular mechanisms should be explored by molecular and biochemical investigations in further studies. When humans spread throughout the Earth, high-altitude environments presented a significant challenge to the people living within them. Low air pressure, hypoxia, strong solar radiation and low temperature exert great pressure on the survival of local people. Genetic factors in both the nuclear genome and mitochondrial DNA (mtDNA) genome play great roles in the adaptation to high-altitude environments, which was considered as natural impacts on human evolution and adaptation 1. In the past few years, an increasing number of genetic studies on the nuclear genome have shown that a series of genes have been involved in high-altitude adaptation in Tibetans 2-8 , Andeans 8,9 and Ethiopians 10,11 , and these genes are mainly distributed in the hypoxia-inducible factor signaling pathway and the TP53 pathway. However, the role of the mtDNA genome in high-altitude adaptation are still in discussion and should receive more attention. Mitochondria are known as the cell's power plant, where cellular fuel is oxidized to provide energy for metabolism. Mitochondrial function is dependent on mtDNA, and mtDNA is well established as a genetic marker. A high mutation rate, small genome size, maternal inheritance, and lack of recombination make mtDNA an important tool for studying genetic structure in different populations. Besides, analyses of mtDNA sequences provide clues for exploring the genetic relationships between different populations, which contributes to deep understanding the role of mtDNA variations in human evolution. In addition to 2 rRNAs and 22 tRNAs, mtDNA encodes 1...

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The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae): Comparative analysis

Cited by 24 publications

References 51 publications

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

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

Mitochondrial DNA genomes revealed different patterns of high-altitude adaptation in high-altitude Tajiks compared with Tibetans and Sherpas

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