Functional Annotation of Alternative Splicing in Plants by the AStafunk Pipeline

Alternative splicing (AS) is an important process in gene regulation and substantially contributes to the proteome diversity. Modern genomics employ increasingly high-throughput technologies to obtain the genome and all forms of expressed genes from a studied plant or animal. To overcome difficulties of maintaining AS databases updated with all newly available transcriptome data, we previously introduced AStalavista, a computer program that reports within minutes all AS events on a genome-wide scale.

Here we present AStafunk, an automated pipeline to annotate the functional impact caused by AS. Employing knowledge about protein families, we integrate algorithms for the prediction of functional domains with the efficient detection of AS events. Such studies have hitherto been hampered by difficulties to map the effect of genomic events on the proteome level, which required cumbersome projections between aminoacid and nucleotide coordinates and also implied the inefficient analysis of highly redundant sequences intrinsic to AS transcriptomes.

In a nutshell, the AStafunk software requires as an input (1^st) the genomic context, (2^nd) gene models and (3^rd) protein domain models to provide the exhaustive landscape of AS events and how these are modifying protein domains (i.e., events creating/disrupting or modifying a domain). In the light of recent advances in plant genomics, with even more transcriptomes expected to become available soon from the 1000 Plants Consortium, we focus in this presentation on AStafunk annotations of publicly available transcriptomes throughout the plant kingdom (green algae, mosses, trees and other flowering plants): http://astalavista.sammeth.net