De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies

Priscilla T.Y. LEUNG; Jack C.H. IP; Sarah ST MAK; Jian Wen QIU; Paul K.S. LAM; Chris KC WONG; Leo L. CHAN; Kenneth M.Y. LEUNG

doi:10.1186/1471-2164-15-804

De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies

Priscilla T.Y. LEUNG, Jack C.H. IP, Sarah ST MAK, Jian Wen QIU, Paul K.S. LAM, Chris KC WONG, Leo L. CHAN, Kenneth M.Y. LEUNG^*

^*Corresponding author for this work

Research output: Journal Publications › Journal Article (refereed) › peer-review

40 Citations (Scopus)

Abstract

Background: The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome database from the tissues of adductor muscle, gills and the hepatopancreas of P. viridis in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses in this sentinel species. Results: Illumina sequencing results yielded 544,272,542 high-quality filtered reads. After de novo assembly using Trinity, 233,257 contigs were generated with an average length of 1,264 bp and an N50 length of 2,868 bp; 192,879 assembled transcripts and 150,111 assembled unigenes were obtained after clustering. A total of 93,668 assembled transcripts (66,692 assembled genes) with putative functions for protein domains were predicted based on InterProScan analysis. Based on similarity searches, 44,713 assembled transcripts and 25,319 assembled unigenes were annotated with at least one BLAST hit. A total of 21,262 assembled transcripts (11,947 assembled genes) were annotated with at least one well-defined Gene Ontology (GO) and 5,131 assembled transcripts (3,181 assembled unigenes) were assigned to 329 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The quantity of assembled unigenes and transcripts obtained from male and female mussels were similar but varied among the three studied tissues, with the highest numbers recorded in the gills, followed by the hepatopancreas, and then the adductor muscle. Multivariate analyses revealed strong tissue-specific patterns among the three different tissues, but not between sexes in terms of expression profiles for annotated genes in various GO terms, and genes associated with stress responses and degradation of xenobiotics. The expression profiles of certain selected genes in each tissue type were further validated using real-time quantitative polymerase chain reaction assays and a similar tissue-specific trend was seen. Conclusions: The extensive sequence data generated from this study will provide a valuable molecular resource for facilitating environmental studies with P. viridis, and highlight the importance of tissue-specific approaches in the future.

Original language	English
Article number	804
Number of pages	14
Journal	BMC Genomics
Volume	15
Issue number	1
DOIs	https://doi.org/10.1186/1471-2164-15-804
Publication status	Published - 19 Sept 2014
Externally published	Yes

Bibliographical note

The authors thank the Centre for Genomic Sciences, HKU for the service support in Illumina sequencing and bioinformatics, and thank Helen Leung and Cecily Law for their technical support. The authors specially thank the two anonymous reviewers for their useful and constructive comments which have greatly improved the clarity of this manuscript. JCHI performed the experiments and data analyses, and drafted the manuscript. PTYL designed and coordinated the experiments. KKYH performed the sample collection and helped the design of the experiments. JWQ contributed to the design, data analysis and revision of the manuscript. KMYL was the principal investigator of this project, designed this study, approved and oversaw the experiments and data analyses, and revised drafts of this manuscript.

Publisher Copyright:
© 2014 Leung et al.

Funding

This work was supported by a research grant awarded to KMY Leung, a Seed Collaborative Research Fund (2011) from the State Key Laboratory in Marine Pollution via Innovation and Technology Commission. JCH Ip thanks the University of Hong Kong (HKU) for providing the Type B postgraduate studentship and support from the Research Grants Council of the Hong Kong SAR Government via a General Research Fund (Project No.: HKU 771212 M) awarded to KMY Leung. The authors thank the Centre for Genomic Sciences, HKU for the service support in Illumina sequencing and bioinformatics, Edward Lau for proofreading early drafts of this manuscript, and Adela Li and Andy Yi for their assistance in the laboratory exposure experiments.

