ntEdit: scalable genome sequence polishing.

MOTIVATION: In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome sequence editing utility that scales to large mammalian and conifer genomes. RESULTS: We first tested ntEdit and the state-of-the-art assembly improvement tools GATK, Pilon and Racon on controlled Escherichia coli and Caenorhabditis elegans sequence data. Generally, ntEdit performs well at low sequence depths (<20×), fixing the majority (>97%) of base substitutions and indels, and its performance is largely constant with increased coverage. In all experiments conducted using a single CPU, the ntEdit pipeline executed in <14 s and <3 m, on average, on E.coli and C.elegans, respectively. We performed similar benchmarks on a sub-20× coverage human genome sequence dataset, inspecting accuracy and resource usage in editing chromosomes 1 and 21, and whole genome. ntEdit scaled linearly, executing in 30-40 m on those sequences. We show how ntEdit ran in <2 h 20 m to improve upon long and linked read human genome assemblies of NA12878, using high-coverage (54×) Illumina sequence data from the same individual, fixing frame shifts in coding sequences. We also generated 17-fold coverage spruce sequence data from haploid sequence sources (seed megagametophyte), and used it to edit our pseudo haploid assemblies of the 20 Gb interior and white spruce genomes in <4 and <5 h, respectively, making roughly 50M edits at a (substitution+indel) rate of 0.0024. AVAILABILITY AND IMPLEMENTATION: https://github.com/bcgsc/ntedit. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Functions of stone cells and oleoresin terpenes in the conifer defense syndrome.

Conifers depend on complex defense systems against herbivores. Stone cells (SC) and oleoresin are physical and chemical defenses of Sitka spruce that have been separately studied in previous work. Weevil oviposit at the tip of the previous year's apical shoot (PYAS). We investigated interactions between weevil larvae and trees in controlled oviposition experiments with resistant (R) and susceptible (S) Sitka spruce. R trees have an abundance of SC in the PYAS cortex. SC are mostly absent in S trees. R trees and S trees also differ in the composition of oleoresin terpenes. Transcriptomes of R and S trees revealed differences in long-term weevil-induced responses. Performance of larvae was significantly reduced on R trees compared with S trees under experimental conditions that mimicked natural oviposition behavior at apical shoot tips and may be attributed to the effects of SC. In oviposition experiments designed for larvae to feed below the area of highest SC abundance, larvae showed an unusual feeding behavior and oleoresin appeared to function as the major defense. The results support a role for both SC and oleoresin terpenes and possible synergies between these traits in the defense syndrome of weevil-resistant Sitka spruce.

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce.

In plants, there can be a trade-off between resource allocations to growth vs defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction. We studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny. We used partial correlations of individual transcripts (expressed sequence tags, ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, for example, those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs. A terpenoid ABC transporter gene showed strongest correlations (P = 0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P = 0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P = 0.004) represented the uncovered positive correlations. Our study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

Function of Sitka spruce stone cells as a physical defence against white pine weevil.

Stone cells are a physical defence of conifers against stem feeding insects such as weevils and bark beetles. In Sitka spruce, abundance of stone cells in the cortex of apical shoot tips is associated with resistance to white pine weevil. However, the mode of action by which stone cells interfere with growth and development of weevil larvae is unknown. We developed a bioassay system for testing potential effects of stone cells, which were isolated from resistant trees, on weevil larvae. Bioassays using artificial diet and controlled amounts of stone cells focused on physical defence. We evaluated the effects of stone cells on establishment of neonate larvae, mandible wear and changes in relative growth rates of third instar larvae. Establishment of neonates and relative growth rates of third instars were significantly reduced by stone cells. Stone cells appeared to be indigestible by weevil larvae. Our results suggest that stone cells affect weevil establishment and development by forming a physical feeding barrier against neonate larvae at the site of oviposition, and by reducing access to nutrients in the cortex of resistant trees, which contain an abundance of stone cells in place of a more nutrient rich tissue in susceptible trees.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.

UNLABELLED: White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20,356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies. AVAILABILITY: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.

Adaptation and exogenous selection in a Picea glauca × Picea engelmannii hybrid zone: implications for forest management under climate change.

The nature of selection responsible for the maintenance of the economically and ecologically important Picea glauca × Picea engelmannii hybrid zone was investigated. Genomic, phenotypic and climatic data were used to test assumptions of hybrid zone maintenance and to model future scenarios under climate change. Genome-wide estimates of admixture based on a panel of 86 candidate gene single nucleotide polymorphisms were combined with long-term quantitative data on growth and survival (over 20 yr), as well as one-time assessments of bud burst and bud set phenology, and cold hardiness traits. A total of 15,498 individuals were phenotyped for growth and survival. Our results suggest that the P. glauca × P. engelmannii hybrid zone is maintained by local adaptation to growing season length and snowpack (exogenous selection). Hybrids appeared to be fitter than pure species in intermediate environments, which fits expectations of the bounded hybrid superiority model of hybrid zone maintenance. Adaptive introgression from parental species has probably contributed to increased hybrid fitness in intermediate habitats. While P. engelmannii ancestry is higher than P. glauca ancestry in hybrid populations, on average, selective breeding in managed hybrid populations is shifting genomic composition towards P. glauca, potentially pre-adapting managed populations to warmer climates.

