Abstract
Coast redwood is a very important endemic conifer timber species in Southern Oregon and Northern California in the USA. Due to its good wood properties and fast growth rate it can be considered as a prospective timber species also in other countries with similar or changing toward similar climatic conditions due to global climate warming, such as Germany. In general, it is frost sensitive and suffers from freezing temperatures. To study genetic mechanisms of frost resistance in this species and to select the most frost tolerant trees we tested 17 clones in climate control chamber experiments and generated two de novo assemblies of the coast redwood transcriptome from a pooled RNA sample using Trinity and CLC Genomic Workbench software, respectively. The hexaploid nature of the coast redwood genome makes it very challenging to successfully assemble and annotate the coast redwood transcriptome. The de novo transcriptome assembly generated by Trinity and CLC considering only reads with a minimum length of 180 bp and contigs no less than 200 bp long resulted in 634,772 and 788,464 unigenes (unique contigs), respectively.
Highlights
Two transcriptome assemblies obtained in our study provide additional invaluable genomic resources and can support further coast redwood genetic studies including those concerning response of this and other conifer species to frost stress or other environmental stresses in general
Code availabilityBlast2GO PRO: https://www.blast2go.com/blast2go-pro Benchmarking Universal Single-Copy Orthologs (BUSCO) v4.0.5: https://busco.ezlab.org FastQC v0.11.5: https://www.bioinformatics.babraham.ac.uk/projects/fastqc Magic-BLAST v1.5.0: https://ncbi.github.io/magicblast MISA: http://pgrc.ipk-gatersleben.de/misa/misa.html PRIMER3: https://github.com/primer3-org/primer[3] Trimmomatic v.0.35: http://www.usadellab.org/cms/?page=trimmomatic Trinity v2.8.4: https://github.com/trinityrnaseq/trinityrnaseq/wiki
Summary
Don) Endl.) is an endemic forest tree conifer species occupying a narrow range along the Pacific Northwest coast in southern Oregon and northern California, USA. It is a valuable timber species characterized by fast growth rate and good quality wood[1]. To study genetic mechanisms of cold-resistance and to select frost-resistant coast redwood trees we tested replicates of 17 different coast redwood clones of diverse origin (Table 1) in a climate control chamber under a freezing temperature of up to −10 °C. Two transcriptome assemblies obtained in our study provide additional invaluable genomic resources and can support further coast redwood genetic studies including those concerning response of this and other conifer species to frost stress or other environmental stresses in general. We hope that our experience with de novo sequencing, assembling and annotating the transcriptome of this difficult non-model polyploid species can help other similar studies
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