Table 1.
Comparison of transcriptome assembly statistics
| Trimmed only, N = 3 reps/tissue | Trimmed only, N = 1 rep/tissue | Trim + error correction, N = 1 rep/tissue | |
|---|---|---|---|
| Transcriptome name | TR333942 | TR118377 | NvecRef32743 |
| Assembled “transcripts”a | 333,942 | 118,377 | 32,743 |
| Transcripts with predicted ORFsb | 29,690 (9 %) | 19,461 (16 %) | 17,346 (53 %) |
| Predicted ORFsc | 135,213 (4.6X) | 77,877 (4X) | 27,511 (1.6X) |
| ORFs with no expressiond | 74,503 (55 %) | 28,975 (37 %) | 10,198 (37 %) |
| CEGMA score (complete) e | 242/248 (98 %) | 241/248 (97 %) | 207/248 (83 %) |
| CEGMA score (partial) | 245/248 (99 %) | 245/248 (99 %) | 231/248 (93 %) |
aTotal number of contigs assembled using Trinity [49, 50]. bOpen reading frames (ORFs) ≥ 100 amino acids (aa) in length were predicted using Transdecoder (http://transdecoder.github.io). cThe average number of ORFs predicted from each transcript is listed in parentheses. dTotal number of transcripts with at least one ORF and abundance estimated at < 2 counts in at least one of the three sampled tissues; counts were assayed using Bedtools [55]. eCEGMA scores are listed as % of the 248 conserved eukaryotic genes that form the CEGMA database [56] that were present in the indicated transcriptome (scores for complete and partial sequences are indicated)