Projections of suitable habitat under climate change scenarios: Implications for trans-boundary assisted colonization.

PREMISE OF THE STUDY: Climate change may threaten endemic species with extinction, particularly relicts of the Arcto-Tertiary Forest, by elimination of their contemporary habitat. Projections of future habitat are necessary to plan for conservation of these species. METHODS: We used spline climatic models and modified Random Forests statistical procedures to predict suitable habitats for Brewer spruce (Picea breweriana), which is endemic to the Klamath Region of California and Oregon. We used three general circulation models and two sets of carbon emission scenarios (optimistic and pessimistic) for future climates. KEY RESULTS: Our procedures predicted present occurrence of Brewer spruce perfectly. For the decades 2030, 2060, and 2090, its projected range within the Klamath Region progressively declined, to the point of disappearance in the decade 2090. The climate niche was projected to move north to British Columbia, the Yukon Territory, and southeastern Alaska. CONCLUSION: The results emphasize the necessity of assisted colonization and trans-boundary movement to prevent extinction of Brewer spruce. The projections provide a framework for formulating conservation plans, but planners must also consider regulations regarding international plant transfers.

Building resiliency in conifer forests: Interior spruce crosses among weevil resistant and susceptible parents produce hybrids appropriate for multi-trait selection.

Tree planting programs now need to consider climate change increasingly, therefore, the resistance to pests plays an essential role in enabling tree adaptation to new ranges through tree population movement. The weevil Pissodes strobi (Peck) is a major pest of spruces and substantially reduces lumber quality. We revisited a large Interior spruce provenance/progeny trial (2,964 genotypes, 42 families) of varying susceptibility, established in British Columbia. We employed multivariate mixed linear models to estimate covariances between, and genetic control of, juvenile height growth and resistance traits. We performed linear regressions and ordinal logistic regressions to test for impact of parental origin on growth and susceptibility to the pest, respectively. A significant environmental component affected the correlations between resistance and height, with outcomes dependent on families. Parents sourced from above 950 m a.s.l. elevation negatively influenced host resistance to attacks, probably due to higher P. engelmannii proportion. For the genetic contribution of parents sourced from above 1,200 m a.s.l., however, we found less attack severity, probably due to a marked mismatch in phenologies. This clearly highlights that interspecific hybrid status might be a good predictor for weevil attacks and delineates the boundaries of successful spruce population movement. Families resulting from crossing susceptible parents generally showed fast-growing trees were the most affected by weevil attacks. Such results indicate that interspecific 'hybrids' with a higher P. glauca ancestry might be genetically better equipped with an optimized resource allocation between defence and growth and might provide the solution for concurrent improvement in resistance against weevil attacks, whilst maintaining tree productivity.

Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada.

Here, we present the complete chloroplast genome sequence of white spruce (Picea glauca, genotype WS77111), a coniferous tree widespread in the boreal forests of North America. This sequence contributes to genomic and phylogenetic analyses of the Picea genus that are part of ongoing research to understand their adaptation to environmental stress.

Complete Chloroplast Genome Sequence of an Engelmann Spruce (Picea engelmannii, Genotype Se404-851) from Western Canada.

Engelmann spruce (Picea engelmannii) is a conifer found primarily on the west coast of North America. Here, we present the complete chloroplast genome sequence of Picea engelmannii genotype Se404-851. This chloroplast sequence will benefit future conifer genomic research and contribute resources to further species conservation efforts.

Genetic differentiation in carbon isotope discrimination and gas exchange in Pseudotsuga menziesii : A common-garden experiment.

Patterns of genetic variation in gas-exchange physiology were analyzed in a 15-year-old Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) plantation that contains 25 populations grown from seed collected from across the natural distribution of the species. Seed was collected from 33°30' to 53°12' north latitude and from 170 m to 2930 m above sea level, and from the coastal and interior (Rocky Mountain) varieties of the species. Carbon isotope discrimination (Δ) ranged from 19.70(‰) to 22.43(‰) and was closely related to geographic location of the seed source. The coastal variety (20.50 (SE=0.21)‰) was not significantly different from the interior variety (20.91 (0.15)‰). Instead, most variation was found within the interior variety; populations from the southern Rockies had the highest discrimination (21.53 (0.20)‰) (lowest water-use efficiency). Carbon isotope discrimination (Δ), stomatal conductance to water vapor (g), the ratio of intercellular to ambient CO2 concentration (ci/ca), and intrinsic water-use efficiency (A/g) were all correlated with altitude of origin (r=0.76, 0.73, 0.74, and -0.63 respectively); all were statistically significant at the 0.01 level. The same variables were correlated with both height and diameter at age 15 (all at P≤0.0005). Observed patterns in the common garden did not conform to our expectation of higher WUE, measured by both A/g and Δ, in trees from the drier habitats of the interior, nor did they agree with published in situ observations of decreasing g and Δ with altitude. The genetic effect opposes the altitudinal one, leading to some degree of homeostasis in physiological characteri tics in situ.

Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce.

In plants, relationships between resistance to herbivorous insect pests and growth are typically controlled by complex interactions between genetically correlated traits. These relationships often result in tradeoffs in phenotypic expression. In this study we used genetical genomics to elucidate genetic relationships between tree growth and resistance to white pine terminal weevil (Pissodes strobi Peck.) in a pedigree population of interior spruce (Picea glauca, P. engelmannii and their hybrids) that was growing at Vernon, B.C. and segregating for weevil resistance. Genetical genomics uses genetic perturbations caused by allelic segregation in pedigrees to co-locate quantitative trait loci (QTLs) for gene expression and quantitative traits. Bark tissue of apical leaders from 188 trees was assayed for gene expression using a 21.8K spruce EST-spotted microarray; the same individuals were genotyped for 384 SNP markers for the genetic map. Many of the expression QTLs (eQTL) co-localized with resistance trait QTLs. For a composite resistance phenotype of six attack and oviposition traits, 149 positional candidate genes were identified. Resistance and growth QTLs also overlapped with eQTL hotspots along the genome suggesting that: 1) genetic pleiotropy of resistance and growth traits in interior spruce was substantial, and 2) master regulatory genes were important for weevil resistance in spruce. These results will enable future work on functional genetic studies of insect resistance in spruce, and provide valuable information about candidate genes for genetic improvement of spruce.

Global transcriptome analysis of constitutive resistance to the white pine weevil in spruce.

Constitutive defense mechanisms are critical to the understanding of defense mechanisms in conifers because they constitute the first barrier to attacks by insect pests. In interior spruce, trees that are putatively resistant and susceptible to attacks by white pine weevil (Pissodes strobi) typically exhibit constitutive differences in traits such as resin duct size and number, bark thickness, and terpene content. To improve our knowledge of their genetic basis, we compared globally the constitutive expression levels of 17,825 genes between 20 putatively resistant and 20 putatively susceptible interior spruce trees from the British Columbia tree improvement program. We identified 54 upregulated and 137 downregulated genes in resistant phenotypes, relative to susceptible phenotypes, with a maximum fold change of 2.24 and 3.91, respectively. We found a puzzling increase of resistance by downregulated genes, as one would think that "procuring armaments" is the best defense. Also, although terpenes and phenolic compounds play an important role in conifer defense, we found few of these genes to be differentially expressed. We found 15 putative small heat-shock proteins (sHSP) and several other stress-related proteins to be downregulated in resistant trees. Downregulated putative sHSP belong to several sHSP classes and represented 58% of all tested putative sHSP. These proteins are well known to be involved in plant response to various kinds of abiotic stress; however, their role in constitutive resistance is not yet understood. The lack of correspondence between transcriptome profile clusters and phenotype classifications suggests that weevil resistance in spruce is a complex trait.

Contrasting microsatellite variation between subalpine and western larch, two closely related species with different distribution patterns.

Subalpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.) represent two closely related species with contrasting abundance and distribution patterns in Western North America. Genetic diversity at seven informative microsatellite loci was determined for 19 populations of subalpine larch and nine populations of western larch. Contrasting genetic diversity and patterns of population differentiation were observed between the two species. The overall within-population genetic diversity parameters were lower in subalpine larch (A = 3.2; A(P) = 3.6; H(E) = 0.418) than in western larch (A(P) = 5.51; H(E) = 0.580), a pattern that is likely related to historical or demographic factors. No evidence of interspecific hybridization was observed. Significantly more population differentiation (theta = 0.15; R(ST) = 0.07), consistent with more restricted gene flow, was observed for subalpine larch as compared to western larch (theta = 0.05; R(ST) = 0.04). Under the assumption of an infinite allele mutation model, 12 of the 19 subalpine larch populations showed signs of deviation from the mutation-drift equilibrium, which suggests Holocene population bottlenecks and fluctuations in effective population size for this species. None of the western larch populations deviated significantly from the mutation-drift equilibrium. For both species, Mantel's test revealed a significant positive relationship between geographical and genetic distances indicative of isolation by distance. A similar geographical structure was detected in both species, suggesting at least two genetically distinct glacial populations in each species. The various implications for gene conservation are discussed.