title: Analysis of de novo sequencing and transcriptome assembly and lignocellulolytic enzymes gene expression of Coriolopsis gallica HTC.
abstract: White-rot basidiomycete Coriolopsis gallica HTC is one of the main biodegraders of poplar. In our previous study, we have shown the strong capacity of C. gallica HTC to degrade lignocellulose. In this study, equal amounts of total RNA fromC. Gallica HTC cultures grown in different conditions were pooled together. Illumina paired-end RNA sequencing was performed, and 13.2 million 90-bp paired-end reads were generated. We chose the Merged Assembly of Oases data-set for the following blast searches and gene ontology analyses. The reads were assembled de novo into 28,034 transcripts (≥ 100 bp) using combined assembly strategy MAO. The transcripts were annotated using Blast2GO. In all, 18,810 transcripts (≥100 bp) achieved BLASTX hits, of which, 7048 transcripts had GO term and 2074 had ECs. The expression level of 11 lignocellulolytic enzyme genes from the assembled C. gallica HTC transcriptome were detected by real-time quantitative polymerase chain reaction. The results showed that expression levels of these genes were affected by carbon source and nitrogen source at the level of transcription. The current abundant transcriptome data allowed the identification of many new transcripts in C. gallica HTC. Data provided here represent the most comprehensive and integrated genomic resources for cloning and identifying genes of interest from C. gallica HTC. Characterization of C. gallica HTC transcriptome provides an effective tool to understand mechanisms underlying cellular and molecular functions of C. gallica HTC.
authors.affiliation: a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.
authors.forename: Yuehong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Cao
authors.affiliation: b Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Tao
authors.affiliation: a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.
authors.forename: Huanhuan
authors.initials: H
authors.lastname: Shao
authors.affiliation: a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.
authors.forename: Kun
authors.initials: K
authors.lastname: Zhang
authors.affiliation: a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.
authors.forename: Yizheng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Tan
mesh_terms: D055453:Coriolaceae / Q000201:enzymology* / Q000235:genetics*; D004798:Enzymes / Q000235:genetics* / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008031:Lignin / Q000235:genetics / Q000378:metabolism*; D016366:Open Reading Frames; D060888:Real-Time Polymerase Chain Reaction; D059467:Transcriptome
chemical_list: D004798:Enzymes; D005656:Fungal Proteins; C036909:lignocellulose; D008031:Lignin
keywords: Coriolopsis gallica HTC; Gene annotation; real-time quantitative PCR; sequence assembler; transcriptome