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 PublicationsJournal Article (refereed)peer-review

38 Citations (Scopus)


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 languageEnglish
Article number804
Number of pages14
JournalBMC Genomics
Issue number1
Publication statusPublished - 19 Sept 2014
Externally publishedYes

Bibliographical note

Funding Information:
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.

Publisher Copyright:
© 2014 Leung et al.


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


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