Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species

Lorenz, W. Walter; Ayyampalayam, Savavanaraj; Bordeaux, John Michael; Howe, Glenn T.; Jermstad, K. D.; Neale, David B.; Rogers, Deborah L.; Dean, Jeffrey F. D.

doi:10.1007/s11295-012-0547-y

Cited by 44 publications

(37 citation statements)

References 38 publications

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“…Genomics progress on the WPBR pathosystem with application of high throughput SNP genotyping technology makes it feasible to undertake the genome-wide association mapping of Pinus partial resistance to Cronartium, which is even more important for whitebark pine, eastern white pine, and other Pinus species where no complete resistance has been discovered. Genome sequencing and RNA-seq analysis of the whole transcriptome have generated SNP data covering the whole genome for several Pinus species [97]. However, any association data between SNPs of candidate genes and partial resistance require verification using large populations (including both partial resistance and non-partial resistance seed families) with field phenotypic evaluation from different geographic areas.…”

Section: Genomic Selection Of Partial Resistancementioning

confidence: 99%

Genetic Resistance to Fusiform Rust in Southern Pines and White Pine Blister Rust in White Pines—A Contrasting Tale of Two Rust Pathosystems—Current Status and Future Prospects

Sniezko

Smith

Liu

et al. 2014

Forests

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Damage or mortality from pathogens can reduce productivity of forest plantations, as well as significantly harm natural forest ecosystems. Genetic resistance within the host species is the first line of defense for tree species. Resistance breeding programs for the native fusiform rust and exotic (to North America) white pine blister rust diseases are two of the longest concerted efforts in forest trees, spanning more than 50 years. Advances in developing greater genetic resistance have been made in both pathosystems, but unique challenges and opportunities in each system translate to different approaches. Fusiform rust resistance programs have mainly emphasized complete resistance, while partial resistance plays a prominent role in white pine blister rust resistance programs. Advances in the development of molecular genetic tools now permit investigations in conifers and their associated rust pathogens. Good progress has been made in identifying resistant populations and understanding resistance in these pathosystems, and resistant stock is now being used extensively for reforestation and restoration. These programs represent great success stories brought to fruition by the OPEN ACCESSForests 2014, 5 2051 long-term efforts. However, continued support will be needed to enhance the level and fully realize the potential of durable genetic resistance in these invaluable North American conifer species.

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Section: Genomic Selection Of Partial Resistancementioning

confidence: 99%

Genetic Resistance to Fusiform Rust in Southern Pines and White Pine Blister Rust in White Pines—A Contrasting Tale of Two Rust Pathosystems—Current Status and Future Prospects

Sniezko

Smith

Liu

et al. 2014

Forests

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“…Microarray and RNA sequencing methods have recently provided critical advances for the genome-wide profiling of gene expression. Transcriptomics is developing rapidly in conifers, with the recent advent of large genomic resources (Lorenz et al 2012;Raherison et al 2012;Canales et al 2014), including draft genomes for Picea (Birol et al 2013;Nystedt et al 2013) and Pinus .…”

Section: Conifer Embryo Developmentmentioning

confidence: 99%

Forest tree genomics: 10 achievements from the past 10 years and future prospects

Plomion

Bastien²,

Bogeat‐Triboulot

et al. 2016

Annals of Forest Science

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strategies in terms of conservation and use, as well as climate changes and associated threats. Genomics will undoubtedly play a major role over the next decade and beyond, not only to further understand the mechanisms underlying adaptation and evolution but also to develop and implement innovative management and policy actions to preserve the adaptability of natural forests and intensively managed plantations.

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“…With these criteria, 40,238 (59%) sequences were assigned a putative protein ID, of which 14,838 were unique. A cutoff E-value set at 1 × 10 −5 was used in the annotation of Conifer DBMagic (Lorenz et al 2012) and a smaller number of putative protein IDs (36,995 sequences (54%)) within the All-Pinus database sequences were identified when this cut-off E-value was used. The annotations for these protein IDs were downloaded from DAVID v6.7, (http://david.abcc.ncifcrf.gov/) (Huang et al 2009).…”

Section: Assembly and Annotation Of The Heterologous Pinus Consensus mentioning

confidence: 99%

Heterologous hybridisation to a Pinus microarray: profiling of gene expression in Pinus radiata saplings exposed to ethephon

Dubouzet¹,

Donaldson²,

Black³

et al. 2014

N.Z. j. of For. Sci.

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Background: The design, construction and application of a Pinus microarray platform are described. The oligonucleotide microarray was developed using publicly available Pinus cDNA sequences mostly derived from Pinus taeda to test whether heterologous hybridisation of microarray probes will generate useful data when hybridised with cRNA constructed from the dominant New Zealand forestry species Pinus radiata.

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Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species

Cited by 44 publications

References 38 publications

Genetic Resistance to Fusiform Rust in Southern Pines and White Pine Blister Rust in White Pines—A Contrasting Tale of Two Rust Pathosystems—Current Status and Future Prospects

Genetic Resistance to Fusiform Rust in Southern Pines and White Pine Blister Rust in White Pines—A Contrasting Tale of Two Rust Pathosystems—Current Status and Future Prospects

Forest tree genomics: 10 achievements from the past 10 years and future prospects

Heterologous hybridisation to a Pinus microarray: profiling of gene expression in Pinus radiata saplings exposed to ethephon

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