The mitochondrial genome of the threatened tideland snail <i>Pirenella pupiformis</i> (Mollusca: Caenogastropoda: Potamididae) determined by shotgun sequencing

Kato, Shintaro; Itoh, Hajime; Fukumori, Hiroaki; Nakajima, Nobuyoshi; Kanaya, Gen; Kojima, Soichi

doi:10.1080/23802359.2022.2060143

Mitochondrial DNA Part B

2022

DOI: 10.1080/23802359.2022.2060143

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The mitochondrial genome of the threatened tideland snail Pirenella pupiformis (Mollusca: Caenogastropoda: Potamididae) determined by shotgun sequencing

Shintaro Kato

Hajime Itoh

Hiroaki Fukumori

et al.

Abstract: The nearly complete mitochondrial genome of the threatened tideland snail Pirenella pupiformis (Mollusca: Cerithioidea: Potamididae) was determined by shotgun next-generation sequencing. The mitogenome is comprised of 13 protein-coding genes (PCGs), two ribosomal RNA (12S and 16S) genes, and 22 transfer RNA genes (tRNAs). This gene order is consistent with the previously published mitochondrial genomes of other species belonging to the family Potamididae. The family Potamididae including… Show more

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Cited by 2 publications

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The mitochondrial genome of Hua aristarchorum (Heude, 1889) (Gastropoda, Cerithioidea, Semisulcospiridae) and its phylogenetic implications

Xu,

Zeng,

Meng

et al. 2024

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Research on complete mitochondrial genomes can help in understanding the molecular evolution and phylogenetic relationships of various species. In this study, the complete mitogenome of Hua aristarchorum was characterized to supplement the limited mitogenomic information on the genus Hua. Three distinct assembly methods, GetOrganelle, NovoPlasty and SPAdes, were used to ensure reliable assembly. The 15,691 bp mitogenome contains 37 genes and an AT-rich region. Notably, the cytochrome c oxidase subunit I (COX1) gene, commonly used for species identification, appears to be slow-evolving and less variable, which may suggest the inclusion of rapidly evolving genes (NADH dehydrogenase subunit 6 [ND6] or NADH dehydrogenase subunit 2 [ND2]) as markers in diagnostic, detection, and population genetic studies of Cerithioidea. Moreover, we identified the unreliability of annotations (e.g., the absence of annotations for NADH dehydrogenase subunit 4L [ND4L] in NC_037771) and potential misidentifications (NC_023364) in public databases, which indicate that data from public databases should be manually curated in future research. Phylogenetic analyses of Cerithioidea based on different datasets generated identical trees using maximum likelihood and Bayesian inference methods. The results confirm that Semisulcospiridae is closely related to Pleuroceridae. The sequences of Semisulcospiridae clustered into three clades, of which H. aristarchorum is one; H. aristarchorum is sister to the other two clades. The findings of this study will contribute to a better understanding of the characteristics of the H. aristarchorum mitogenome and the phylogenetic relationships of Semisulcospiridae. The inclusion of further mitochondrial genome sequences will improve knowledge of the phylogeny and origin of Cerithioidea.

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The mitochondrial genome of Hua aristarchorum (Heude, 1889) (Gastropoda, Cerithioidea, Semisulcospiridae) and its phylogenetic implications

Xu,

Zeng,

Meng

et al. 2024

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A new species of Semisulcospira O. Boettger, 1886 (Gastropoda, Cerithoidea, Semisulcospiridae) from Fujian, China with mitochondrial genome and its phylogenetic implications

Xu,

Meng,

Zeng

et al. 2025

ZSE

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During our investigation of the diversity and phylogeny of the family Semisulcospiridae in China, we have found a presumed new species in mountain streams of Xiamen, Fujian Province on both morphology and molecular evidence. This new species, Semisulcospira egrettasp. nov., is characterized by its thin and smooth shell, retaining about 0.5 mm long embryonic shells in its brood pouch, and by distinctive features of its radular morphology. Phylogenetic analyses of partial sequences of the mitochondrial markers 16S ribosomal RNA (16S) and cytochrome c oxidase subunit I (COI) and complete sequences of the nuclear ribosomal internal transcribed spacer (ITS, including internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2) supported the distinctiveness of S. egrettasp. nov. from other Semisulcospira species. These analyses consistently placed S. egrettasp. nov. in Semisulcospira confirming its monophyly. Phylogenetic analyses based on just COI and 16S exhibited low resolution rendering the phylogenetic position of the new species within the genus uncertain. In contrast, phylogenetic tree analyses of complete mitochondrial genomes, which include 13 protein-coding genes (PCGs), were better resolved. However, the mitogenome dataset included a more restricted sampling of taxa (16), impeding a detailed exploration of the phylogenetic position of the new species. To address this deficit, we provide seven complete mitochondrial genomes for S. egrettasp. nov., obtained using the genome skimming sequencing method. This study contributes important molecular and genomic data, aiding in the understanding of semisulcospirid phylogeny, and highlights the need for further taxonomic sampling and phylogenomic methods to resolve the evolutionary relationships within Semisulcospiridae.

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The mitochondrial genome of the threatened tideland snail Pirenella pupiformis (Mollusca: Caenogastropoda: Potamididae) determined by shotgun sequencing

Cited by 2 publications

References 21 publications

The mitochondrial genome of Hua aristarchorum (Heude, 1889) (Gastropoda, Cerithioidea, Semisulcospiridae) and its phylogenetic implications

The mitochondrial genome of Hua aristarchorum (Heude, 1889) (Gastropoda, Cerithioidea, Semisulcospiridae) and its phylogenetic implications

A new species of Semisulcospira O. Boettger, 1886 (Gastropoda, Cerithoidea, Semisulcospiridae) from Fujian, China with mitochondrial genome and its phylogenetic implications

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