Changes to the FlyBase gene model annotation set in the era of high-throughput data. Changes to the FlyBase gene model annotation set in the era of high-throughput.

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Changes to the FlyBase gene model annotation set in the era of high-throughput data. Changes to the FlyBase gene model annotation set in the era of high-throughput data. The gene model annotation set of FlyBase version FB2010_01 (R5.24), the last version to predate FlyBase incorporation of high-throughput data, was compared to that of FlyBase version FB2014_06 (R6.03) to determine the degree of change over the course of 26 annotation updates. Gene model annotations common to both sets (white) were identified. Gene model annotations specific to R6.03 were then examined to identify those derived from R5.24-specific gene model annotations through gene merge/split or reclassification (yellow). The remaining R5.24-specific annotations were classified as “withdrawn” (red), and the R6.03-specific annotations were classified as “new” (blue). The number of gene models within each category of status change is shown for protein-coding genes (A). For 13,003 of the 13,112 protein-coding genes common to both R5.24 and R6.03 (excluding nine complex cases), we also examined the degree to which the number of associated transcripts changed: a measure of gene model complexity. For these genes, the numbers of associated transcripts that persisted (white), were deleted (red), or were added (blue) at some point between R5.24 and R6.03 are shown (B). Changes to the set of annotated pseudogenes (C) and non-coding RNA genes (D) are also shown. Beverley B. Matthews et al. G3 2015;5:1721-1736 ©2015 by Genetics Society of America