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men12278-sup-0001-AppendixS1.xlsapplication/msexcel6852KAppendix S1. The breadth of coverage of all genes in the predicted gene set of the oyster genome mapped by transcriptome sequencing reads. The file contains the breadth of coverage from Qingdao, Qinhuangdao, Dalian and the combined population, in addition to the coordinates of the coding regions with a minimum sequencing depth of 4 in the combined population.
men12278-sup-0002-AppendixS2.xlsapplication/msexcel7720KAppendix S2. List of the 0.58 million putative SNPs found in the study. The file contains the putative SNP information including the scaffold ID, coordinate, the reference base at the corresponding position, SNP type and gene ID.
men12278-sup-0003-AppendixS3.xlsapplication/msexcel885KAppendix S3. Summary of the 1,671 putative SNPs genotyped by HRM analysis. The table contains putative SNP type, primer sequences, melting temperature of PCR, expected product sequence and gene annotation.
men12278-sup-0004-AppendixS4.xlsapplication/msexcel260KAppendix S4. Expression values of the 275 stress-responsive genes under varying degrees of different stimuli, including salinity, temperature and exposure to air and heavy metals. The expression levels were estimated by the reads per kilobase per million reads (RPKM) measure. The annotation of GO, KEGG and Swiss-Prot was provided for each gene.
men12278-sup-0005-AppendixS5.pdfapplication/PDF1696KAppendix S5. SNP confirmation by Sanger sequencing. A) Melting curves with three types of genotypes marked with c, d and g. B) PCR sequence alignment. Three types of amplicons corresponding to different melting curves were sequenced, respectively, and four clones were listed in each type of selected amplicon. Ref: reference sequence; a and c: sequence of the two homozygotes; b: sequence of the heterozygote.
men12278-sup-0006-AppendixS6.pdfapplication/PDF2782KAppendix S6. Existence of unpredicted SNPs in addition to the target SNP in the same amplicon. A) High-resolution melting peaks of the amplicons that contained an unpredicted SNP in addition to the target SNP. a: Melting curves of one homozygote; b, c and d: melting curves of different heterozygotes. B) Sequence alignment of the amplicons indicates the presence of the extra SNP in the same amplicon. Light grey is used to highlight the target SNP, whereas dark grey shows the unpredicted SNP. Ref: the reference sequence.
men12278-sup-0007-AppendixS7.pdfapplication/PDF1525KAppendix S7. The genotyping result of Cg_cSNP_635 with different numbers of samples. A) Melting curves of Cg_cSNP_635 for eight samples. B) Melting curves of Cg_cSNP_635 for 48 samples. The same regular melting curves were acquired with different numbers of samples.
men12278-sup-0008-AppendixS8.pdfapplication/PDF3596KAppendix S8. High-resolution melting peaks with/without temperature calibration of Cg_cSNP_1965 (A1 and A2) and Cg_cSNP_2012 (B1 and B2). A1, B1) High-resolution melting peaks without temperature calibration. A2, B2) High-resolution melting peaks with temperature calibration. After temperature calibration, the tightly integrated melting curves made it easier to distinguish one peak from the other.

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