De novo transcriptome assembly of cold stressed clones of the hexaploid Sequoia sempervirens (D. Don) Endl.

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. Background & Summary Coast redwood (Sequoia sempervirens (D. 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. 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. However, some coast redwood trees survived freezing temperatures in Germany demonstrating cold-tolerance. Considering global warming and climate change, this species can be potentially considered as a prospective commercial timber species for future German sustainable forestry. 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. Samples included the 'Filoli-phenotype' clones and clones from two trees growing in Germany that are considered as frost resistant. 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

Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin

“…The overall alignment rate of the RNA-seq needle libraries, SRX7171900 and ERX2099880, was 80% and 87.96%, respectively. The concatenated transcripts and fragments contained 409,920, 622,955, and 128,005 transcripts from the PacBio Iso-Seq long-read transcripts, de novo short read assembled needle transcripts from Breidenbach et al (2020) and de novo short read assembled transcripts from Scott et al (2016) , respectively. After clustering, these transcripts collapsed into 131,842 PacBio Iso-Seq high quality transcripts, 568,778 transcripts from Breidenbach et al (2020) , and 97:764 from Scott et al (2016) .…”

“…Currently, there are two RNA-seq libraries available, SRX7171900 (150 bp PE) ( Breidenbach et al 2020 ), which represents a pooled needle tissue library from multiple clones, and ERX2099880 (100 bp PE) ( Matasci et al 2014 ), which represents branch apex, including needle, tissue generated for the 1000 Plants (1KP) project. The Illumina sequencing reads were trimmed using Sickle v.1.33 ( Joshi and Fass 2011 ) with the following parameters, quality threshold = 30, length threshold = 50.…”

“…Three independent transcriptomes were concatenated and clustered at 98% identity with vsearch V.2.15.0 ( Rognes et al 2016 ). These included the Iso-seq transcriptome generated by us for our annotation, the short-read Illumina-derived transcriptome ( Scott et al 2016 ) available at https://datadryad.org/stash/dataset/doi :10.5061/dryad.7nb70, and the cold-stressed transcriptome (TSA: GIBU01000000) ( Breidenbach et al 2020 ). The combined resource was frame-selected based on ORF prediction from TransDecoder v.5.0.2.…”

The 3D Genome: From Structure to Function

“…The nucleus of a human cell contains 46 densely packed chromosomes [ 12 ]. In contrast, octoploid ( Opuntia ) [ 13 ], hexaploid (Sequoia) [ 14 ], and tetraploid ( Coffea ) [ 15 ] genomes contain 88, 66, and 44 chromosomes, respectively. However, Ophioglossum contains 1260 (decaploid, 630 pairs) chromosomes per cell [ 16 ], and these chromosomes can directly and accurately segregate themselves to the next cell during mitosis.…”

Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

“…Both coast redwood and giant sequoia are currently listed as endangered species by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species [45]. Despite their unique ecological and economic importance, the genomics of local adaptation in coast redwood and giant sequoia are insufficiently studied [38,40,[46][47][48][49][50]. The objectives of this research were to dissect the genomic basis of local adaptation to climate in natural populations of giant sequoia and coast redwood by (i) locating genomic regions showing signals of natural selection that might provide information about the mode of adaptation, (ii) identifying the main environmental variables driving adaptation in the species, and (iii) understanding the main biological functions of genes associated with environmental variation.…”