Characterisation of the mantle transcriptome and biomineralisation genes in the blunt-gaper clam, Mya truncata

Victoria A. Sleight; Michael A.S. Thorne; Lloyd S. Peck; Jaison Arivalagan; Sophie Berland; Arul Marie; Melody S. Clark

doi:10.1016/j.margen.2016.01.003

Characterisation of the mantle transcriptome and biomineralisation genes in the blunt-gaper clam, Mya truncata

Victoria A. Sleight^*, Michael A.S. Thorne, Lloyd S. Peck, Jaison Arivalagan, Sophie Berland, Arul Marie, Melody S. Clark

^*Corresponding author for this work

Aberdeen Centre For Environmental Sustainability

Research output: Contribution to journal › Article › peer-review

27 Citations (Scopus)

Abstract

Members of the Myidae family are ecologically and economically important, but there is currently very little molecular data on these species. The present study sequenced and assembled the mantle transcriptome of Mya truncata from the North West coast of Scotland and identified candidate biomineralisation genes. RNA-Seq reads were assembled to create 20,106 contigs in a de novo transciptome, 18.81% of which were assigned putative functions using BLAST sequence similarity searching (cuttoff E-value 1E - 10). The most highly expressed genes were compared to the Antarctic clam (Laternula elliptica) and showed that many of the dominant biological functions (muscle contraction, energy production, biomineralisation) in the mantle were conserved. There were however, differences in the constitutive expression of heat shock proteins, which were possibly due to the M. truncata sampling location being at a relatively low latitude, and hence relatively warm, in terms of the global distribution of the species. Phylogenetic analyses of the Tyrosinase proteins from M. truncata showed a gene expansion which was absent in L. elliptica. The tissue distribution expression patterns of putative biomineralisation genes were investigated using quantitative PCR, all genes showed a mantle specific expression pattern supporting their hypothesised role in shell secretion. The present study provides some preliminary insights into how clams from different environments - temperate versus polar - build their shells. In addition, the transcriptome data provides a valuable resource for future comparative studies investigating biomineralisation.

Original language	English
Pages (from-to)	47-55
Number of pages	9
Journal	Marine Genomics
Volume	27
DOIs	https://doi.org/10.1016/j.margen.2016.01.003
Publication status	Published - 1 Jun 2016

Bibliographical note

Funding Information:
VAS was funded by a NERC DTG studentship (Project Reference: NE/J500173/1) to the British Antarctic Survey. MSC, MAST and LSP were financed by NERC core funding to the British Antarctic Survey, Polar Sciences for Planet Earth Programme. JA was funded by the European Union Seventh Framework Programme under grant agreement no. 605051. We would like to thank Laura J. Weir for technical assistance, Elizabeth M. Harper for advice on shell microstructure and Felipe Aguilera for providing a molluscan Tyrosinase alignment. We thank the dive team at the NERC National Centre for Scientific Diving, Oban for animal collection and Dr Kim Last at the Scottish Association for Marine Science for overseeing animal husbandry.

Publisher Copyright:
© 2016 The Authors.

Keywords

Bioinformatics
Calcification
Gene expression
Phylogenetics
Shell

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10.1016/j.margen.2016.01.003

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title = "Characterisation of the mantle transcriptome and biomineralisation genes in the blunt-gaper clam, Mya truncata",

abstract = "Members of the Myidae family are ecologically and economically important, but there is currently very little molecular data on these species. The present study sequenced and assembled the mantle transcriptome of Mya truncata from the North West coast of Scotland and identified candidate biomineralisation genes. RNA-Seq reads were assembled to create 20,106 contigs in a de novo transciptome, 18.81% of which were assigned putative functions using BLAST sequence similarity searching (cuttoff E-value 1E - 10). The most highly expressed genes were compared to the Antarctic clam (Laternula elliptica) and showed that many of the dominant biological functions (muscle contraction, energy production, biomineralisation) in the mantle were conserved. There were however, differences in the constitutive expression of heat shock proteins, which were possibly due to the M. truncata sampling location being at a relatively low latitude, and hence relatively warm, in terms of the global distribution of the species. Phylogenetic analyses of the Tyrosinase proteins from M. truncata showed a gene expansion which was absent in L. elliptica. The tissue distribution expression patterns of putative biomineralisation genes were investigated using quantitative PCR, all genes showed a mantle specific expression pattern supporting their hypothesised role in shell secretion. The present study provides some preliminary insights into how clams from different environments - temperate versus polar - build their shells. In addition, the transcriptome data provides a valuable resource for future comparative studies investigating biomineralisation.",

keywords = "Bioinformatics, Calcification, Gene expression, Phylogenetics, Shell",

author = "Sleight, {Victoria A.} and Thorne, {Michael A.S.} and Peck, {Lloyd S.} and Jaison Arivalagan and Sophie Berland and Arul Marie and Clark, {Melody S.}",

