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

2015 ◽  
Vol 83 (2) ◽  
pp. 189-212 ◽  
Author(s):  
René L. Warren ◽  
Christopher I. Keeling ◽  
Macaire Man Saint Yuen ◽  
Anthony Raymond ◽  
Greg A. Taylor ◽  
...  
2019 ◽  
Author(s):  
Joel Vizueta ◽  
Alejandro Sánchez-Gracia ◽  
Julio Rozas

AbstractGene annotation is a critical bottleneck in genomic research, especially for the comprehensive study of very large gene families in the genomes of non-model organisms. Despite the recent progress in automatic methods, the tools developed for this task often produce inaccurate annotations, such as fused, chimeric, partial or even completely absent gene models for many family copies, which require considerable extra efforts to be amended. Here we present BITACORA, a bioinformatics solution that integrates sequence similarity search tools and Perl scripts to facilitate both the curation of these inaccurate annotations and the identification of previously undetected gene family copies directly from DNA sequences. We tested the performance of the BITACORA pipeline in annotating the members of two chemosensory gene families of different sizes in seven available chelicerate genome drafts. Despite the relatively high fragmentation of some of these drafts, BITACORA was able to improve the annotation of many members of these families and detected thousands of new chemoreceptors encoded in genome sequences. The program generates an output file in the general feature format (GFF) files, with both curated and novel gene models, and a FASTA file with the predicted proteins. These outputs can be easily integrated in genomic annotation editors, greatly facilitating subsequent manual annotation and downstream evolutionary analyses.


1997 ◽  
Vol 129 (2) ◽  
pp. 291-318 ◽  
Author(s):  
Robert K. Lawrence ◽  
William J. Mattson ◽  
Robert A. Haack

AbstractSynchrony of insect and host tree phenologies has often been suggested as an important factor influencing the susceptibility of white spruce, Picea glauca (Moench) Voss, and other hosts to the spruce budworm, Choristoneura fumiferana (Clemens) (Lepidoptera: Tortricidae). We evaluated this hypothesis by caging several cohorts of spruce budworm larvae on three white spruce populations at different phenological stages of the host trees, and then comparing budworm performance with host phenology and variation of 13 foliar traits. The beginning of the phenological window of susceptibility in white spruce occurs several weeks prior to budbreak, and the end of the window is sharply defined by the end of shoot growth. Performance was high for the earliest budworm cohorts that we tested. These larvae began feeding 3–4 weeks prior to budbreak and completed their larval development prior to the end of shoot elongation. Optimal synchrony occurred when emergence preceded budbreak by about 2 weeks. Larval survival was greater than 60% for individuals starting development 1–3 weeks prior to budbreak, but decreased to less than 10% for those starting development 2 or more weeks after budbreak and thus completing development after shoot elongation ceased. High performance by the budworm was most strongly correlated with high levels of foliar nitrogen, phosphorous, potassium, copper, sugars, and water and low levels of foliar calcium, phenolics, and toughness. These results suggest that advancing the usual phenological window of white spruce (i.e. advancing budbreak prior to larval emergence) or retarding budworm phenology can have a large negative effect on the spruce budworm’s population dynamics.


Botany ◽  
2011 ◽  
Vol 89 (5) ◽  
pp. 323-338 ◽  
Author(s):  
A. Tsuneda ◽  
M.L. Davey ◽  
R.S. Currah

An endoconidial, black meristematic taxon Atramixtia arboricola gen. et. sp. nov. (Dothideales) from the black subicula found on twigs of declining white spruce, Picea glauca (Moench) Voss, in Alberta is described. It is morphologically distinguishable from other endoconidial taxa by the conidioma composed of clumps of endoconidial conidiogenous cells, scattered meristematically dividing cells, dematiaceous hyphae, abundant brown, granular matrix materials, and sometimes plant tissue. Endoconidia also occur in conidiogenous cellular clumps that are not organized into a conidioma but develop directly from stromatic cells on the bark. In culture, it forms similar endoconidial conidiomata and also a mycelial, blastic synanamorph that superficially resembles Hormonema . Atramixtia arboricola is a member of the Dothideales and shows phylogenetic affinities to a clade of conifer-stem and -needle pathogens, including Sydowia and Delphinella , although no teleomorph was found either on the natural substrate or in culture. It has not been determined whether A. arboricola is pathogenic to its host, but the occurrence of abundant intracellular hyphae in the host periderm suggests that the fungus is at least parasitic.