Keywords

Biomonitor
De novo transcriptome
Mussel
Perna viridis
RNA-seq
Tissue specificity

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10.1186/1471-2164-15-804Licence: CC BY

Cite this

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title = "De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies",

abstract = "Background: The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome database from the tissues of adductor muscle, gills and the hepatopancreas of P. viridis in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses in this sentinel species. Results: Illumina sequencing results yielded 544,272,542 high-quality filtered reads. After de novo assembly using Trinity, 233,257 contigs were generated with an average length of 1,264 bp and an N50 length of 2,868 bp; 192,879 assembled transcripts and 150,111 assembled unigenes were obtained after clustering. A total of 93,668 assembled transcripts (66,692 assembled genes) with putative functions for protein domains were predicted based on InterProScan analysis. Based on similarity searches, 44,713 assembled transcripts and 25,319 assembled unigenes were annotated with at least one BLAST hit. A total of 21,262 assembled transcripts (11,947 assembled genes) were annotated with at least one well-defined Gene Ontology (GO) and 5,131 assembled transcripts (3,181 assembled unigenes) were assigned to 329 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The quantity of assembled unigenes and transcripts obtained from male and female mussels were similar but varied among the three studied tissues, with the highest numbers recorded in the gills, followed by the hepatopancreas, and then the adductor muscle. Multivariate analyses revealed strong tissue-specific patterns among the three different tissues, but not between sexes in terms of expression profiles for annotated genes in various GO terms, and genes associated with stress responses and degradation of xenobiotics. The expression profiles of certain selected genes in each tissue type were further validated using real-time quantitative polymerase chain reaction assays and a similar tissue-specific trend was seen. Conclusions: The extensive sequence data generated from this study will provide a valuable molecular resource for facilitating environmental studies with P. viridis, and highlight the importance of tissue-specific approaches in the future.",

keywords = "Biomonitor, De novo transcriptome, Mussel, Perna viridis, RNA-seq, Tissue specificity",

author = "LEUNG, {Priscilla T.Y.} and IP, {Jack C.H.} and MAK, {Sarah ST} and QIU, {Jian Wen} and LAM, {Paul K.S.} and WONG, {Chris KC} and CHAN, {Leo L.} and LEUNG, {Kenneth M.Y.}",

note = "The authors thank the Centre for Genomic Sciences, HKU for the service support in Illumina sequencing and bioinformatics, and thank Helen Leung and Cecily Law for their technical support. The authors specially thank the two anonymous reviewers for their useful and constructive comments which have greatly improved the clarity of this manuscript. JCHI performed the experiments and data analyses, and drafted the manuscript. PTYL designed and coordinated the experiments. KKYH performed the sample collection and helped the design of the experiments. JWQ contributed to the design, data analysis and revision of the manuscript. KMYL was the principal investigator of this project, designed this study, approved and oversaw the experiments and data analyses, and revised drafts of this manuscript. Publisher Copyright: {\textcopyright} 2014 Leung et al.",

year = "2014",

month = sep,

day = "19",

doi = "10.1186/1471-2164-15-804",

language = "English",

volume = "15",

journal = "BMC Genomics",

issn = "1471-2164",

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TY - JOUR

T1 - De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies

AU - LEUNG, Priscilla T.Y.

AU - IP, Jack C.H.

AU - MAK, Sarah ST

AU - QIU, Jian Wen

AU - LAM, Paul K.S.

AU - WONG, Chris KC

AU - CHAN, Leo L.

AU - LEUNG, Kenneth M.Y.

N1 - The authors thank the Centre for Genomic Sciences, HKU for the service support in Illumina sequencing and bioinformatics, and thank Helen Leung and Cecily Law for their technical support. The authors specially thank the two anonymous reviewers for their useful and constructive comments which have greatly improved the clarity of this manuscript. JCHI performed the experiments and data analyses, and drafted the manuscript. PTYL designed and coordinated the experiments. KKYH performed the sample collection and helped the design of the experiments. JWQ contributed to the design, data analysis and revision of the manuscript. KMYL was the principal investigator of this project, designed this study, approved and oversaw the experiments and data analyses, and revised drafts of this manuscript. Publisher Copyright: © 2014 Leung et al.

