Poplar carbohydrate-active enzymes - whole genome annotation and functional analyses based on RNA expression data
Plant J. 2019 May 20 [Epub ahead of print]
Kumar V, Hainaut M, Delhomme N, Mannapperuma C, Immerzeel P, Street NR, Henrissat B, Mellerowicz EJ
Carbohydrate-Active enZymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites, and cell wall biopolymers. They are the key enzymes for biosynthesis of food and renewable biomass. Woody biomass is particularly important for long-term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents de-novo annotation of CAZymes genes in the current Populus trichocarpa genome assembly, and their in silico functional characterization based on high resolution RNA-Seq datasets. Altogether 1914 CAZyme and expansin genes were annotated in 101 families. 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and A. thaliana (with exception of CBM13 found only in poplar), a few families had significantly different copy number between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co-expression network analysis of CAZymes in wood forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v 3.0/) for P. tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue-specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for modification of secondary cell wall biosynthesis, and other developmental processes in woody plants.
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