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.

Forest tree species are increasingly subject to severe mortalities from exotic pests, pathogens, and invasive organisms, accelerated by climate change. Such forest health issues are threatening multiple species and ecosystem sustainability globally. One of the most extreme examples of forest ecosystem disruption is the extirpation of the American chestnut (Castanea dentata) caused by the introduction of chestnut blight and root rot pathogens from Asia. Asian species of chestnut are being employed as donors of disease resistance genes to restore native chestnut species in North America and Europe. To aid in the restoration of threatened chestnut species, we present the assembly of a reference genome for Chinese chestnut (C. mollissima) "Vanuxem," one of the donors of disease resistance for American chestnut restoration. From the de novo assembly of the complete genome (725.2 Mb in 14,110 contigs), over half of the sequences have been anchored to the 12 genetic linkage groups. The anchoring is validated by genetic maps and in situ hybridization to chromosomes. We demonstrate the value of the genome as a platform for research and species restoration, including signatures of selection differentiating American chestnut from Chinese chestnut to identify important candidate genes for disease resistance, comparisons of genome organization with other woody species, and a genome-wide examination of progress in backcross breeding for blight resistance. This reference assembly should prove of great value in the understanding, improvement, and restoration of chestnut species.

Background Sugar maple (Acer saccharum Marsh.) is a hardwood tree species native to northeastern North America and economically valued for its wood and sap. Yet, few molecular genetic resources have been developed for this species to date. Microsatellite markers have been a useful tool in population genetics, e.g., to monitor genetic variation and to analyze gene flow patterns. The objective of this study is to develop a reference transcriptome and microsatellite markers in sugar maple.FindingsA set of 117,861 putative unique transcripts were assembled using 29.2 Gb of RNA sequencing data derived from different tissues and stress treatments. From this set of sequences a total of 1068 microsatellite motifs were identified. Out of 58 genic microsatellite markers tested on a population of 47 sugar maple trees in upper Michigan, 22 amplified well, of which 16 were polymorphic and 6 were monomorphic. Values for expected heterozygosity varied from 0.224 to 0.726 for individual loci. Of the 16 polymorphic markers, 15 exhibited transferability to other Acer L. species.ConclusionsGenic microsatellite markers can be applied to analyze genetic variation in potentially adaptive genes relative to genomic reference markers as a basis for the management of sugar maple genetic resources in the face of climate change.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-017-2653-2) contains supplementary material, which is available to authorized users.

Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally.

Teak is one of the highly famous woody plant species for its premier quality of wood. Teak has problem on productivity because of long reproductive cycle. The problem is basically related to mechanism of flower development. The aim of this study was preliminary development of expressed gene database to characterize the floral transcriptome in teak. Two subtracted cDNA libraries were constructed from vegetative and generative bud tissues. Libraries were sequenced using Illumina MiSeq technology which generated paired-end read sequences 3,778,316 for vegetative and 3,701,878 for generative. The sequences assembled de novo into 87,365 transcript contigs consisting of 42,435,728 bases with N50 of 498 bp using CLC-Genomics Workbench. 76,169 (87.18%) of the 87,365 assembled contigs exhibited significant similarity BLASTN to Solanum lycopersicum database (www.phytozome.com). The assembled contigs were annotated through high stringency BLASTX analysis to proteome of S. lycopersicum. Distribution of contigs abundance between vegetative and generative stages analyzed using the DEGseq approach. The numbers of contigs distribution are 24,730 in vegetative, 28,912 in generative and 33,723 in both stages. The functionally protein datasets characterized by Gene Ontology (GO) annotation and KEGG metabolic pathways assignments for the result of DEG analysis. These contigs, 18,756 (75.84%) from vegetative, 22,089 (76.40%) from generative and 22,917 (67.96%) from both stages were assigned to GO classes. A total of 1455 (13.77%) were mapped to 30 pathways from vegetative, 1,638 (13.70%) were mapped to 27 pathways from generative and 1,652 (12.20%) were mapped to 30 pathways from both by BLAST comparison against the KEGG database. The biological processes of flowering developments were identified in the biological process dataset and the numbers of contigs were discovered different between stages. This transcriptome dataset information will act as a valuable resource for further molecular genetic studies teak, as well as for isolation and characterization of functional genes involved in flowering development pathways.