note = "Funding Information: VAS was funded by a NERC DTG studentship (Project Reference: NE/J500173/1) to the British Antarctic Survey. MSC, MAST and LSP were financed by NERC core funding to the British Antarctic Survey, Polar Sciences for Planet Earth Programme. JA was funded by the European Union Seventh Framework Programme under grant agreement no. 605051. We would like to thank Laura J. Weir for technical assistance, Elizabeth M. Harper for advice on shell microstructure and Felipe Aguilera for providing a molluscan Tyrosinase alignment. We thank the dive team at the NERC National Centre for Scientific Diving, Oban for animal collection and Dr Kim Last at the Scottish Association for Marine Science for overseeing animal husbandry. Publisher Copyright: {\textcopyright} 2016 The Authors.",

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doi = "10.1016/j.margen.2016.01.003",

language = "English",

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AU - Peck, Lloyd S.

AU - Arivalagan, Jaison

AU - Berland, Sophie

AU - Marie, Arul

AU - Clark, Melody S.

N1 - Funding Information: VAS was funded by a NERC DTG studentship (Project Reference: NE/J500173/1) to the British Antarctic Survey. MSC, MAST and LSP were financed by NERC core funding to the British Antarctic Survey, Polar Sciences for Planet Earth Programme. JA was funded by the European Union Seventh Framework Programme under grant agreement no. 605051. We would like to thank Laura J. Weir for technical assistance, Elizabeth M. Harper for advice on shell microstructure and Felipe Aguilera for providing a molluscan Tyrosinase alignment. We thank the dive team at the NERC National Centre for Scientific Diving, Oban for animal collection and Dr Kim Last at the Scottish Association for Marine Science for overseeing animal husbandry. Publisher Copyright: © 2016 The Authors.

PY - 2016/6/1

Y1 - 2016/6/1

N2 - Members of the Myidae family are ecologically and economically important, but there is currently very little molecular data on these species. The present study sequenced and assembled the mantle transcriptome of Mya truncata from the North West coast of Scotland and identified candidate biomineralisation genes. RNA-Seq reads were assembled to create 20,106 contigs in a de novo transciptome, 18.81% of which were assigned putative functions using BLAST sequence similarity searching (cuttoff E-value 1E - 10). The most highly expressed genes were compared to the Antarctic clam (Laternula elliptica) and showed that many of the dominant biological functions (muscle contraction, energy production, biomineralisation) in the mantle were conserved. There were however, differences in the constitutive expression of heat shock proteins, which were possibly due to the M. truncata sampling location being at a relatively low latitude, and hence relatively warm, in terms of the global distribution of the species. Phylogenetic analyses of the Tyrosinase proteins from M. truncata showed a gene expansion which was absent in L. elliptica. The tissue distribution expression patterns of putative biomineralisation genes were investigated using quantitative PCR, all genes showed a mantle specific expression pattern supporting their hypothesised role in shell secretion. The present study provides some preliminary insights into how clams from different environments - temperate versus polar - build their shells. In addition, the transcriptome data provides a valuable resource for future comparative studies investigating biomineralisation.

AB - Members of the Myidae family are ecologically and economically important, but there is currently very little molecular data on these species. The present study sequenced and assembled the mantle transcriptome of Mya truncata from the North West coast of Scotland and identified candidate biomineralisation genes. RNA-Seq reads were assembled to create 20,106 contigs in a de novo transciptome, 18.81% of which were assigned putative functions using BLAST sequence similarity searching (cuttoff E-value 1E - 10). The most highly expressed genes were compared to the Antarctic clam (Laternula elliptica) and showed that many of the dominant biological functions (muscle contraction, energy production, biomineralisation) in the mantle were conserved. There were however, differences in the constitutive expression of heat shock proteins, which were possibly due to the M. truncata sampling location being at a relatively low latitude, and hence relatively warm, in terms of the global distribution of the species. Phylogenetic analyses of the Tyrosinase proteins from M. truncata showed a gene expansion which was absent in L. elliptica. The tissue distribution expression patterns of putative biomineralisation genes were investigated using quantitative PCR, all genes showed a mantle specific expression pattern supporting their hypothesised role in shell secretion. The present study provides some preliminary insights into how clams from different environments - temperate versus polar - build their shells. In addition, the transcriptome data provides a valuable resource for future comparative studies investigating biomineralisation.

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KW - Calcification

KW - Gene expression

KW - Phylogenetics

KW - Shell

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DO - 10.1016/j.margen.2016.01.003

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SN - 1874-7787

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EP - 55

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JF - Marine Genomics

ER -

Characterisation of the mantle transcriptome and biomineralisation genes in the blunt-gaper clam, Mya truncata

Abstract

Bibliographical note

Keywords

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