Skip to main content
Dryad logo

Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence

Citation

Luo, Chaobing et al. (2020), Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence, Dryad, Dataset, https://doi.org/10.5061/dryad.05qfttdzr

Abstract

Neosinocalamus affinis, a type of cluster bamboo, is a good candidate feedstock for biomass energy. In the study, we found a total of 686 genes were identified as belonging to CAZyme families in the N. affinis transcriptome, including 222 glycoside hydrolases (GHs), 288 glycosyltransferases (GTs), 64 carbohydrate esterases (CEs), 70 auxiliary activities (AAs), 37 carbohydrate binding modules (CBMs) and five polysaccharide lyases (PLs). Expression profiles revealed that several CAZyme genes were up-regulated after insect infestation, particularly the GT, GH, AA and CE family members. Lignocellulose assays showed that the contents of three components, cellulose, hemicellulose and lignin, increased after insect infestation. Our findings showed that CAZyme genes were abundant in the N. affinis transcriptome and were involved in the response to herbivory. These findings could be applied to protect bamboo against herbivores, such as the bamboo snout beetle Cyrtotrachelus buqueti, and develop low-cost chemical feedstock from bamboo.

Methods

Transcriptome data from Neosinocalamus affinis and CAZyme family analysis

The N. affinis transcriptome data were retrieved from the National Center for Biotechnology Information (NCBI) database Sequence Read Archive (SRA; BioProject PRJNA396472), accessed through the accession number SRX3051434 using NCBI (https://www.ncbi.nlm.nih.gov/) and focused on CAZyme genes. To identify CAZyme genes, coding sequences of all the assembled unigenes were submitted for local BLASTx search using the dbCAN CAZyme annotation algorithm, which provides the hidden Markov model index files of various carbohydrate enzyme domains by hmmscan,16 with an E-value cutoff of 1E−5.

Phylogenetic analysis of the CAZymes

ClustalX 2.1 program and DNAMAN software version 8.0 (Lynnon Biosoft) were used to align CAZyme protein sequences with default parameters. The MEGA 7.0 program17 was used to establish a tree between N. affinis and A. thaliana to survey the phylogenetic relationships using the Neighbor-Joining method with 1000 bootstrap replicates.

Funding

Department of Sichuan Science and Technology, Award: 2019YFG0139

Department of Sichuan Science and Technology, Award: 2019YFG0139