Alignments of C. gigas in vitro sequences

• Main Authors: Lapègue, Sylvie, Heurtebise, Serge, Flahauw, Emilie
• Format: Report
• Language: unknown
• Published: 2014
• Subjects: Aquaculture; Invertebrates; Population Genetics - Empirical; Adaptation; Pacific; Pacific oyster
• Online Access: http://hdl.handle.net/10255/dryad.58488; https://doi.org/10.5061/dryad.jr233/4

For the Pacific oyster, in vitro sequencing investigated 103 loci from ESTs retrieved from the Genbank database (http://www.ncbi.nlm.nih.gov/) or from specific libraries that had been obtained to detect genes differentially regulated during summer mortality events (Fleury et al. 2009). Primers were designed using the Primer3 software package (Rozen and Skaletsky 2000). For a first set of ESTs (n = 61), 24 oysters belonging to a third generation of selection for summer mortality resistance were used in the SNP discovery phase (Sauvage 2008; Sauvage et al. 2007). A second set of ESTs (n = 42) was then added and 10 of the 24 oysters were used for sequencing, as described in Sauvage et al. (2007), together with a third set of five SNPs from the 20 developed by Bai et al. (2009). Sequence alignment was performed with ClustalW via the BioEdit interface (Hall 1999) and DNAMAN version 4.1 (www.lynnon.com). The validity of each SNP was checked manually on the chromatograms and sequence alignments. A total of 321 in vitro SNPs were detected in the first dataset of 61 sequenced fragments, and 380 in the second dataset of 42 sequenced fragments. Among those 701 SNPs, 72 were selected (39 and 33 from the two datasets, respectively) because they had high functionality scores and no neighboring polymorphisms. However, as we wanted to be sure that some genes of interest were represented in the SNP dataset, for several ESTs we kept two SNPs. Therefore, our 72 selected in vitro SNPs were obtained from 65 different ESTs.