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Next generation sequencing facilitates quantitative analysis of wild type and overexpression of LbDREB6 transgenic line transcriptomes

ABSTRACT: Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between overexpression of LbDREB6 transgenic lines and Wild Type expose to pathogen stress Methods:After 2 days of inoculation with the pathogen, leaves of WT, OE14 and OE18 plants were harvested and frozen in liquid nitrogen immediately for RNA extraction. For each sample, ~20 μg total RNA of stem tip with 2 pieces of leaves was sent to Annoroad Gene Technology Co., Ltd, Beijing, China for high throughout Illumina HiSeq 4000 sequencing (Illumina, San Diego, CA, USA). Results: To determine the possible pathways of LbDREB6 in pathogen defense, we conduct the transcriptomotic sequencing. After sequence, we achieved 53.20 Gb clean reads (18.2–24.7 million per library, Q30 ≥95.02%). About 68.3%-70.42% clean reads per library could be mapped to the Populus trichocarpa genome (see Table S2). The quality of the assembled transcriptome is good enough for functional annotation and further analysis compared with WT. Conclusions: Our study represents the detailed analysis of pathogen response transcriptomes , with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that next generation sequencing offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

ORGANISM(S): Populus ussuriensis

PROVIDER: GSE120118 | GEO | 2020/09/19

REPOSITORIES: GEO

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