[en] Plantae (Archaeplastida) are a natural group of organisms with plastids of primary endosymbiotic origin. Within this group, members of the red algae show evidence of a reduction of their genomic content. In this work, we designed a bioinformatics approach to investigate the few, sometimes incomplete, genomic datasets available for red algae, with the purpose of pointing out possible gene family losses and expansions. Our pipeline first populates a relational database with precomputed orthology relationships between green plant genomes and red algal datasets and then efficiently queries the database for computing statistics of losses and expansions for a series of gene families of interest.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Di Franco, Arnaud ; Université de Liège - ULiège > Doct. sc. (bioch., biol. mol.&cell., bioinf.&mod.-Bologne)
Hanikenne, Marc ; Université de Liège - ULiège > Département des sciences de la vie > Génomique fonctionnelle et imagerie moléculaire végétale
Baurain, Denis ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes
Language :
English
Title :
Identifying losses and expansions of selected gene families in incomplete genomic datasets