Leung Priscilla T Y, Ip Jack C H, Mak Sarah S T, Qiu Jian Wen, Lam Paul K S, Wong Chris K C, Chan Leo L, Leung Kenneth M Y
The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
BMC Genomics. 2014 Sep 19;15(1):804. doi: 10.1186/1471-2164-15-804.
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.
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.
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.
热带绿唇贻贝（Perna viridis）是整个印度 - 太平洋地区常用的生物监测器，用于环境监测和生态毒理学研究。然而，关于该物种的分子数据有限。我们试图从绿唇贻贝的闭壳肌、鳃和肝胰腺组织建立一个全球转录组数据库，以增进我们对这个指示物种在特定毒性反应中涉及的分子方面的理解。
Illumina测序结果产生了544,272,542条高质量过滤后的 reads。使用Trinity进行从头组装后，生成了233,257个contig，平均长度为1,264 bp，N50长度为2,868 bp；聚类后获得了192,879个组装转录本和150,111个组装单基因。基于InterProScan分析，预测了总共93,668个具有蛋白质结构域推定功能的组装转录本（66,692个组装基因）。基于相似性搜索，44,713个组装转录本和25,319个组装单基因至少有一个BLAST匹配注释。总共21,262个组装转录本（11,947个组装基因）至少有一个明确的基因本体（GO）注释，5,131个组装转录本（3,181个组装单基因）被分配到329个京都基因与基因组百科全书（KEGG）通路。从雄性和雌性贻贝获得的组装单基因和转录本数量相似，但在三个研究组织中有所不同，鳃中的数量最高，其次是肝胰腺，然后是闭壳肌。多变量分析显示，在三个不同组织之间存在强烈的组织特异性模式，但在不同GO术语中注释基因的表达谱以及与应激反应和异生物质降解相关的基因方面，性别之间没有差异。使用实时定量聚合酶链反应分析进一步验证了每种组织类型中某些选定基因的表达谱，并且观察到了类似的组织特异性趋势。
本研究产生的大量序列数据将为促进绿唇贻贝的环境研究提供有价值的分子资源，并突出未来组织特异性方法的重要性。
