The complete mitochondrial genome of the mudsnail
            <i>Cipangopaludina cathayensis</i>
            (Gastropoda: Viviparidae)

Yang, Huirong; Zhang, Jiaen; Luo, Hao; Luo, Ming; Guo, Jing; Deng, Zhixin; Zhao, Benliang

doi:10.3109/19401736.2014.971274

Cited by 15 publications

(25 citation statements)

References 13 publications

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“…Two other helicid species had PORs located between COIII and tRNA Ser with lengths of 158–186 bp, whereas the PORs of Albinaria caerulea (65 bp), Aegista diversifamilia (93 bp), Cylindrus obtusus (395 bp) and Euhadra herklotsi (78 bp) were specific, respectively between ND3 and tRNA Ser , tRNA Met and tRNA Ser , ND5 and tRNA Ala , tRNA Se r (UCN) and tRNA Ser(AGN) . The absence of a control region was consistent with other gastropods (Deng et al 2014; Wang et al 2014; Yang et al 2014). In the present study, the longest noncoding region was 149 bp, which was the second longest one by far.…”

Section: Discussionsupporting

confidence: 87%

“…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%

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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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Section: Discussionsupporting

confidence: 87%

Section: Methodsmentioning

confidence: 99%

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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“…S-rRNA and L-rRNA genes are 877 and 1381 bp, respectively, located between the tRNA Glu and tRNA Leu genes and separated by the tRNA Val gene. Overall nucleotide compositions of the light strand in descending order are 40.97% of A, 30.78% of T, 20.48% of C and 12.60% of G. Gene arrangement and distribution are different from the typical vertebrates (Yang et al 2014a(Yang et al , 2016a) and similar to Cipangopaludina cathayensis (Yang et al 2014b). The absence of D-loop is consistent with the Gastropoda (Liu et al 2012;Zeng et al 2015;Zhou et al 2016), but, at least, one lengthy non-coding region is an essential regulatory element for the initiation of transcription and replication (Wolstenholme 1992).…”

mentioning

confidence: 88%

The complete mitochondrial genome of the golden apple snail Pomacea canaliculata (Gastropoda: Ampullariidae)

Yang

Zhang

Deng

et al. 2016

Mitochondrial DNA Part B

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We present the complete mitochondrial genome of Cipangopaludina cathayensis in this study. The mitochondrial genome is 15 706 bp in length, containing 13 protein-coding genes, two rRNA genes and 22 tRNA genes. Overall nucleotide compositions of the light strand are 40.97% of A, 30.78% of T, 20.48% of C and 12.60% of G. Its gene arrangement and distribution are different from the typical vertebrates. The absence of D-loop is consistent with the Gastropoda, but, at least, one lengthy non-coding region is an essential regulatory element for the initiation of transcription and replication. A phylogenetic tree is constructed using the maximum-likelihood method based on the complete mitogenomes of the closely related 21 Gastropoda species to assess their actual phylogenetic relationship and evolution. The result provides fundamental data for resolving phylogenetic and genetic problems related to effective management strategies.

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“…As mitogenomes of some molluscan groups are known to exhibit extensive genome length and architecture instability [26], besides its use as a phylogenetic marker, the availability of complete mitogenomic sequences for different organisms provides a good model system for decoding the mechanisms of mitogenomic evolution [24, 27]. Only one complete viviparid mitogenome has been published so far, Cipangopaludina cathayensis [28], and two more are currently (Feb 2017) available from the GenBank: Bellamya quadrata and another C . cathayensis (both unpublished).…”

Section: Introductionmentioning

confidence: 99%

Sequencing of the complete mitochondrial genomes of eight freshwater snail species exposes pervasive paraphyly within the Viviparidae family (Caenogastropoda)

et al. 2017

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Phylogenetic relationships among snails (Caenogastropoda) are still unresolved, and many taxonomic categories remain non-monophyletic. Paraphyly has been reported within a large family of freshwater snails, Viviparidae, where the taxonomic status of several species remains questionable. As many endemic Chinese viviparid species have become endangered during the last few decades, this presents a major obstacle for conservation efforts. Mitochondrial genomes (mitogenomes) carry a large amount of data, so they can often provide a much higher resolution for phylogenetic analyses in comparison to the traditionally used molecular markers. To help resolve their phylogenetic relationships, the complete mitogenomes of eight Chinese viviparid snails, Viviparus chui, Cipangopaludina chinensis, C. ussuriensis, C. dianchiensis (endangered), Margarya melanioides (endangered), M. monodi (critically endangered), Bellamya quadrata and B. aeruginosa, were sequenced and compared to almost all of the available caenogastropod mitogenomes. Viviparidae possess the largest mitogenomes (16 392 to 18 544 bp), exhibit the highest A+T bias (72.5% on average), and some exhibit unique gene orders (a rearrangement of the standard MYCWQGE box), among the Caenogastropoda. Apart from the Vermetidae family and Cerithioidea superfamily, which possessed unique gene orders, the remaining studied caenogastropod mitogenomes exhibited highly conserved gene order, with minimal variations. Maximum likelihood and Bayesian inference analyses, used to reconstruct the phylogenetic relationships among 49 almost complete (all 37 genes) caenogastropod mitogenomes, produced almost identical tree topologies. Viviparidae were divided into three clades: a) Margarya and Cipangopaludina (except C. ussuriensis), b) Bellamya and C. ussuriensis, c) Viviparus chui. Our results present evidence that some Cipangopaludina species (dianchiensis and cathayensis) should be renamed into the senior genus Margarya. The phylogenetic resolution obtained in this study is insufficient to fully resolve the relationships within the ‘b’ clade, but if C. chinensis proves to be a valid representative of the genus, C. ussuriensis may have to be reassigned a different genus (possibly Bellamya, or even a new genus). Non-monophyly also remains pervasive among the higher (above the family-level) Caenogastropod taxonomic classes. Gene order distance matrix produced a different phylogenetic signal from the nucleotide sequences, which indicates a limited usability of this approach for inferring caenogastropod phylogenies. As phenotypic homoplasy appears to be widespread among some viviparid genera, in order to effectively protect the rapidly diminishing endemic Viviparid populations in China, further detailed molecular phylogenetic studies are urgently needed to resolve the taxonomic status of several species.

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The complete mitochondrial genome of the mudsnail Cipangopaludina cathayensis (Gastropoda: Viviparidae)

Cited by 15 publications

References 13 publications

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

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

The complete mitochondrial genome of the golden apple snail Pomacea canaliculata (Gastropoda: Ampullariidae)

Sequencing of the complete mitochondrial genomes of eight freshwater snail species exposes pervasive paraphyly within the Viviparidae family (Caenogastropoda)

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