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.
authors.forename: Priscilla T Y
authors.initials: PT
authors.lastname: Leung
authors.forename: Jack C H
authors.initials: JC
authors.lastname: Ip
authors.forename: Sarah S T
authors.initials: SS
authors.lastname: Mak
authors.forename: Jian Wen
authors.initials: JW
authors.lastname: Qiu
authors.forename: Paul K S
authors.initials: PK
authors.lastname: Lam
authors.forename: Chris K C
authors.initials: CK
authors.lastname: Wong
authors.forename: Leo L
authors.initials: LL
authors.lastname: Chan
authors.affiliation: The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. kmyleung@hku.hk.
authors.forename: Kenneth M Y
authors.initials: KM
authors.lastname: Leung
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D020451:Contig Mapping; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D058977:Molecular Sequence Annotation; D009132:Muscles / Q000378:metabolism; D049883:Perna / Q000235:genetics*; D025341:Principal Component Analysis; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological; D059467:Transcriptome