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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3052-0) contains supplementary material, which is available to authorized users.

Genes for ash tree resistance to an insect pest identified via comparative genomics

“…None of the EAB-resistance associated amino acid states were found in the putatively resistant F. pennsylvanica genotype (Supplementary Table 8), suggesting that different genes, or different variants within these genes, are involved in the intraspecific variation in susceptibility of this species. Despite this, transcripts inferred to be from 11 of our candidate genes showed evidence for differential expression subsequent to EAB-7 feeding in F. pennsylvanica (Supplementary Note 6 and Supplementary Table 10) and two gene families that were highlighted as potentially important for response to tissue damage in F. pennsylvanica 25 are also represented among our candidates (see above).…”

“…Fraxinus species has been previously suggested on the basis of chemical 24 and transcriptomic 25 data, and several metabolomic studies have indicated that products of the phenylpropanoid pathway could be involved 26 .…”

“…OG11720 is putatively orthologous to NRT1.5/NPF7. 3., a member of the NRT1/PTR family 32 which is involved in transport of multiple phytohormones (Supplementary Note 4.3); a transcript matching this gene family had decreased expression in response to both mechanical wounding and EAB feeding in F. pennsylvanica 25 . Putative functions of further candidates relate to other signalling molecules involved in triggering defence response (Supplementary Note 4.5), including calcium (OG50989) 17,33 , nitric oxide (NO; OG21033) 34,35 and spermine (OG33348) 36 .…”

Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

“…Root tissues of heat, cold, drought and unstressed honeylocust half-sib seedlings were used to generate five transcriptome libraries as described in Lane et al (2016). After TruSeq Stranded mRNA library preparation we performed paired-end sequencing of the five libraries on an Illumina MiSeq (San Diego, Ca) with a read length of 151 bp and deposited raw reads in the NCBI Short Read Archive (SRA) (BioProject accession number PRJNA273269).…”

“…After TruSeq Stranded mRNA library preparation we performed paired-end sequencing of the five libraries on an Illumina MiSeq (San Diego, Ca) with a read length of 151 bp and deposited raw reads in the NCBI Short Read Archive (SRA) (BioProject accession number PRJNA273269). Error correction, trimming and assembly of reads were performed as described in Lane et al (2016). Open Reading Frames (ORFs) were predicted with TransDecoder 2.01 (Haas et al 2013).…”