Complete mitochondrial genome of the mangrove whipray
            <i>Himantura granulata</i>
            (Myliobatiformes: Dasyatidae)

Chen, Xiao; Xiang, Dan; Arunrugstichai, Sirachai; Cai, Ling; Xu, Yuziwei

doi:10.3109/19401736.2013.865178

Cited by 22 publications

(22 citation statements)

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“…The unorthodox trnS1 (AGN) is commonplace among all sequenced monogeneans [ 12 , 15 , 16 , 22 – 24 , 45 – 51 ], and possibly even all flatworms [ 42 ]. The unpaired DHU-arm in tRNA cys was also reported in most monogeneans apart from Pseudochauhanea macrorchis , M. sebastis , Polylabris halichoeres (Wang & Yang, 1998), T. nebulosi and N. melleni [ 16 , 22 , 23 , 45 , 52 ]. A slight preference for the A nucleotide (AT skewness, 0.013) was found in concatenated tRNAs of the P. inermis mt genome, which is an exclusive feature among the analyzed monogeneans (Fig.…”

Section: Resultsmentioning

confidence: 74%

Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny

Zhang

Zou

et al. 2017

Parasites Vectors

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Background Paratetraonchoides inermis (Monogenea: Tetraonchoididae) is a flatworm parasitising the gills of uranoscopid fishes. Its morphological characteristics are ambiguous, and molecular data have never been used to study its phylogenetic relationships, which makes its taxonomic classification controversial. Also, several decades of unsuccessful attempts to resolve the relationships within the Monogenea present a strong indication that morphological datasets may not be robust enough to be used to infer evolutionary histories. As the use of molecular data is currently severely limited by their scarcity, we have sequenced and characterized the complete mitochondrial (mt) genome of P. inermis. To investigate its phylogenetic position, we performed phylogenetic analyses using Bayesian inference and maximum likelihood approaches using concatenated amino acid sequences of all 12 protein-coding genes on a dataset containing all available monogenean mt genomes.ResultsThe circular mt genome of P. inermis (14,654 bp) contains the standard 36 genes: 22 tRNAs, two rRNAs, 12 protein-encoding genes (PCGs; Atp8 is missing) and a major non-coding region (mNCR). All genes are transcribed from the same strand. The A + T content of the whole genome (82.6%), as well as its elements, is the highest reported among the monogeneans thus far. Three tRNA-like cloverleaf structures were found in mNCR. Several results of the phylogenomic analysis are in disagreement with previously proposed relationships: instead of being closely related to the Gyrodactylidea, Tetraonchidea exhibit a phylogenetic affinity with the Dactylogyridea + Capsalidea clade; and the order Capsalidea is neither basal within the subclass Monopisthocotylea, nor groups with the Gyrodactylidea, but instead forms a sister clade with the Dactylogyridea. The mt genome of P. inermis exhibits a unique gene order, with an extensive reorganization of tRNAs. Monogenea exhibit exceptional gene order plasticity within the Neodermata.ConclusionsThis study shows that gene order within monopisthocotylid mt genomes is evolving at uneven rates, which creates misleading evolutionary signals. Furthermore, our results indicate that all previous attempts to resolve the evolutionary history of the Monogenea may have produced at least partially erroneous relationships. This further corroborates the necessity to generate more molecular data for this group of parasitic animals.Electronic supplementary materialThe online version of this article (10.1186/s13071-017-2404-1) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 74%

Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny

Zhang

Zou

et al. 2017

Parasites Vectors

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“…In the previous sequenced complete mt genome of the order Stylommatophora, the noncoding regions range from 1 bp to 65 bp (Hatzoglou et al 1995; Terrett et al 1995; Yamazaki et al 1997; White et al 2011; Groenenberg et al 2012; Gaitán-Espitia et al 2013; Deng et al 2014; Wang et al 2014) except Achatina fulica with 551 bp length (He et al 2014). In metazoan mt genomes, these noncoding regions are normal.…”

