# A genome sequence for the threatened whitebark pine

## TL;DR

Scientists created a high-quality genome sequence for whitebark pine to help restore populations threatened by disease and climate change.

## Contribution

A high-quality genome assembly and annotation for whitebark pine, improving identification of disease resistance genes.

## Key findings

- The genome assembly includes 27.6 Gb of sequence with 87.2% placed on 12 chromosomes.
- 25,362 protein-coding genes were annotated, with over 77% of the genome identified as repeats.
- Candidate genes for resistance to white pine blister rust were identified, including nucleotide-binding leucine-rich repeat receptors (NLRs).

## Abstract

Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine
regions in the Western contiguous United States and Canada. WBP has become critically
threatened throughout a significant part of its natural range due to mortality from the
introduced fungal pathogen white pine blister rust (WPBR, Cronartium
ribicola) and additional threats from mountain pine beetle
(Dendroctonus ponderosae), wildfire, and maladaptation due to changing
climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic
technologies can contribute to a faster, more cost-effective approach to the traditional
practices of identifying disease-resistant, climate-adapted seed sources for restoration.
With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford
Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly
approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs
(N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total
sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding
genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the
greatest variation in resistance to WPBR among the North American white pines. Candidate
genes for quantitative resistance include disease resistance genes known as
nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain
alignments and direct genome scanning was employed to fully describe the 3 subclasses of
NLRs. Our high-quality reference sequence and annotation provide a marked improvement in
NLR identification compared to previous assessments that leveraged de novo-assembled
transcriptomes.

Whitebark pine (Pinus albicaulis), a white pine of western North
American subalpine regions, has become critically threatened throughout its range by white
pine blister rust fungus (WPBR), mountain pine beetle, wildfire, and maladaptation from
changing climate—vast acreages have suffered nearly complete mortality from WPBR. As
genomic data can contribute to faster, cost-effective approaches for identifying
disease-resistant, climate-adapted seed sources for restoration, Neale et al. present a
high-quality reference sequence and annotation—a marked improvement in candidate
WPBR-disease-resistance gene identification compared to previous assessments.