Expression and phylogenetic analyses of the genome-unpredicted RNAseq only novel Hydra gene families. A) Graph showing the proportion of the sequence covered by the ORF among the genome-unpredicted 7’103 RNAseq transcripts that encode short ORFs (<100 AA). 2’209 (31%) transcripts encode ORFs that cover >98% of their full length. B) Nucleotide sequence length of the transcripts analyzed in A: 81 are larger than 1’000 nt long (red line). The 25 largest contigs were tested by RT-PCR and all were successfully amplified (green dots). See Additional file 1: Figure S5. C) RT-PCR analysis of the expression of 25 genome-predicted Hydra transcripts not confirmed by RNAseq. To distinguish between gene and transcript amplification, PCR were performed on total RNA treated (+) or not (-) with DNAse (DN) and reverse transcribed (RT+) or not (RT-). D) The RNAseq only genes (i.e. genome-unpredicted), were sorted into three classes according to the presence (full dot) or the absence (empty dot) of the criteria specified above the first row. The expression of 18 sequences of class I and 25 sequences of classes II, III and IV was tested by RT-PCR.
Wenger and Galliot BMC Genomics 2013 14:204 doi:10.1186/1471-2164-14-204