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Updated: Jun 29, 2025

Processing the Loblolly Pine PtGen2 cDNA Microarray

Processing the Loblolly Pine PtGen2 cDNA Microarray

Published on: March 20, 2009

A genome sequence for the threatened whitebark pine.

David B Neale^1,2, Aleksey V Zimin³, Amy Meltzer³

¹Department of Plant Sciences, University of California, Davis, CA 95616, USA.

G3 (Bethesda, Md.)

|March 25, 2024

Summary

This summary is machine-generated.

Genomic sequencing of whitebark pine (WBP) provides a vital tool for conservation. This high-quality genome assembly aids in identifying genes for disease resistance, crucial for WBP restoration efforts.

Keywords:

Pinus albicaulis annotation conifer genome assembly gymnosperm whitebark pine

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An Improved Method of RNA Isolation from Loblolly Pine P. taeda L. and Other Conifer Species

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An Improved Method of RNA Isolation from Loblolly Pine P. taeda L. and Other Conifer Species

An Improved Method of RNA Isolation from Loblolly Pine P. taeda L. and Other Conifer Species

Published on: February 22, 2010

Area of Science:

Genomics
Forestry
Conservation Biology

Background:

Whitebark pine (WBP) is critically threatened by white pine blister rust (WPBR), mountain pine beetle, wildfire, and climate change.
WBP populations have experienced significant mortality across their natural range in Western North America.
Genomic technologies offer a promising avenue for accelerating the identification of resilient seed sources for WBP restoration.

Purpose of the Study:

To generate a high-quality reference genome assembly for whitebark pine (Pinus albicaulis).
To facilitate the identification of genes associated with resistance to white pine blister rust (WPBR) and adaptation to changing climates.
To improve genomic resources for WBP conservation and restoration.

Main Methods:

Hybrid assembly using Illumina short reads (haploid megagametophyte) and Oxford Nanopore long reads (diploid needle tissue).
Deep sequencing coverage and a multistep assembly approach.
Genome annotation to identify protein-coding genes and repeat content, with a focus on nucleotide-binding leucine-rich repeat receptors (NLRs).

Main Results:

A comprehensive WBP genome assembly of 27.6 Gb in 92,740 contigs and 34,716 scaffolds, with 87.2% anchored to 12 chromosomes.
Annotation identified 25,362 protein-coding genes, with over 77% of the genome characterized as repeats.
Detailed characterization of three NLR subclasses, revealing significant improvements in identification compared to previous transcriptome-based assessments.

Conclusions:

The high-quality WBP genome assembly and annotation represent a significant advancement for WBP research and conservation.
This resource will accelerate the identification of genetic markers for WPBR resistance and climate adaptation.
Enables more effective and cost-efficient restoration strategies for this imperiled species.