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      A genome sequence for the threatened whitebark pine

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          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.

          Abstract

          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.

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          Most cited references62

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          BEDTools: a flexible suite of utilities for comparing genomic features

          Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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            Minimap2: pairwise alignment for nucleotide sequences

            Heng Li (2018)
            Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.
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              Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

              Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT2, for representing and searching an expanded model of the human reference genome, in which a large catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate two initial applications of HISAT2: HLA typing, a critical need in human organ transplantation, and DNA fingerprinting, widely used in forensics. These applications are part of HISAT-genotype, with performance not only surpassing earlier computational methods, but matching or exceeding the accuracy of laboratory-based assays.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press (US )
                2160-1836
                May 2024
                25 March 2024
                25 March 2024
                : 14
                : 5
                : jkae061
                Affiliations
                Department of Plant Sciences, University of California , Davis, CA 95616, USA
                Whitebark Pine Ecosystem Foundation , Missoula, MT 59808, USA
                Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University , Baltimore, MD 21218, USA
                Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University , Baltimore, MD 21218, USA
                Department of Ecology and Evolutionary Biology, University of Connecticut , Storrs, CT 06269, USA
                Department of Ecology and Evolutionary Biology, University of Connecticut , Storrs, CT 06269, USA
                School of Forestry, Northern Arizona University , Flagstaff, AZ 86011, USA
                Department of Plant Sciences, University of California , Davis, CA 95616, USA
                University of California Cooperative Extension, Central Sierra , Jackson, CA 95642, USA
                Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University , Baltimore, MD 21218, USA
                USDA Forest Service, Pacific Southwest Research Station , Davis, CA 95618, USA
                School of Forestry, Northern Arizona University , Flagstaff, AZ 86011, USA
                Department of Plant Sciences, University of California , Davis, CA 95616, USA
                Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University , Baltimore, MD 21218, USA
                Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University , Baltimore, MD 21218, USA
                Departments of Computer Science and Biostatistics, Johns Hopkins University , Baltimore, MD 21218, USA
                Department of Ecology and Evolutionary Biology, University of Connecticut , Storrs, CT 06269, USA
                Institute for Systems Genomics, University of Connecticut , Storrs, CT 06269, USA
                Author notes
                Corresponding author: Department of Plant Sciences, University of California, One Shields Ave., Davis, CA 95616, USA. Email: dbneale@ 123456ucdavis.edu
                Corresponding author: Department of Plant Sciences, University of California, One Shields Ave., Davis, CA 95616, USA. Email: pemcguire@ 123456ucdavis.edu

                Conflicts of interest Any use of product names is for informational purposes only and does not imply endorsement by the US Government. The findings and conclusions in this publication are those of the authors and should not be construed to represent any official USDA or US Government determination or policy.

                Author information
                https://orcid.org/0000-0002-0380-1634
                https://orcid.org/0000-0003-2872-5428
                https://orcid.org/0000-0001-6647-723X
                https://orcid.org/0000-0003-2083-6027
                https://orcid.org/0000-0002-8859-7432
                https://orcid.org/0000-0001-5923-0888
                Article
                jkae061
                10.1093/g3journal/jkae061
                11075562
                38526344
                bebb6f19-e534-4f32-b9d2-4f13e237aa63
                © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 11 December 2023
                : 12 March 2024
                : 04 April 2024
                Page count
                Pages: 12
                Funding
                Funded by: USDA Forest Service Forest Health Protection;
                Funded by: American Forests;
                Funded by: Krieber Charitable Trust;
                Funded by: NIH, DOI 10.13039/100000002;
                Award ID: R01-HG006677
                Funded by: NSF, DOI 10.13039/100000001;
                Award ID: IOS-1744309
                Funded by: Computational Biology Core;
                Funded by: Institute for Systems Genomics;
                Funded by: University of Connecticut for High Performance Computing Resources;
                Funded by: NSF CAREER;
                Award ID: 1943371
                Categories
                Genome Report
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140
                Featured

                Genetics
                genome assembly,whitebark pine,pinus albicaulis,annotation,conifer,gymnosperm
                Genetics
                genome assembly, whitebark pine, pinus albicaulis, annotation, conifer, gymnosperm

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