A total of 4,690 transcripts possessed assembled transcript support by both Cufflinks and Scripture.
Between JGI and this study, there is transcript support for 27,016 loci, a number that compares well with 28,457 predicted genes in the BGI Shandong E. salsugineum genome release [ 13] and 28,901 protein-coding genes for the closely related Eutrema parvulum (also known as T. parvula) [ 24].
Notably, recent RNAseq experiments revealed some discrepancies between transcripts and annotated genes, and supported the existence of new genes and/or putative non-coding RNAs ([ 55], and RNAseq evidences in ToxoDB v9.0).
In addition, the functionality of these platelet transcripts was supported by a strong correlation between transcript abundance and protein expression [ 63, 64].
The higher similarity seen between Anopheles and Mayetiola transcripts supports their closer evolutionary relationship and suggests that the higher Dipteran split occurred prior to the divergence of the Hessian fly and mosquito.
We next investigated possible biases between intron support and other characteristics of introns, including size, splice site consensus sequence, and position within the spliced transcript.
For example, transcripts supporting molecular function and cell component were different between the two interaction types.
The yellow stage has the highest number of genes expressed (43,552 transcripts, TPM > 1), compared to red and green stages (43,257 and 36,388 transcripts) (Supporting Information Fig. S1).
