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Article ; Online: Transcriptome features of stone cell development in weevil-resistant and susceptible Sitka spruce.

Whitehill, Justin G A / Yuen, Macaire M S / Chiang, Angela / Ritland, Carol E / Bohlmann, Jörg

2023 Volume 239, Issue 6, Page(s) 2138–2152

Abstract: Stone cells are a specialized, highly lignified cell type found in both angiosperms and gymnosperms. In conifers, abundance of stone cells in the cortex provides a robust constitutive physical defense against stem feeding insects. Stone cells are a major ...

Abstract	Stone cells are a specialized, highly lignified cell type found in both angiosperms and gymnosperms. In conifers, abundance of stone cells in the cortex provides a robust constitutive physical defense against stem feeding insects. Stone cells are a major insect-resistance trait in Sitka spruce (Picea sitchensis), occurring in dense clusters in apical shoots of trees resistant (R) to spruce weevil (Pissodes strobi) but being rare in susceptible (S) trees. To learn more about molecular mechanisms of stone cell formation in conifers, we used laser microdissection and RNA sequencing to develop cell-type-specific transcriptomes of developing stone cells from R and S trees. Using light, immunohistochemical, and fluorescence microscopy, we also visualized the deposition of cellulose, xylan, and lignin associated with stone cell development. A total of 1293 genes were differentially expressed at higher levels in developing stone cells relative to cortical parenchyma. Genes with potential roles in stone cell secondary cell wall formation (SCW) were identified and their expression evaluated over a time course of stone cell formation in R and S trees. The expression of several transcriptional regulators was associated with stone cell formation, including a NAC family transcription factor and several genes annotated as MYB transcription factors with known roles in SCW formation.
MeSH term(s)	Animals ; Transcriptome/genetics ; Weevils ; Picea/genetics ; Phenotype ; Insecta ; Gene Expression Regulation, Plant
Language	English
Publishing date	2023-07-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19103
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Article ; Online: Transcriptome features of stone cell development in weevil‐resistant and susceptible Sitka spruce

Whitehill, Justin G. A. / Yuen, Macaire M. S. / Chiang, Angela / Ritland, Carol E. / Bohlmann, Jörg

New Phytologist. 2023 Sept., v. 239, no. 6 p.2138-2152

2023

Abstract	Stone cells are a specialized, highly lignified cell type found in both angiosperms and gymnosperms. In conifers, abundance of stone cells in the cortex provides a robust constitutive physical defense against stem feeding insects. Stone cells are a major insect‐resistance trait in Sitka spruce (Picea sitchensis), occurring in dense clusters in apical shoots of trees resistant (R) to spruce weevil (Pissodes strobi) but being rare in susceptible (S) trees. To learn more about molecular mechanisms of stone cell formation in conifers, we used laser microdissection and RNA sequencing to develop cell‐type‐specific transcriptomes of developing stone cells from R and S trees. Using light, immunohistochemical, and fluorescence microscopy, we also visualized the deposition of cellulose, xylan, and lignin associated with stone cell development. A total of 1293 genes were differentially expressed at higher levels in developing stone cells relative to cortical parenchyma. Genes with potential roles in stone cell secondary cell wall formation (SCW) were identified and their expression evaluated over a time course of stone cell formation in R and S trees. The expression of several transcriptional regulators was associated with stone cell formation, including a NAC family transcription factor and several genes annotated as MYB transcription factors with known roles in SCW formation.
Keywords	Picea sitchensis ; Pissodes strobi ; RNA ; cell walls ; cellulose ; cortex ; fluorescence microscopy ; immunohistochemistry ; lignin ; microdissection ; transcription (genetics) ; transcription factors ; transcriptome ; xylan
Language	English
Dates of publication	2023-09
Size	p. 2138-2152.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19103
Database	NAL-Catalogue (AGRICOLA)

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Article: Subalpine fir microsatellite variation reveals the complex relationship between var. lasiocarpa and var. bifolia

Ritland, Kermit / Miscampbell, Allyson / Cartwright, Charlie / Bohlmann, Nikhil / Ritland, Carol

Canadian journal of forest research. 2022 Mar. 22, v. 52, no. 6

2022

Abstract: Subalpine fir, Abies lasiocarpa, occurs throughout western North America, often in forest–tundra parkland. To resolve the presence of varieties in this species, we surveyed microsatellite genetic markers in 11 populations containing three putative ... ...