PY - 2014/9/19

Y1 - 2014/9/19

N2 - Background: The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome database from the tissues of adductor muscle, gills and the hepatopancreas of P. viridis in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses in this sentinel species. Results: Illumina sequencing results yielded 544,272,542 high-quality filtered reads. After de novo assembly using Trinity, 233,257 contigs were generated with an average length of 1,264 bp and an N50 length of 2,868 bp; 192,879 assembled transcripts and 150,111 assembled unigenes were obtained after clustering. A total of 93,668 assembled transcripts (66,692 assembled genes) with putative functions for protein domains were predicted based on InterProScan analysis. Based on similarity searches, 44,713 assembled transcripts and 25,319 assembled unigenes were annotated with at least one BLAST hit. A total of 21,262 assembled transcripts (11,947 assembled genes) were annotated with at least one well-defined Gene Ontology (GO) and 5,131 assembled transcripts (3,181 assembled unigenes) were assigned to 329 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The quantity of assembled unigenes and transcripts obtained from male and female mussels were similar but varied among the three studied tissues, with the highest numbers recorded in the gills, followed by the hepatopancreas, and then the adductor muscle. Multivariate analyses revealed strong tissue-specific patterns among the three different tissues, but not between sexes in terms of expression profiles for annotated genes in various GO terms, and genes associated with stress responses and degradation of xenobiotics. The expression profiles of certain selected genes in each tissue type were further validated using real-time quantitative polymerase chain reaction assays and a similar tissue-specific trend was seen. Conclusions: The extensive sequence data generated from this study will provide a valuable molecular resource for facilitating environmental studies with P. viridis, and highlight the importance of tissue-specific approaches in the future.

AB - Background: The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome database from the tissues of adductor muscle, gills and the hepatopancreas of P. viridis in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses in this sentinel species. Results: Illumina sequencing results yielded 544,272,542 high-quality filtered reads. After de novo assembly using Trinity, 233,257 contigs were generated with an average length of 1,264 bp and an N50 length of 2,868 bp; 192,879 assembled transcripts and 150,111 assembled unigenes were obtained after clustering. A total of 93,668 assembled transcripts (66,692 assembled genes) with putative functions for protein domains were predicted based on InterProScan analysis. Based on similarity searches, 44,713 assembled transcripts and 25,319 assembled unigenes were annotated with at least one BLAST hit. A total of 21,262 assembled transcripts (11,947 assembled genes) were annotated with at least one well-defined Gene Ontology (GO) and 5,131 assembled transcripts (3,181 assembled unigenes) were assigned to 329 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The quantity of assembled unigenes and transcripts obtained from male and female mussels were similar but varied among the three studied tissues, with the highest numbers recorded in the gills, followed by the hepatopancreas, and then the adductor muscle. Multivariate analyses revealed strong tissue-specific patterns among the three different tissues, but not between sexes in terms of expression profiles for annotated genes in various GO terms, and genes associated with stress responses and degradation of xenobiotics. The expression profiles of certain selected genes in each tissue type were further validated using real-time quantitative polymerase chain reaction assays and a similar tissue-specific trend was seen. Conclusions: The extensive sequence data generated from this study will provide a valuable molecular resource for facilitating environmental studies with P. viridis, and highlight the importance of tissue-specific approaches in the future.

KW - Biomonitor

KW - De novo transcriptome

KW - Mussel

KW - Perna viridis

KW - RNA-seq

KW - Tissue specificity

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U2 - 10.1186/1471-2164-15-804

DO - 10.1186/1471-2164-15-804

M3 - Journal Article (refereed)

C2 - 25239240

AN - SCOPUS:84922611093

SN - 1471-2164

VL - 15

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 804

ER -

De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies

Abstract

Bibliographical note

Funding

Keywords

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