A putative species complex in the
            <scp>S</scp>
            ea of
            <scp>J</scp>
            apan revealed by
            <scp>DNA</scp>
            sequence data: a study on
            <i>
              <scp>L</scp>
              ottia
            </i>
            cf. 
            <i>kogamogai</i>
            (
            <scp>G</scp>
            astropoda:
            <scp>P</scp>
            atellogastropoda)

Kristof, Alen; Oliveira, André Luiz de; Kolbin, K. G.; Wanninger, Andreas

doi:10.1111/jzs.12120

Cited by 3 publications

(1 citation statement)

References 35 publications

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“…Most species from this group feed by scraping a fine film of microalgae from what appears to be a bare rock surface. Their shells have the appearance of hats of different sizes, generally reaching no more than 20 cm 3 , 4 . These limpets, which are ecologically important in coastal regions, separated from other gastropods early in molluscan evolution 5 .…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda

Jiao

Guo

Yan

et al. 2020

Sci Rep

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To improve the systematics and taxonomy of Patellogastropoda within the evolution of gastropods, we determined the complete mitochondrial genome sequences of Lottia goshimai and Nipponacmea fuscoviridis in the family Lottiidae, which presented sizes of 18,192 bp and 18,720 bp, respectively. In addition to 37 common genes among metazoa, we observed duplication of the trnM gene in L. goshimai and the trnM and trnW genes in N. fuscoviridis. The highest A + T contents of the two species were found within protein-coding genes (59.95% and 54.55%), followed by rRNAs (56.50% and 52.44%) and tRNAs (56.42% and 52.41%). trnS1 and trnS2 could not form the canonical cloverleaf secondary structure due to the lack of a dihydrouracil arm in both species. The gene arrangements in all Patellogastropoda compared with those of ancestral gastropods showed different levels of gene rearrangement, including the shuffling, translocation and inversion of single genes or gene fragments. This kind of irregular rearrangement is particularly obvious in the Lottiidae family. The results of phylogenetic and gene rearrangement analyses showed that L. goshimai and Lottia digitalis clustered into one group, which in turn clustered with N. fuscoviridis in Patellogastropoda. This study demonstrates the significance of complete mitogenomes for phylogenetic analysis and enhances our understanding of the evolution of Patellogastropoda.

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Section: Introductionmentioning

confidence: 99%

Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda

Jiao

Guo

Yan

et al. 2020

Sci Rep

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The potential for using shell proteins in gastropod systematics, assessed in patellogastropod limpets

Colgan

2021

Zoological Journal of the Linnean Society

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This investigation of the application of shell protein information to gastropod systematics initially utilized available Lottia gigantea sequences and a transcriptome of Patelloida mimula developed here. Levels of differentiation between predicted sequences of reciprocal best-hit potential homologues in P. mimula and L. gigantea suggested that they could be useful within families, and possibly in higher taxa using some shell-associated proteins, particularly the peroxidases. Subsequently, proteomic analyses of the acid-soluble fraction of extractions from 17 shells and five tissue samples were conducted by combined liquid chromatography/mass spectrometry with nano-electrospray ionization. All proteins with abundance more than 1.2% in the L. gigantea shell proteome were identified with 100% confidence in most extractions by SearchGui/PeptideShaker analyses. In total, 259 of 379 peptides predicted from in silico digestion of L. gigantea shell proteins were represented by validated peptide spectrum matches in one or more specimens. Systematics applications were investigated by analysing metrics such as protein coverage by peptides and phylogenetic analyses of peptide presence/absence. The investigation suggested that diagnostic profiles based on fixed presence/absence differences can be used to separate species pairs. However, further development of analytical techniques and accumulation of reference databases is required for realising fully the systematics potential of the shell proteome.

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Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

et al. 2016

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BackgroundMollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal for studies into animal evolution. Despite being one of the most species-rich phyla, molecular and in silico studies concerning specific key developmental gene families are still scarce, thus hampering deeper insights into the molecular machinery that governs the development and evolution of the various molluscan class-level taxa.ResultsNext-generation sequencing was used to retrieve transcriptomes of representatives of seven out of the eight recent class-level taxa of mollusks. Similarity searches, phylogenetic inferences, and a detailed manual curation were used to identify and confirm the orthology of numerous molluscan Hox and ParaHox genes, which resulted in a comprehensive catalog that highlights the evolution of these genes in Mollusca and other metazoans. The identification of a specific molluscan motif in the Hox paralog group 5 and a lophotrochozoan ParaHox motif in the Gsx gene is described. Functional analyses using KEGG and GO tools enabled a detailed description of key developmental genes expressed in important pathways such as Hedgehog, Wnt, and Notch during development of the respective species. The KEGG analysis revealed Wnt8, Wnt11, and Wnt16 as Wnt genes hitherto not reported for mollusks, thereby enlarging the known Wnt complement of the phylum. In addition, novel Hedgehog (Hh)-related genes were identified in the gastropod Lottia cf. kogamogai, demonstrating a more complex gene content in this species than in other mollusks.ConclusionsThe use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3080-9) contains supplementary material, which is available to authorized users.

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A putative species complex in the S ea of J apan revealed by DNA sequence data: a study on L ottia cf. kogamogai ( G astropoda: P atellogastropoda)

Cited by 3 publications

References 35 publications

Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda

Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda

The potential for using shell proteins in gastropod systematics, assessed in patellogastropod limpets

Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks

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