Abstract	Subalpine fir, Abies lasiocarpa, occurs throughout western North America, often in forest–tundra parkland. To resolve the presence of varieties in this species, we surveyed microsatellite genetic markers in 11 populations containing three putative varieties of Abies lasiocarpa: (1) var. lasiocarpa, (2) var. bifolia, and (3) var. arizonica. We tested primers from related taxa, and 13 of the best primer pairs were used for assays. Within populations, both heterozygosity and allelic richness were approximately 10% lower in var. lasiocarpa. The STRUCTURE procedure struggled to assign populations to groups correctly; at K = 3, individuals were assigned to their putative varieties with approximately 70% accuracy. Regardless, both lasiocarpa and bifolia were correctly assigned more than expected by chance, indicating that these taxa are distinct. A dendrogram of genetic distances showed var. arizonica to exhibit higher evolutionary distance from the other two varieties and serves as an outgroup. The dendrogram also showed a nesting of var. bifolia clades within var. lasiocarpa, indicating a complex relationship between var. lasiocarpa and var. bifolia. Comparisons among the STRUCTURE population assignments for K = 2, K = 3, and K = 4 identified populations with cryptic admixture and indicate a “lasiocarpa–bifolia” subspecies complex that warrants further study.
Keywords	Abies lasiocarpa ; forests ; heterozygosity ; microsatellite repeats ; research ; North America
Language	English
Dates of publication	2022-0322
Size	p. 901-909.
Publishing place	Canadian Science Publishing
Document type	Article
ZDB-ID	1473096-0
ISSN	1208-6037 ; 0045-5067
ISSN (online)	1208-6037
ISSN	0045-5067
DOI	10.1139/cjfr-2021-0303
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Article ; Online: Genomic virulence features of Beauveria bassiana as a biocontrol agent for the mountain pine beetle population.

Li, Janet X / Fernandez, Kleinberg X / Ritland, Carol / Jancsik, Sharon / Engelhardt, Daniel B / Coombe, Lauren / Warren, René L / van Belkum, Marco J / Carroll, Allan L / Vederas, John C / Bohlmann, Joerg / Birol, Inanc

BMC genomics

2023 Volume 24, Issue 1, Page(s) 390

Abstract: Background: The mountain pine beetle, Dendroctonus ponderosae, is an irruptive bark beetle that causes extensive mortality to many pine species within the forests of western North America. Driven by climate change and wildfire suppression, a recent ... ...

Abstract	Background: The mountain pine beetle, Dendroctonus ponderosae, is an irruptive bark beetle that causes extensive mortality to many pine species within the forests of western North America. Driven by climate change and wildfire suppression, a recent mountain pine beetle (MPB) outbreak has spread across more than 18 million hectares, including areas to the east of the Rocky Mountains that comprise populations and species of pines not previously affected. Despite its impacts, there are few tactics available to control MPB populations. Beauveria bassiana is an entomopathogenic fungus used as a biological agent in agriculture and forestry and has potential as a management tactic for the mountain pine beetle population. This work investigates the phenotypic and genomic variation between B. bassiana strains to identify optimal strains against a specific insect. Results: Using comparative genome and transcriptome analyses of eight B. bassiana isolates, we have identified the genetic basis of virulence, which includes oosporein production. Genes unique to the more virulent strains included functions in biosynthesis of mycotoxins, membrane transporters, and transcription factors. Significant differential expression of genes related to virulence, transmembrane transport, and stress response was identified between the different strains, as well as up to nine-fold upregulation of genes involved in the biosynthesis of oosporein. Differential correlation analysis revealed transcription factors that may be involved in regulating oosporein production. Conclusion: This study provides a foundation for the selection and/or engineering of the most effective strain of B. bassiana for the biological control of mountain pine beetle and other insect pests populations.
MeSH term(s)	Animals ; Coleoptera ; Beauveria/genetics ; Virulence/genetics ; Genomics
Chemical Substances	oosporein (708AUK232A)
Language	English
Publishing date	2023-07-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-023-09473-4
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Article: Genetic architecture of terpene chemistry and growth traits and the impact of inbreeding on these traits in western redcedar (

Shalev, Tal J / Gamal El-Dien, Omnia / Yuen, Macaire M S / van der Merwe, Lise / Kirst, Matias / Yanchuk, Alvin D / Ritland, Carol / Russell, John H / Bohlmann, Joerg

Evolutionary applications

2023 Volume 16, Issue 3, Page(s) 673–687

Abstract: Western redcedar (WRC; ...

