Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica

BMC Genomics

Table 2 Comparison of quality statistics for transcriptome assembly at unclustered, 95% and 80% sequence identity thresholds

	Unclustered	95% sequence identity threshold	80% sequence identity threshold
Composition
Total # Reftigs	136,000	114,716	98,729
% Contigs	16.4%	18.9%	20.5%
% Singletons	83.6%	81.1%	79.5%
Annotation
Total reftigs annotated		58,811	50,736
% Reftigs annotated		51.3%	51.4%
% of Contigs		62.6%	64.3%
% of Singletons		48.6%	48.1%
# of Osmoregulation candidates		1014	1007
Sample illumina reads mapped to annotated transcriptome
% Reftigs with mapped reads		86.7%	88.3%
% of Reads mapped uniquely		40.8%	42.8%

With more permissive clustering, the number of unique sequences in the transcriptome (reftigs) decreases and the proportion of non-singleton reftigs (contigs) increases. The clustering threshold has a trivial effect on the proportion of reftigs annotated and the number of osmoregulatory candidates recovered. With 42.8% of Illumina reads uniquely mapping, transcriptomes based on more permissive clustering have a greater percentage of annotated reftigs with reads mapped to them as well as a greater percentage of uniquely mapped reads.

ISSN: 1471-2164