4/15/2023 0 Comments Clc genomics workbench assembly![]() We also 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. 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. Published transcriptome data are also limited 3. Its genome has only recently been sequenced, and the genome assembly has been made publicly available (, accessed in May 2019), but it is still unpublished and not annotated. Coast redwood is a hexaploid species and is very difficult to study. RNA isolated from 12 clones from different temperature treatments was used to generate two de novo assemblies of a coast redwood transcriptome using Trinity and CLC Genomic Workbench software considering only reads with a minimum length of 180 bp and contigs no less than 200 bp long. Samples included the ‘Filoli-phenotype’ clones and clones from two trees growing in Germany that are considered as frost resistant. 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 ☌. Considering global warming and climate change, this species can be potentially considered as a prospective commercial timber species for future German sustainable forestry. However, some coast redwood trees survived freezing temperatures in Germany demonstrating cold-tolerance. The species has been planted successfully in some other countries for commercial wood production 2, but in Germany it is used currently rather as a decorative, exotic species, mainly due to its sensitivity to freezing temperatures. It is a valuable timber species characterized by fast growth rate and good quality wood 1. 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. ![]() 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.Ĭoast redwood ( Sequoia sempervirens (D. ![]() The hexaploid nature of the coast redwood genome makes it very challenging to successfully assemble and annotate the coast redwood transcriptome. 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. In general, it is frost sensitive and suffers from freezing temperatures. 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. Coast redwood is a very important endemic conifer timber species in Southern Oregon and Northern California in the USA.
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