Abstract	Western redcedar (WRC;
Language	English
Publishing date	2023-01-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2405496-3
ISSN	1752-4563 ; 1752-4571
ISSN (online)	1752-4563
ISSN	1752-4571
DOI	10.1111/eva.13526
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Article ; Online: Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.

Lo, Theodora / Coombe, Lauren / Gagalova, Kristina K / Marr, Alex / Warren, René L / Kirk, Heather / Pandoh, Pawan / Zhao, Yongjun / Moore, Richard A / Mungall, Andrew J / Ritland, Carol / Pavy, Nathalie / Jones, Steven J M / Bohlmann, Joerg / Bousquet, Jean / Birol, Inanç / Thomson, Ashley

G3 (Bethesda, Md.)

2023 Volume 14, Issue 1

Abstract: Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of ...

Abstract	Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.
MeSH term(s)	Phylogeny ; Picea/genetics ; North America
Language	English
Publishing date	2023-12-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkad247
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Article ; Online: Slow but not low

Buschiazzo Emmanuel / Ritland Carol / Bohlmann Jörg / Ritland Kermit

BMC Evolutionary Biology, Vol 12, Iss 1, p

genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

2012 Volume 8

Abstract: Background Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka ... ...

Abstract	Background Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce ( Picea sitchensis ) and loblolly pine ( Pinus taeda ), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar ( Populus trichocarpa ), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. Results Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10 -9 synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar- Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. Conclusions Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.
Keywords	Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Evolution ; QH359-425
Subject code	580
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
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Article: Genomic selection reveals hidden relatedness and increased breeding efficiency in western redcedar polycross breeding.

Gamal El-Dien, Omnia / Shalev, Tal J / Yuen, Macaire M S / Stirling, Rod / Daniels, Lori D / Breinholt, Jesse W / Neves, Leandro G / Kirst, Matias / Van der Merwe, Lise / Yanchuk, Alvin D / Ritland, Carol / Russell, John H / Bohlmann, Joerg

Evolutionary applications

2022 Volume 15, Issue 8, Page(s) 1291–1312

Abstract: Western redcedar (WRC) is an ecologically and economically important forest tree species characterized by low genetic diversity with high self-compatibility and high heartwood durability. Using sequence capture genotyping of target genic and non-genic ... ...

Abstract	Western redcedar (WRC) is an ecologically and economically important forest tree species characterized by low genetic diversity with high self-compatibility and high heartwood durability. Using sequence capture genotyping of target genic and non-genic regions, we genotyped 44 parent trees and 1520 offspring trees representing 26 polycross (PX) families collected from three progeny test sites using 45,378 SNPs. Trees were phenotyped for eight traits related to growth, heartwood and foliar chemistry associated with wood durability and deer browse resistance. We used the
Language	English
Publishing date	2022-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2405496-3
ISSN	1752-4563 ; 1752-4571
ISSN (online)	1752-4563
ISSN	1752-4571
DOI	10.1111/eva.13463
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Article ; Online: Physical disturbance by recovering sea otter populations increases eelgrass genetic diversity.

Foster, Erin / Watson, Jane / Lemay, Matthew A / Tinker, M Tim / Estes, James A / Piercey, Rebecca / Henson, Lauren / Ritland, Carol / Miscampbell, Allyson / Nichol, Linda / Hessing-Lewis, Margot / Salomon, Anne K / Darimont, Chris T

Science (New York, N.Y.)

2021 Volume 374, Issue 6565, Page(s) 333–336

Abstract: Most knowledge regarding the role of predators is ecological in nature. Here, we report how disturbance generated by sea otters ( ...

Abstract	Most knowledge regarding the role of predators is ecological in nature. Here, we report how disturbance generated by sea otters (
MeSH term(s)	Animals ; Food Chain ; Genetic Variation ; Otters/physiology ; Zosteraceae/genetics
Language	English
Publishing date	2021-10-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abf2343
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Article ; Online: Comparative genomics of resistance of spruce to the white pine weevil in British Columbia

Ritland Kermit / Verne Sébastien / Jaquish Barry / Ritland Carol

BMC Proceedings , Vol 5, Iss Suppl 7, p O

2011 Volume 10

Keywords	Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Medicine (General) ; R5-920 ; Medicine ; R ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
Language	English
Publishing date	2011-09-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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