title: Mining tissue-specific contigs from peanut (Arachis hypogaea L.) for promoter cloning by deep transcriptome sequencing.
abstract: Peanut (Arachis hypogaea L.), one of the most important oil legumes in the world, is heavily damaged by white grubs. Tissue-specific promoters are needed to incorporate insect resistance genes into peanut by genetic transformation to control the subterranean pests. Transcriptome sequencing is the most effective way to analyze differential gene expression in this non-model species and contribute to promoter cloning. The transcriptomes of the roots, seeds and leaves of peanut were sequenced using Illumina technology. A simple digital expression profile was established based on number of transcripts per million clean tags (TPM) from different tissues. Subsequently, 584 root-specific candidate transcript assembly contigs (TACs) and 316 seed-specific candidate TACs were identified. Among these candidate TACs, 55.3% were root-specific and 64.6% were seed-specific by semi-quantitative RT-PCR analysis. Moreover, the consistency of semi-quantitative RT-PCR with the simple digital expression profile was correlated with the length and TPM value of TACs. The results of gene ontology showed that some root-specific TACs are involved in stress resistance and respond to auxin stimulus, whereas, seed-specific candidate TACs are involved in embryo development, lipid storage and long-chain fatty acid biosynthesis. One root-specific promoter was cloned and characterized. We developed a high-yield screening system in peanut by establishing a simple digital expression profile based on Illumina sequencing. The feasible and rapid method presented by this study can be used for other non-model crops to explore tissue-specific or spatially specific promoters.
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Geng
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Duan
authors.affiliation: Department of Biology, Miami University, Oxford, OH 45056, USA Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA.
authors.forename: Chun
authors.initials: C
authors.lastname: Liang
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Changlong
authors.initials: C
authors.lastname: Shu
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors.forename: Fuping
authors.initials: F
authors.lastname: Song
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China jzhang@ippcaas.cn.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
mesh_terms: D010367:Arachis / Q000235:genetics*; D003001:Cloning, Molecular; D059014:High-Throughput Nucleotide Sequencing; D011401:Promoter Regions, Genetic; D059467:Transcriptome
keywords: Arachis hypogaea; Digital gene expression profile; Root-specific transcript assembly contigs; Seed-specific transcript assembly contigs; Tissue-specific promoters