Transcriptomic Analysis of the Clam Meretrix meretrix on Different Larval Stages
- 897 Downloads
The clam Meretrix meretrix (Mollusca: Bivalvia) is an important commercial species in China. The deficiency of genomic and transcriptomic data is becoming the bottleneck of further researches on its complex and unique developmental processes. To improve this situation, in this study, a large-scale RNA sequencing was conducted on M. meretrix on larval stages. In particular, mRNAs of trochophore, D-veliger, pediveliger, and postlarva were purified, reverse transcribed, and sequenced through 454 sequencing technology. A total of 704,671 reads were obtained and assembled into 124,737 unique sequences (35,205 contigs and 89,532 singletons). Further analysis showed that 118,075 (94.66%) of these sequences were low-expression-level transcripts. Fifteen thousand two hundred fifteen (12.20%) of the unique sequences were annotated by searching against Uniprot Protein Knowledgebase, while the others (109,522, 87.80%) were left as novel sequences. Gene ontology analysis of the annotated sequences showed that most of them were assigned to certain gene ontology terms. By analyzing the depth of each unique sequence, a preliminary quantification analysis was conducted. An amount of sequences that showed a dramatic transcript discrepancy among the four larval stages were screened, which were related to development, growth, shell formation, and immune responses etc. As the first attempt on large-scale RNA sequencing of marine bivalve larvae, this work would enrich the knowledge of larval development of marine bivalves and provide fundamental support for further researches.
KeywordsTransctriptome Larval development Meretrix meretrix Bivalve
The authors thank Dr. Jiquan Zhang and Dr. ChengZhang Liu for the technical support. This project was financially supported by the National Basic Research Program of China (2010CB126403) and the National Natural Science Foundation of China (31072249, 30871910).
- Badhai J, Fröjmark A-S, Davey E, Schuster J, Dahl N (2009) Ribosomal protein S19 and S24 insufficiency cause distinct cell cycle defects in Diamond–Blackfan anemia. Biochim Biophys Acta Mol Basis Dis 1792(10):1036–1042Google Scholar
- Fleury E, Huvet A, Lelong C, De Lorgeril J, Boulo V, Gueguen Y, Bachere E, Tanguy A, Moraga D, Fabioux C, Lindeque P, Shaw J, Reinhardt R, Prunet P, Davey G, Lapegue S, Sauvage C, Corporeau C, Moal J, Gavory F, Wincker P, Moreews F, Klopp C, Mathieu M, Boudry P, Favrel P (2009) Generation and analysis of a 29,745 unique expressed sequence tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase. BMC Genomics 10(1):341PubMedCrossRefGoogle Scholar
- Gricourt L, Bonnec G, Boujard D, Mathieu M, Kellner K (2003) Insulin-like system and growth regulation in the Pacific oyster Crassostrea gigas: hrIGF-1 effect on protein synthesis of mantle edge cells and expression of an homologous insulin receptor-related receptor. Gen Comp Endocrinol 134(1):44–56PubMedCrossRefGoogle Scholar
- Gricourt L, Mathieu M, Kellner K (2006) An insulin-like system involved in the control of Pacific oyster Crassostrea gigas reproduction: hrIGF-1 effect on germinal cell proliferation and maturation associated with expression of an homologous insulin receptor-related receptor. Aquaculture 251(1):85–98CrossRefGoogle Scholar
- Lee SW, Hong SM, Choi CS (2006) Characteristics of calcification processes in embryos and larvae of the Pacific oyster, Crassostrea gigas. Bull Mar Sci 78(2):309–317Google Scholar
- Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, Deweese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39(suppl 1):D225–D229PubMedCrossRefGoogle Scholar