The green ash transcriptome and identification of genes responding to abiotic and biotic stresses

BMC Genomics

Research Article

Stephan Schuster¹  John McGraw¹  Donghwan Shim²  Teodora Best²  John E. Carlson²  Nicole Zembower²  Jack Davitt³  Nathan Henry³  Thomas Lane³  Margaret E. Staton³  Mark V. Coggeshall⁴  Haiying Liang⁵  Yi Xu⁶  Jennifer Koch⁷ 

[1] Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 16802, University Park, PA, USA;Department of Ecosystem Science and Management, Pennsylvania State University, 16802, University Park, PA, USA;Department of Entomology and Plant Pathology, University of Tennessee, 37966, Knoxville, TN, USA;Department of Forestry, University of Missouri, 65211, Columbia, MO, USA;Department of Plant Biology and Pathology, Rutgers University, 08901, New Brunswick, NJ, USA;Department of Plant Biology and Pathology, Rutgers University, 08901, New Brunswick, NJ, USA;Department of Genetics and Biochemistry, Clemson University, 29634, Clemson, SC, USA;Northern Research Station, USDA Forest Service, 43015, Delaware, OH, USA;

关键词: Transcriptome;    RNASeq;    Assembly;    Fraxinus;    Emerald ash borer;    Heat;    Drought;    Cold;    Ozone;    Stress response;   

DOI  :  10.1186/s12864-016-3052-0

 received in 2016-03-11, accepted in 2016-08-27,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundTo develop a set of transcriptome sequences to support research on environmental stress responses in green ash (Fraxinus pennsylvanica), we undertook deep RNA sequencing of green ash tissues under various stress treatments. The treatments, including emerald ash borer (EAB) feeding, heat, drought, cold and ozone, were selected to mimic the increasing threats of climate change and invasive pests faced by green ash across its native habitat.ResultsWe report the generation and assembly of RNA sequences from 55 green ash samples into 107,611 putative unique transcripts (PUTs). 52,899 open reading frames were identified. Functional annotation of the PUTs by comparison to the Uniprot protein database identified matches for 63 % of transcripts and for 98 % of transcripts with ORFs. Further functional annotation identified conserved protein domains and assigned gene ontology terms to the PUTs. Examination of transcript expression across different RNA libraries revealed that expression patterns clustered based on tissues regardless of stress treatment. The transcripts from stress treatments were further examined to identify differential expression. Tens to hundreds of differentially expressed PUTs were identified for each stress treatment. A set of 109 PUTs were found to be consistently up or down regulated across three or more different stress treatments, representing basal stress response candidate genes in green ash. In addition, 1956 simple sequence repeats were identified in the PUTs, of which we identified 465 high quality DNA markers and designed flanking PCR primers.ConclusionsNorth American native ash trees have suffered extensive mortality due to EAB infestation, creating a need to breed or select for resistant green ash genotypes. Stress from climate change is an additional concern for longevity of native ash populations. The use of genomics could accelerate management efforts. The green ash transcriptome we have developed provides important sequence information, genetic markers and stress-response candidate genes.

【 授权许可】

CC BY   
© The Author(s). 2016