Characterization of the Whole Mitogenome of Largehead Hairtail Trichiurus lepturus (Trichiuridae): Insights into Special Characteristics

Mukundan, Lakshmi; Sukumaran, Sandhya; Sebastian, Wilson; Gopalakrishnan, A

doi:10.1007/s10528-020-09956-z

Cited by 7 publications

(15 citation statements)

References 67 publications

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“…One of the 13 PCGs (ND6), seven tRNAcoding genes (Gln, Ala, Asn, Cys, Tyr, Ser, Glu), and one noncoding region (OL) are encoded on the L-strand, and the other 28 genes (12 PCGs, 14 tRNA-coding genes, and 2 rRNA-coding genes) and d-loop are encoded on the H-strand. The composition and arrangement of the mitochondrial genes in these four species were the same as those in T. gangeticus in the Indian Ocean (MK333401 in Mukundan et al 2020). To characterize variation among the Trichiurus mitogenomes, we analyzed the base composition of T. gangeticus in the Indian Ocean (Mukundan et al 2020).…”

Section: Genome Organization Base Composition and Ratesmentioning

confidence: 68%

“…The composition and arrangement of the mitochondrial genes in these four species were the same as those in T. gangeticus in the Indian Ocean (MK333401 in Mukundan et al 2020). To characterize variation among the Trichiurus mitogenomes, we analyzed the base composition of T. gangeticus in the Indian Ocean (Mukundan et al 2020). We found the mean AT nucleotide content of the five complete mitogenomes to be similar (55.0% in T. japonicus, 55.1% in T. lepturus, 54.4% in T. nanhaiensis, 54.3% in T. gangeticus and 54.6% in T. brevis; Table 5).…”

Section: Genome Organization Base Composition and Ratesmentioning

confidence: 68%

“…3), the sequences of the genus Trichiurus were grouped into five lineages (I-V). Trichiurus haumela (MH846121 in Zheng et al 2019) was included within T. japonicus (lineage I), and T. lepturus (MW719078) in our study and "T. lepturus" (MK333401 in Mukundan et al 2020) were not considered monophyletic (lineages II and III). Thus, our study used COI sequences to examine the taxonomic status of Trichiurus species.…”

Section: Species Identificationmentioning

confidence: 97%

“…The remaining high-quality reads were assembled using SPAdes v3.10 (https://github.com/ablab/spades). Compared with the corresponding complete mitogenome sequences of the genus Trichiurus (Liu and Cui 2009;Liu et al 2013;Xu et al 2019;Zheng et al 2019;Mukundan et al 2020; Table 1), protein-coding genes (PCGs), tRNA-coding genes and ribosome-coding genes were identified by BLAST. Codon usage, nucleotide substitution and base composition were determined using MEGA-X and DnaSP version 5.10 (Librado and Rozas 2009), and the rules for the vertebrate mitochondrial genetic code was used.…”

Section: Sequence Assembly Annotation and Analysismentioning

confidence: 99%

“…Trichiurus haumela (MH846121 in Zheng et al 2019) was also included within T. japonicus in lineage A. The specimen from the Indian Ocean (MK333401 in Mukundan et al 2020) might be not T. lepturus, as it was grouped with other specimens of T. gangeticus in lineage E. The genetic distance within the six lineages ranged from 0.0013 (lineage F, T. brevis) to 0.0333 (lineage C, T. lepturus), and the genetic distance between lineages ranged from 0.0435 (between T. japonicus and T. auriga) to 0.1600 (between T. japonicus and T. brevis) (Table 2). Based on the mitogenomes, the genetic distances between these five species ranged from 0.0507 (T. nanhaiensis and T. gangeticus) to 0.1331 (T. gangeticus and T. brevis), including the d-loop region, and from 0.0476 (T. nanhaiensis and T. gangeticus) to 0.1288 (T. lepturus and T. brevis), excluding the d-loop region (Table 2).…”

Section: Species Identificationmentioning

confidence: 99%

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Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

Yi¹,

Hsu²,

Gu³

et al. 2022

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Four Trichiurus species, T. japonicus, T. lepturus, T. nanhaiensis, and T. brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T. gangeticus. The mitogenomes contained 16.568–16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T. lepturus nor T. nanhaiensis but they are T. gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.

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Section: Genome Organization Base Composition and Ratesmentioning

confidence: 68%

Section: Genome Organization Base Composition and Ratesmentioning

confidence: 68%

Section: Species Identificationmentioning

confidence: 97%

Section: Sequence Assembly Annotation and Analysismentioning

confidence: 99%

Section: Species Identificationmentioning

confidence: 99%

See 3 more Smart Citations

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

Yi¹,

Hsu²,

Gu³

et al. 2022

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Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data

Mthethwa

Merwe

Roodt‐Wilding

2023

Ecology and Evolution

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The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we assembled eight complete novel mitochondrial genomes for five Gempylidae species (Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun) using Ion Torrent sequencing to supplement publicly available mitogenome data for gempylids. Using Bayesian inference and maximum-likelihood tree search methods, we investigated the evolutionary relationships of 17 Gempylidae species using mitogenome data. In addition, we estimated divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89-52.04) million years ago: Gempylidae 1 (Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus) and Gempylidae 2 (Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis). The present study demonstrated the superior performance of complete mitogenome data compared with individual genes in phylogenetic reconstruction. By including T. atun individuals from different regions, we demonstrated the potential for the application of mitogenomes in species phylogeography.

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Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS‐2019 and phylogenetic analysis of the Myriapoda

Zuo

Zhang

Shen

2022

Ecology and Evolution

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The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS‐2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT‐skew (−0.236). Several genes rearrangements were detected and we propose a new rearrangement model: “TD (N\R) L + C” based on the genome‐scale duplication + (non‐random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.

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Characterization of the Whole Mitogenome of Largehead Hairtail Trichiurus lepturus (Trichiuridae): Insights into Special Characteristics

Cited by 7 publications

References 67 publications

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data

Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS‐2019 and phylogenetic analysis of the Myriapoda

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Characterization of the Whole Mitogenome of Largehead Hairtail Trichiurus lepturus (Trichiuridae): Insights into Special Characteristics

Cited by 7 publications

References 67 publications

﻿Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

﻿Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data

Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS‐2019 and phylogenetic analysis of the Myriapoda

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Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex