Mitochondrial genome of Chinese grass shrimp, Palaemonetes sinensis and comparison with other Palaemoninae species

AbstractThe mitogenome of Chinese grass shrimp, Palaemonetes sinensis, was determined through Illumina sequencing, and the basic characteristics and gene arrangement were analyzed. The mitogenome of P. sinensis was 15955 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and one control region, with tightly packed. 33 of these genes were encoded on the heavy strand, and the remainders encoded on the light strand. The composition of P. sinensis mitogenome presented a strong A + T bias, which account for 66.7%. All PCGs were initiated by a canonical ATN codon, except nad5, which was initiated by GTG. The termination codons of the PCGs were TAA, TAG and T–. The secondary structures of 22 tRNAs of P. sinensis had the typical clover structure, except of trnS1 owing to the lack of dihydroxyuridine (DHU) arm. Gene order comparison of P. sinensis and previously-sequenced Palaemoninae revealed a unique translocation between trnT and trnP in Macrobrachium. The phylogenetic analyses showed that three Exopalaemon species formed a monophyletic group and then clustered with two Palaemon species and P. sinensis successively whereas Macrobrachium clustered with Palaemon capensis in the other clade.

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A novel rearrangement in the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region translocation and a tRNA gene inversion

Genome ◽

10.1139/g09-069 ◽

2009 ◽

Vol 52 (12) ◽

pp. 975-984 ◽

Cited By ~ 48

Author(s):

Xiaoyu Kong ◽

Xiaoli Dong ◽

Yanchun Zhang ◽

Wei Shi ◽

Zhongming Wang ◽

...

Keyword(s):

Control Region ◽

Molecular Mechanisms ◽

Cynoglossus Semilaevis ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Heavy Strand ◽

Light Strand ◽

Putative Control Region

The organization of fish mitochondrial genomes (mitogenomes) is quite conserved, usually with the heavy strand encoding 12 of 13 protein-coding genes and 14 of 22 tRNA genes, and the light strand encoding ND6 and the remaining 8 tRNA genes. Currently, there are only a few reports on gene reorganization of fish mitogenomes, with only two types of rearrangements (shuffling and translocation) observed. No gene inversion has been detected in approximately 420 complete fish mitogenomes available so far. Here we report a novel rearrangement in the mitogenome of Cynoglossus semilaevis (Cynoglossinae, Cynoglossidae, Pleuronectiformes). The genome is 16 371 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 main noncoding regions, the putative control region and the light-strand replication origin. A striking finding of this study is that the tRNAGln gene is translocated from the light to the heavy strand (Q inversion). This is accompanied by shuffling of the tRNAIle gene and long-range translocation of the putative control region downstream to a site between ND1 and the tRNAGln gene. The remaining gene order is identical to that of typical fish mitogenomes. Additionally, unique characters of this mitogenome, including a high A+T content and length variations of 8 protein-coding genes, were found through comparison of the mitogenome sequence with those from other flatfishes. All the features detected and their relationships with the rearrangements, as well as a possible rearrangement pathway, are discussed. These data provide interesting information for better understanding the molecular mechanisms of gene reorganization in fish mitogenomes.

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Characterization of the mitochondrial genome of Diphyllobothrium latum (Cestoda: Pseudophyllidea) – implications for the phylogeny of eucestodes

Parasitology ◽

10.1017/s003118200600206x ◽

2006 ◽

Vol 134 (5) ◽

pp. 749-759 ◽

Cited By ~ 19

Author(s):

J.-K. PARK ◽

K.-H. KIM ◽

S. KANG ◽

H. K. JEON ◽

J.-H. KIM ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Amino Acid Sequences ◽

Hymenolepis Diminuta ◽

Rrna Genes ◽

Gene Arrangement ◽

Protein Coding ◽

Protein Coding Genes ◽

Diphyllobothrium Latum

SUMMARYThe complete nucleotide sequence of the mitochondrial genome was determined for the fish tapeworm Diphyllobothrium latum. This genome is 13 608 bp in length and encodes 12 protein-coding genes (but lacks the atp8), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes, corresponding to the gene complement found thus far in other flatworm mitochondrial (mt) DNAs. The gene arrangement of this pseudophyllidean cestode is the same as the 6 cyclophyllidean cestodes characterized to date, with only minor variation in structure among these other genomes; the relative position of trnS2 and trnL1 is switched in Hymenolepis diminuta. Phylogenetic analyses of the concatenated amino acid sequences for 12 protein-coding genes of all complete cestode mtDNAs confirmed taxonomic and previous phylogenetic assessments, with D. latum being a sister taxon to the cyclophyllideans. High nodal support and phylogenetic congruence between different methods suggest that mt genomes may be of utility in resolving ordinal relationships within the cestodes. All species of Diphyllobothrium infect fish-eating vertebrates, and D. latum commonly infects humans through the ingestion of raw, poorly cooked or pickled fish. The complete mitochondrial genome provides a wealth of genetic markers which could be useful for identifying different life-cycle stages and for investigating their population genetics, ecology and epidemiology.

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The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): insight into the deep-sea adaptive evolution of vesicomyids

10.1101/648121 ◽

2019 ◽

Cited By ~ 1

Author(s):

Mei Yang ◽

Lin Gong ◽

Jixing Sui ◽

Xinzheng Li

Keyword(s):

Energy Metabolism ◽

Mitochondrial Genome ◽

Adaptive Evolution ◽

Deep Sea ◽

Phylogenetic Analyses ◽

Gene Arrangement ◽

Protein Coding ◽

Mitochondrial Energy Metabolism ◽

Protein Coding Genes ◽

Rna Genes

AbstractThe deep sea is one of the most extreme environments on earth, with low oxygen, high hydrostatic pressure and high levels of toxins. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, “G(A)nT” motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea environment.

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Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

Scientific Reports ◽

10.1038/s41598-020-78082-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Meng-Yuan Zhao ◽

Qing-Bo Huo ◽

Yu-Zhou Du

Keyword(s):

Ribosomal Rna ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

The Other ◽

Mitochondrial Genomes ◽

Stem Loop ◽

Protein Coding ◽

Protein Coding Genes ◽

Noncoding Control Region ◽

Rna Genes

AbstractIn this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

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Novel Gene Rearrangement in the Mitochondrial Genome of Anastatus Fulloi (Hymenoptera Chalcidoidea) and Phylogenetic Implications for Chalcidoidea

10.21203/rs.3.rs-1123217/v1 ◽

2021 ◽

Author(s):

Jiequn Yi ◽

Han Wu ◽

Jianbai Liu ◽

Jihu Li ◽

Yinglin Lu ◽

...

Keyword(s):

Large Scale ◽

Phylogenetic Analyses ◽

Rrna Genes ◽

Gene Arrangement ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Novel Gene ◽

Phylogenetic Implications ◽

Relationship Of

Abstract The genus Anastatus comprises a large group of parasitoids, including several biological control agents in agricultural and forest systems. The taxonomy and phylogeny of these species remain controversial. In this study, the mitogenome of A. fulloi Sheng and Wang was sequenced and characterized. The nearly full-length mitogenome of A. fulloi was 15,692 bp, compromising 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes and a control region (CR). The total A + T contents were 83.83%, 82.18%, 87.58%, 87.27%, and 82.13% in the whole mitogenome, 13 PCGs, 22 tRNA genes, 2 rRNA genes, and CR, respectively. The mitogenome presented negative AT skews and positive GC skews, except for the CR. Most PCGs were encoded on the majority strand, started with ATN codons, and ended with TAA codons. Among the 3736 amino acid-encoding codons, TTA (Leu1), CGA (Arg), TCA (Ser2), and TCT (Ser2) were predominant. Most tRNAs had cloverleaf secondary structures, except trnS1, with the absence of a dihydrouridine (DHU) arm. Compared with mitogenomes of the ancestral insect and another parasitoid within Eupelmidae, large-scale rearrangements were found in the mitogenome of A. fulloi, especially inversions and inverse transpositions of tRNA genes. The gene arrangements of parasitoid mitogenomes within Chalcidoidea were variable. A novel gene arrangement was presented in the mitogenome of A. fulloi. Phylogenetic analyses based on the 13 protein-coding genes of 20 parasitoids indicated that the phylogenetic relationship of 6 superfamilies could be presented as Mymaridae + (Eupelmidae + (Encyrtidae + (Trichogrammatidae + (Pteromalidae + Eulophidae)))). This study presents the first complete mitogenome of the Anastatus genus and offers insights into the identification, taxonomy, and phylogeny of these parasitoids.

