A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species

Table 1 Number of genes obtained by each annotation method

Method	D. melanogaster	D. simulans	D. mauritiana	Comparable
Published annotation	13,676	11,837 (86.55 %)	12,005 (87.78 %)	9,994 (73.08 %)
after filtering				8,810 (64.42 %)
Direct re-annotation	13,676	13,436 (98.24 %)	13,401 (97.99 %)	13,328 (97.45 %)
after filtering				12,334 (90.19 %)
Reciprocal re-annotation	13,457 (98.40 %)	13,373 (97.78 %)	13,346 (97.59 %)	13,311 (97.33 %)
after filtering				13,239 (96.80 %)

The last column contains the number of genes for which 1:1 orthologs were identified in the three species. “after filtering” indicates the remaining common genes after filtering out genes with length difference larger than 49 bp. Percentages in brackets are always given in relation to the total number of gene models in D. melanogaster (r5.55; 13,676 gene models)

ISSN: 1471-2164