Hard clam, Meretrix spp. , are widely commercial aquaculture species in Asia. Various breeding programs, such as mass selection, family selection, and hybridization between different geographic populations, have been used in hard clam. Their growth and survival are often influenced by environmental factors, pathogens or genetic defect. However, the production of hard clam farming declined recently in Taiwan. There are five major aquaculture species in Taiwan: Meretrix meretrix, M. lusoria, M. lamarckii, M. petechialis, M. lyrata. Next-generation sequencing (NGS) can allow us to collect gene data and establish gene library much more quickly and cheaply than previous methods. In this project, genetic samples of Meretrix spp. from major farming area in Taiwan will be analyzed by NGS for species detection and gene variation to explore the causes of declined production:
In this project:
1. The COI sequence of 52 hard clam individuals from Taishi, Yunlin and DongShih, Chiayi were amplified by PCR. In sequence alignment and phylogenetic tree analysis, 49 individuals belonged to one clade and 3 individuals belong to another clade. These results showed the clade distribution of aquacultured hard clam and the sample picking of NGS experiments.
2. Assembled sequences of hard clams transcriptome were annotated with Function Annotator pipeline. Several methods were used to infer their potential functions. Briefly, assembled sequences were aligned to NCBI nr database with blastx program and potential coding regions were predicted with TransCoder program. The transcriptome of hard clam showed lower similarity of mRNA sequences of other Mollusca species, the highest is Pacific oyster with 33.6% by taxonomic distribution analysis. 11 candidates of temperature-tolerant genes were picked by sequence expression comparison between hard calms individuals cultured in different temperatures. More tests and experiments are needed for confirmation.