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Legionella becoming a mutualist: adaptive processes shaping the genome of symbiont in the louse Polyplax serrata

10.1101/155820 ◽

2017 ◽

Author(s):

Jana Říhová ◽

Eva Nováková ◽

Filip Husník ◽

Václav Hypša

Keyword(s):

Convergent Evolution ◽

Phylogenetic Analyses ◽

Gc Content ◽

The Other ◽

Intracellular Bacteria ◽

Metabolic Function ◽

Protein Coding ◽

Protein Coding Genes ◽

Adaptive Processes ◽

Insect Symbionts

AbstractLegionellaceae are intracellular bacteria known as important pathogens of man. In the environment, they are mainly found in biofilms associated with amoebas. In contrast to another gammaproteobacterial family Enterobacteriaceae which established a broad spectrum of symbioses with many insect taxa, the only instance of legionella-like symbiont has been reported from lice of the genus Polyplax. Here, we sequenced the complete genome of this symbiont and compared its main characteristics to other Legionella species and insect symbionts. Based on rigorous multigene phylogenetic analyses, we confirm this bacterium as a member of the genus Legionella and propose the name Candidatus Legionella polyplacis, sp.n. We show that the genome of Ca. Legionella polyplacis underwent massive degeneration, including considerable size reduction (529.746 bp, 484 protein coding genes) and a severe decrease in GC content (23%). We identify several possible constraints underlying the evolution of this bacterium. On one hand, Ca. Legionella polyplacis and the louse symbionts Riesia and Puchtella experienced convergent evolution, perhaps due to adaptation to similar hosts. On the other hand, some metabolic differences are likely to reflect different phylogenetic positions of the symbionts and hence availability of particular metabolic function in the ancestor. This is exemplified by different arrangements of thiamine metabolism in Ca. Legionella polyplacis and Riesia. Finally, horizontal gene transfer is shown to play a significant role in the adaptive and diversification process. Particularly, we show that Ca. L. polyplacis horizontally acquired a complete biotin operon (bioADCHFB) that likely assisted this bacterium when becoming an obligate mutualist.

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Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽

10.11646/zootaxa.4952.2.7 ◽

2021 ◽

Vol 4952 (2) ◽

pp. 331-353

Author(s):

CHAO YANG ◽

LE ZHAO ◽

QINGXIONG WANG ◽

HAO YUAN ◽

XUEJUAN LI ◽

...

Keyword(s):

Secondary Structure ◽

Gene Order ◽

Phylogenetic Relationships ◽

Gene Rearrangement ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Comparative Analyses ◽

Protein Coding Genes ◽

Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies.

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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 ◽

10.7717/peerj.10364 ◽

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.

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Phylogenetics and revised taxonomy of the Australian freshwater cod genus, Maccullochella (Percichthyidae)

Marine and Freshwater Research ◽

10.1071/mf09145 ◽

2010 ◽

Vol 61 (9) ◽

pp. 980 ◽

Cited By ~ 12

Author(s):

Catherine J. Nock ◽

Martin S. Elphinstone ◽

Stuart J. Rowland ◽

Peter R. Baverstock

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Strong Support ◽

Taxonomic Revision ◽

Protein Coding ◽

Protein Coding Genes ◽

Allopatric Populations ◽

Murray Darling Basin ◽

Murray Cod ◽

Australian Freshwater

Determining the phylogenetic and taxonomic relationships among allopatric populations can be difficult, especially when divergence is recent and morphology is conserved. We used mitochondrial sequence data from the control region and three protein-coding genes (1253 bp in total) and genotypes determined at 13 microsatellite loci to examine the evolutionary relationships among Australia’s largest freshwater fish, the Murray cod, Maccullochella peelii peelii, from the inland Murray–Darling Basin, and its allopatric sister taxa from coastal drainages, the eastern freshwater cod, M. ikei, and Mary River cod, M. peelii mariensis. Phylogenetic analyses provided strong support for taxon-specific clades, with a clade containing both of the eastern taxa reciprocally monophyletic to M. peelii peelii, suggesting a more recent common ancestry between M. ikei and M. peelii mariensis than between the M. peelii subspecies. This finding conflicts with the existing taxonomy and suggests that ancestral Maccullochella crossed the Great Dividing Range in the Pleistocene and subsequently diverged in eastern coastal drainages. Evidence from the present study, in combination with previous morphological and allozymatic data, demonstrates that all extant taxa are genetically and morphologically distinct. The taxonomy of Maccullochella is revised, with Mary River cod now recognised as a species, Maccullochella mariensis, a sister species to eastern freshwater cod, M. ikei. As a result of the taxonomic revision, Murray cod is M. peelii.

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Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

International Journal of Molecular Sciences ◽

10.3390/ijms19082383 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2383 ◽

Cited By ~ 8

Author(s):

Qixiang Lu ◽

Wenqing Ye ◽

Ruisen Lu ◽

Wuqin Xu ◽

Yingxiong Qiu

Keyword(s):

Gene Order ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Early Pleistocene ◽

Disjunct Distribution ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Intergenic Spacers ◽

Protein Coding Genes

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

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