During the assisted assembling (Supplementary Data), 779,694 SNPs and 156,376 Indels with combined length of 1,779,694 and 1,075,154 bp, respectively, were used as a guide of the genome revision to obtain IR.
Of 283 predicted extensions, 256 were consistent with FlyBase genome annotation revision 5.43.
The Flybase Consortium, Data from: D. melanogaster genome annotation revision 5.43, ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.43_FB2012_01/gff/dmel-all-no-analysis-r5.43.gff.gz, Freely available online.
It is likely that increased numbers of platyhelminth MBDs (especially within the 'Monogenea') will be identified once existing genomes undergo revision [ 36] or new genomes/transcriptomes are sequenced.
Before describing the applications of CVTree3, we recall the significant fact that for prokaryotes with sequenced genomes, all taxonomic revisions or new proposals published thus far agree with CVTree or at least do not contradict the CVTree branching order.
The high number of reads in intronic and intergenic regions, together with the high percentage of reads that did not map at all (14%), strongly indicates that the Vitis reference genome may require revision.
After revision of Genome Studio plots (Online Resource 4), we identified discrepancies for 15 of those samples.
The procedure followed the standard protocol for Illumina Whole Genome Gene Expression with IntelliHyb, revision A. Hybridisation was detected using 1 µg/mL Cy3-streptavidin (GE Healthcare, Little Chalfont, UK).
The use of GenePRIMP for genome annotation enabled manual revision of 132 long genes, 130 short genes, 99 broken genes and 76 interrupted genes.
