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Picea sitchensis

ABSTRACT: Stone cells and the conifer defense syndrome

PROVIDER: PRJNA398042 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5949080_1.fastq.gz	Fastqsanger.gz
	SRR5949080_2.fastq.gz	Fastqsanger.gz
	SRR5949090_1.fastq.gz	Fastqsanger.gz
	SRR5949090_2.fastq.gz	Fastqsanger.gz
	SRR5949100_1.fastq.gz	Fastqsanger.gz

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Predicting adaptive phenotypes from multilocus genotypes in Sitka spruce (Picea sitchensis) using random forest.

Project description:Climate is the primary driver of the distribution of tree species worldwide, and the potential for adaptive evolution will be an important factor determining the response of forests to anthropogenic climate change. Although association mapping has the potential to improve our understanding of the genomic underpinnings of climatically relevant traits, the utility of adaptive polymorphisms uncovered by such studies would be greatly enhanced by the development of integrated models that account for the phenotypic effects of multiple single-nucleotide polymorphisms (SNPs) and their interactions simultaneously. We previously reported the results of association mapping in the widespread conifer Sitka spruce (Picea sitchensis). In the current study we used the recursive partitioning algorithm 'Random Forest' to identify optimized combinations of SNPs to predict adaptive phenotypes. After adjusting for population structure, we were able to explain 37% and 30% of the phenotypic variation, respectively, in two locally adaptive traits--autumn budset timing and cold hardiness. For each trait, the leading five SNPs captured much of the phenotypic variation. To determine the role of epistasis in shaping these phenotypes, we also used a novel approach to quantify the strength and direction of pairwise interactions between SNPs and found such interactions to be common. Our results demonstrate the power of Random Forest to identify subsets of markers that are most important to climatic adaptation, and suggest that interactions among these loci may be widespread.

| S-EPMC3429923 | biostudies-literature

Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure.

Project description:Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

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Somatic mutations substantially increase the per-generation mutation rate in the conifer <i>Picea sitchensis</i>.

Project description:The rates and biological significance of somatic mutations have long been a subject of debate. Somatic mutations in plants are expected to accumulate with vegetative growth and time, yet rates of somatic mutations are unknown for conifers, which can reach exceptional sizes and ages. We investigated somatic mutation rates in the conifer Sitka spruce (Picea sitchensis (Bong.) Carr.) by analyzing a total of 276 Gb of nuclear DNA from the tops and bottoms of 20 old-growth trees averaging 76 m in height. We estimate a somatic base substitution rate of 2.7 × 10-8 per base pair within a generation. To date, this is one of the highest estimated per-generation rates of mutation among eukaryotes, indicating that somatic mutations contribute substantially to the total per-generation mutation rate in conifers. Nevertheless, as the sampled trees are centuries old, the per-year rate is low in comparison with nontree taxa. We argue that although somatic mutations raise genetic load in conifers, they generate important genetic variation and enable selection both among cell lineages within individual trees and among offspring.

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