TY - JOUR
T1 - De novo transcriptome assembly of the marine gastropod Reishia clavigera for supporting toxic mechanism studies
AU - Ip, Jack C.H.
AU - Leung, Priscilla T.Y.
AU - Ho, Kevin K.Y.
AU - Qiu, J. W.
AU - Leung, Kenneth M.Y.
N1 - Funding Information:
This work was substantially supported by the General Research Fund (Project no.: HKU 771212M) granted by the Research Grants Council of the Hong Kong SAR Government. JCHI thanks The University of Hong Kong (HKU) for providing him a Type B postgraduate studentship. 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.
PY - 2016/9/1
Y1 - 2016/9/1
N2 - The intertidal whelk Reishia clavigera is commonly used as a biomonitor of chemical contamination in the marine environment along Western Pacific region, and as a model for mechanistic studies of organotin-mediated imposex development. However, limited genomic resources of R. clavigera have restricted its role for the investigation of molecular mechanisms of such endocrine disruptions. This study, therefore, aimed to establish tissue-specific transcriptomes of the digestive gland, gonad, head ganglia, penis and the remaining body part of the male and female R. clavigera. By combining the results, a global transcriptome was obtained. A total of 578,134,720 high-quality filtered reads were obtained using Illumina sequencing. The R. clavigera transcriptome comprised of 38,466 transcripts and 32,798 unigenes with predicted open reading frames. The average length of transcripts was 1,709 bp with N50 of 2,236 bp. Based on sequence similarity searches against public databases, 28,657 transcripts and 24,403 unigenes had at least one BLAST hit. There were 17,530 transcripts and 14,897 unigenes annotated with at least one Gene Ontology (GO) term. Moreover, 5,776 transcripts and 5,137 unigenes were associated with 333 Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. The numbers of unigenes were similar among the five target tissues and between sexes, but tissue-specific expression profiles were revealed by multivariate analyses. Based on the functional annotation, putative steroid hormone-associated unigenes were identified. In particular, we highlighted the presence of steroid hormone receptor homologues that could be the targets for mechanistic studies of the organotin-mediated imposex development in marine gastropods. This newly generated transcriptome assembly of R. clavigera provides a valuable molecular resource for ecotoxicological and environmental genomic studies.
AB - The intertidal whelk Reishia clavigera is commonly used as a biomonitor of chemical contamination in the marine environment along Western Pacific region, and as a model for mechanistic studies of organotin-mediated imposex development. However, limited genomic resources of R. clavigera have restricted its role for the investigation of molecular mechanisms of such endocrine disruptions. This study, therefore, aimed to establish tissue-specific transcriptomes of the digestive gland, gonad, head ganglia, penis and the remaining body part of the male and female R. clavigera. By combining the results, a global transcriptome was obtained. A total of 578,134,720 high-quality filtered reads were obtained using Illumina sequencing. The R. clavigera transcriptome comprised of 38,466 transcripts and 32,798 unigenes with predicted open reading frames. The average length of transcripts was 1,709 bp with N50 of 2,236 bp. Based on sequence similarity searches against public databases, 28,657 transcripts and 24,403 unigenes had at least one BLAST hit. There were 17,530 transcripts and 14,897 unigenes annotated with at least one Gene Ontology (GO) term. Moreover, 5,776 transcripts and 5,137 unigenes were associated with 333 Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. The numbers of unigenes were similar among the five target tissues and between sexes, but tissue-specific expression profiles were revealed by multivariate analyses. Based on the functional annotation, putative steroid hormone-associated unigenes were identified. In particular, we highlighted the presence of steroid hormone receptor homologues that could be the targets for mechanistic studies of the organotin-mediated imposex development in marine gastropods. This newly generated transcriptome assembly of R. clavigera provides a valuable molecular resource for ecotoxicological and environmental genomic studies.
KW - Endocrine disruption
KW - Nuclear receptor
KW - Organotin
KW - Thais clavigera
KW - Transcriptomic
UR - http://www.scopus.com/inward/record.url?scp=84978676907&partnerID=8YFLogxK
U2 - 10.1016/j.aquatox.2016.07.006
DO - 10.1016/j.aquatox.2016.07.006
M3 - Journal article
C2 - 27450239
AN - SCOPUS:84978676907
SN - 0166-445X
VL - 178
SP - 39
EP - 48
JO - Aquatic Toxicology
JF - Aquatic Toxicology
ER -
