Biology subjects

Jaquish, B.

Publications and source records attributed to Jaquish, B..

3 recordsLinked to original sources

bioRxiv2022

Multi-trait selection to build resilience in conifer forests: a case study on spruce-shoot weevil interactions

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 hybrid status might be a good predictor for weevil attacks and delineates the boundaries of successful spruce population movement. Families resulting from crossing susceptible with resistant parents generally showed fast-growing trees were the least affected by weevil attacks. Such results indicate that these "hybrids" 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.

genetics↗

bioRxiv2019

ntEdit: scalable genome sequence polishing

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.\n\nWe first tested ntEdit and the state-of-the-art assembly improvement tools GATK, Pilon and Racon on controlled E. coli and C. elegans sequence data. Generally, ntEdit performs well at low sequence depths (<20X), 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 <14s and <3m, on average, on E. coli and C. elegans, respectively. We performed similar benchmarks on a sub-20X coverage human genome sequence dataset, inspecting accuracy and resource usage in editing chromosomes 1 and 21, and whole genome. ntEdit scaled linearly, executing in 30-40m on those sequences. We show how ntEdit ran in <2h20m to improve upon long and linked read human genome assemblies of NA12878, using high coverage (54X) 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 Gbp interior and white spruce genomes in <4 and <5h, respectively, making roughly 50M edits at a (substitution+indel) rate of 0.0024.\n\nAvailabilityhttps://github.com/bcgsc/ntedit\n\nSupplemental materialavailable online.

bioinformatics↗

bioRxiv2018

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

O_LIIn plants, there can be a trade-off between resource allocations to growth versus defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction.\nC_LIO_LIWe 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.\nC_LIO_LIWe used partial correlations of individual transcripts (ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, e.g., those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs.\nC_LIO_LIA 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.\nC_LIO_LIOur 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.\nC_LI

plant biology↗