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Conference Paper: Developing a platform of environmental omics for the green-lipped mussel Perna viridis

TitleDeveloping a platform of environmental omics for the green-lipped mussel Perna viridis
Authors
Issue Date2014
PublisherThe Society of Environmental Toxicology and Chemistry (SETAC).
Citation
The 24th Annual Meeting of the SETAC Europe, Basel, Switzerland, 11-15 May 2014, abstract no. 462 How to Cite?
AbstractThe green-lipped mussel Perna viridis is an important marine biomonitor species in pollution monitoring and ecotoxicological studies in Asia-Pacific region, and considered as a subtropical equivalent biomonitor of the temperate Mytilus species. However, the genomic information of P. viridis is still largely unexplored when compared with Mytilus species. This study aimed to establish a transcriptomic profile of P. viridis using the next generation sequencing technology and provide a good representative set of genomic information for elucidation of toxic mechanisms upon pollution stresses and identification of a suite of suitable biomarkers for monitoring marine pollution and environmental stresses. To obtain a wide spectrum of environmental-associated transcripts, adult mussels (4-5 cm shell length) were collected from different locations in Hong Kong and from those after 24-hour exposures to various challenges of physical stresses and chemical pollutants, so as to cover a wide range of stress-associated transcription patterns for future environmental studies. Two males and females from each location and from each treatment were chosen for obtaining the three target tissues (i.e., hepatopancreas, gill and adductor muscle). For each sex and each tissue type, a total RNA sample was extracted from pooled tissues from the field and laboratory treated mussels. The RNA sample was subjected to cDNA library construction, followed by the RNA-sequencing using a Solexa GAIIx (Illumina). Including the splicing variants, a de novo assembly of a total length of 295,064,579 base-pair (bp) contig was obtained, with 233,257 contigs assembled of an average size of 1264 bp. The 192,879 non-redundant assembled transcripts were blasted against the NCBI nr database and three molluscan EST databases, and resulted in 44,713 transcripts with at least a blast hit, and having a top match with the sequences from the Pacific oyster, Crassostrea gigas (27,651 transcripts). A total of 5,131 transcripts were assigned with KEGG annotation involving in 329 pathways. Based on multivariate statistical analysis, expression patterns of genes from stress associated responses and detoxification were strongly tissue-specific but the differences between genders were little. The anticipated genomic database generated from this study will further strengthen the role of P. viridis as a universal marine biomonitor in the Asia-Pacific region.
DescriptionConference Theme: Science across bridges, borders and boundaries
Oral presentation
Session Track: Aquatic and terrestrial ecotoxicology
Persistent Identifierhttp://hdl.handle.net/10722/205052

 

DC FieldValueLanguage
dc.contributor.authorIp, CHen_US
dc.contributor.authorLeung, TYen_US
dc.contributor.authorQiu, JWen_US
dc.contributor.authorChan, LLen_US
dc.contributor.authorLam, PKSen_US
dc.contributor.authorLeung, KMYen_US
dc.date.accessioned2014-09-20T01:19:58Z-
dc.date.available2014-09-20T01:19:58Z-
dc.date.issued2014en_US
dc.identifier.citationThe 24th Annual Meeting of the SETAC Europe, Basel, Switzerland, 11-15 May 2014, abstract no. 462en_US
dc.identifier.urihttp://hdl.handle.net/10722/205052-
dc.descriptionConference Theme: Science across bridges, borders and boundaries-
dc.descriptionOral presentation-
dc.descriptionSession Track: Aquatic and terrestrial ecotoxicology-
dc.description.abstractThe green-lipped mussel Perna viridis is an important marine biomonitor species in pollution monitoring and ecotoxicological studies in Asia-Pacific region, and considered as a subtropical equivalent biomonitor of the temperate Mytilus species. However, the genomic information of P. viridis is still largely unexplored when compared with Mytilus species. This study aimed to establish a transcriptomic profile of P. viridis using the next generation sequencing technology and provide a good representative set of genomic information for elucidation of toxic mechanisms upon pollution stresses and identification of a suite of suitable biomarkers for monitoring marine pollution and environmental stresses. To obtain a wide spectrum of environmental-associated transcripts, adult mussels (4-5 cm shell length) were collected from different locations in Hong Kong and from those after 24-hour exposures to various challenges of physical stresses and chemical pollutants, so as to cover a wide range of stress-associated transcription patterns for future environmental studies. Two males and females from each location and from each treatment were chosen for obtaining the three target tissues (i.e., hepatopancreas, gill and adductor muscle). For each sex and each tissue type, a total RNA sample was extracted from pooled tissues from the field and laboratory treated mussels. The RNA sample was subjected to cDNA library construction, followed by the RNA-sequencing using a Solexa GAIIx (Illumina). Including the splicing variants, a de novo assembly of a total length of 295,064,579 base-pair (bp) contig was obtained, with 233,257 contigs assembled of an average size of 1264 bp. The 192,879 non-redundant assembled transcripts were blasted against the NCBI nr database and three molluscan EST databases, and resulted in 44,713 transcripts with at least a blast hit, and having a top match with the sequences from the Pacific oyster, Crassostrea gigas (27,651 transcripts). A total of 5,131 transcripts were assigned with KEGG annotation involving in 329 pathways. Based on multivariate statistical analysis, expression patterns of genes from stress associated responses and detoxification were strongly tissue-specific but the differences between genders were little. The anticipated genomic database generated from this study will further strengthen the role of P. viridis as a universal marine biomonitor in the Asia-Pacific region.-
dc.languageengen_US
dc.publisherThe Society of Environmental Toxicology and Chemistry (SETAC).-
dc.relation.ispartofAnnual Meeting of the SETAC Europeen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleDeveloping a platform of environmental omics for the green-lipped mussel Perna viridisen_US
dc.typeConference_Paperen_US
dc.identifier.emailLeung, TY: ptyleung@hku.hken_US
dc.identifier.emailLeung, KMY: kmyleung@hku.hken_US
dc.identifier.authorityLeung, KMY=rp00733en_US
dc.description.naturepublished_or_final_version-
dc.identifier.hkuros238270en_US
dc.publisher.placeBelgium-

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