2004 ◽  
Vol 34 (7) ◽  
pp. 1538-1542 ◽  
Author(s):  
Heidi Steltzer

Soil carbon (C) and nitrogen (N) pools were measured under the canopy of 29 white spruce (Picea glauca (Moench) Voss) trees and in the surrounding tundra 3 and 6 m away from each tree at three sites of recent forest expansion along the Agashashok River in northwestern Alaska. The aim was to characterize the potential for forest expansion to lead to increased soil C pools across diverse tundra types. Soil C beneath the trees correlated positively with tree age, suggesting that tree establishment has led to C storage in the soils under their canopy at a rate of 18.5 ± 4.6 g C·m–2·year–1. Soil C in the surrounding tundra did not differ from those under the trees and showed no relationship to tree age. This characterization of the soil C pools at the 3-m scale strengthens the assertion that the pattern associated with the trees is an effect of the trees, because tree age cannot explain variation among tundra sampling locations at this scale. Potential mechanisms by which these white spruce trees could increase soil C pools include greater production and lower litter quality.


Author(s):  
Andrei Lapenis ◽  
George Robinson ◽  
Gregory B. Lawrence

Here we investigate the possible<sup></sup> future response of white spruce (Picea glauca) to a warmer climate by studying trees planted 90 years ago near the southern limit of their climate tolerance in central New York, 300 km south of the boreal forest where this species is prevalent. We employed high-frequency recording dendrometers to determine radial growth phenology of six mature white spruce trees during 2013-2017. Results demonstrate significant reductions in the length of radial growth periods inversely proportional to the number of hot days with air temperature exceeding 30 oC. During years with very hot summers, the start of radial growth began about 3 days earlier than the 2013-2017 average. However, in those same years the end of radial growth was also about 17 days earlier resulting in a shorter (70 versus 100 day), radial growth season. Abundant (350-500 mm) summer precipitation, which resulted in soil moisture values of 20-30% allowed us to dismiss drought as a factor. Instead, a likely cause of reduced radial growth was mean temperature that exceeded daily average of 30<sup> o</sup>C that lead to photoinhibition.


Life ◽  
2016 ◽  
Vol 6 (3) ◽  
pp. 32 ◽  
Author(s):  
Philipp Schiffer ◽  
Jan Gravemeyer ◽  
Martina Rauscher ◽  
Thomas Wiehe
Keyword(s):  

2018 ◽  
Vol 48 (4) ◽  
pp. 324-332 ◽  
Author(s):  
Nicola A. Kokkonen ◽  
S. Ellen Macdonald ◽  
Ian Curran ◽  
Simon M. Landhäusser ◽  
Victor J. Lieffers

Given a seed source, the quality of available substrates is a key factor in determining the success of white spruce (Picea glauca (Moench) Voss) natural regeneration. We examined the influence of substrate and competing vegetation on survival and growth of natural regeneration of white spruce up to 4 years following harvesting in deciduous-dominated upland boreal mixedwood sites. Feather moss, thick soil surface organic layers, litter, and solid wood were poor substrates for establishment. Early successional mosses establishing on mineral soil, thin organics, and rotten wood were generally favourable microsites but were not highly available on postharvest sites. Mineral soil substrates were not as suitable as expected, likely because on a postlogged site, they are associated with unfavourable environmental characteristics (e.g., low nutrient availability, exposure). There was some evidence that survival and growth of seedlings were improved by surrounding vegetation in the first years, but heavy competing vegetation had a negative impact on older seedlings. Burial by aspen litter greatly increased seedling mortality, especially when combined with a brief period of submergence due to heavy spring snowmelt. The results provide insight into conditions under which natural regeneration could be an option for establishing white spruce following harvesting of deciduous-dominated boreal mixedwood forests.


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