Section: Discussionmentioning

confidence: 99%

“…Usually, changes in length of the whole mt genome are mainly caused by difference of the control region (Zhang and Hewitt 1997). However, the control region may not be aligned accurately in gastropods (Groenenberg et al 2012) except in Achatina fulica which included a 551 bp (POR)putative control region between COI and tRNA Val (He et al 2014). Another ten sequenced stylommatophoran species may possess short putative control region located in different places (Hatzoglou et al 1995; Terrett et al 1995; Yamazaki et al 1997; White et al 2011; Groenenberg et al 2012; Gaitán-Espitia et al 2013; Deng et al 2014; Wang et al 2014; Huang et al 2015; 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Annotations and editing procedures of the mitochondrial genomes of Cernuella virgata were performed in MEGA5.0. Mitochondrial PCGs and rRNA genes were identified by BLAST searches at NCBI against other Eupulmonata sequences (Wang et al 2014; He et al 2014; Deng et al 2014; Yang et al 2014). The limits of both protein coding and rRNA genes were adjusted manually based on location of adjacent genes, and the presence of start and stop codons.…”

Section: Methodsmentioning

confidence: 99%

“…It has been extensively used to study the origin of species, phylogeography and population genetic structure and so on due to its small genome size, fast evolution, uniparental inheritance and lack of extensive recombination (Saccone et al 1999; Elmerot et al 2002). To date, only nine species from the order Stylommatophora have been determined as dispersing in Helicidae (Terrett et al 1995; Groenenberg et al 2012; Gaitán-Espitia et al 2013), Bradybaenidae (Yamazaki et al 1997; Deng et al 2014), Clausiliidae (Hatzoglou et al 1995), Succineidae (White et al 2011), Achatinidae (He et al 2014) and Camaenidae (Wang et al 2014). However, there are no reports on the mt genome of the family Hygromiidae.…”

Section: Introductionmentioning

confidence: 99%

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The mitochondrial genome of the land snail Cernuella virgata (Da Costa, 1778): the first complete sequence in the family Hygromiidae (Pulmonata, Stylommatophora)

Lin¹,

Zhou²,

Ding³

et al. 2016

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The land snail Cernuella virgata (da Costa, 1778) is widely considered as a pest to be quarantined in most countries. In this study, the complete mitochondrial genome of Cernuella virgata is published. The mitochondrial genome has a length of 14,147 bp a DNA base composition of 29.07% A, 36.88% T, 15.59% C and 18.46% G, encoding 13 (PCGs)protein-coding genes , 22 (tRNA)transfer RNA genes and two (rRNA)ribosomal RNA genes. The complete nucleotide composition was biased toward adenine and thymine, A+T accounting for 69.80%. Nine PCGs and 14 tRNA genes are encoded on the J strand, and the other four PCGs and eight tRNA genes are encoded on the N strand. The genome also includes 16 intergenic spacers. All PCGs start strictly with ATN, and have conventional stop codons (TAA and TAG). All tRNAs fold into the classic cloverleaf structure, except tRNAArg, tRNASer(UCN), tRNASer(AGN) and tRNAPro. The first three lack the dihydrouridine arm while the last lacks the TψC arm. There are 502 bp long noncoding regions and 418bp long gene overlaps in the whole mitochondrial genome, accounting for 3.54% and 2.95% of the total length respectively. Phylogenetic analyses based on the sequences of the protein coding genes revealed a sister group relationship between the Hygromiidae and the Helicidae.

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Characterization and comparison of the complete mitochondrial genomes of two stingrays, Dasyatis pastinaca and Dasyatis tortonesei (Myliobatiformes: Dasyatidae) from the Mediterranean Sea

Vella

2021

Mol Biol Rep

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Complete mitochondrial genome of the mangrove whipray Himantura granulata (Myliobatiformes: Dasyatidae)

Cited by 22 publications

References 1 publication

Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny

Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny

The mitochondrial genome of the land snail Cernuella virgata (Da Costa, 1778): the first complete sequence in the family Hygromiidae (Pulmonata, Stylommatophora)

Characterization and comparison of the complete mitochondrial genomes of two stingrays, Dasyatis pastinaca and Dasyatis tortonesei (Myliobatiformes: Dasyatidae) from the Mediterranean Sea

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