The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev1,
- Omnia Gamal El-Dien1,2,
- Macaire M.S. Yuen1,
- Shu Shengqiang3,
- Shaun D. Jackman4,
- René L. Warren4,
- Lauren Coombe4,
- Lise van der Merwe5,
- Ada Stewart6,
- Lori B. Boston6,
- Christopher Plott6,
- Jerry Jenkins6,
- Guifen He3,
- Juying Yan3,
- Mi Yan3,
- Jie Guo3,
- Jesse W. Breinholt7,8,
- Leandro G. Neves7,
- Jane Grimwood6,
- Loren H. Rieseberg9,
- Jeremy Schmutz3,6,
- Inanc Birol4,
- Matias Kirst10,
- Alvin D. Yanchuk5,
- Carol Ritland1,
- John H. Russell5 and
- Joerg Bohlmann1
- 1Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
- 2Pharmacognosy Department, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt;
- 3Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;
- 4Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada;
- 5British Columbia Ministry of Forests, Victoria, British Columbia V8W 9E2, Canada;
- 6HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
- 7Rapid Genomics, Gainesville, Florida 32601, USA;
- 8Intermountain Healthcare, Intermountain Precision Genomics, St. George, Utah 84790, USA;
- 9Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
- 10School of Forest, Fisheries and Geomatic Sciences, University of Florida, Gainesville, Florida 32603, USA
Abstract
We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species of the Cupressaceae. The genome assembly, derived from a uniquely inbred tree produced through five generations of self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one of the most complete genome assemblies for a conifer. Population genomic analysis revealed WRC to be one of the most genetically depauperate wild plant species, with an effective population size of approximately 300 and no significant genetic differentiation across its geographic range. Nucleotide diversity, π, is low for a continuous tree species, with many loci showing zero diversity, and the ratio of π at zero- to fourfold degenerate sites is relatively high (approximately 0.33), suggestive of weak purifying selection. Using an array of genetic lines derived from up to five generations of selfing, we explored the relationship between genetic diversity and mating system. Although overall heterozygosity was found to decline faster than expected during selfing, heterozygosity persisted at many loci, and nearly 100 loci were found to deviate from expectations of genetic drift, suggestive of associative overdominance. Nonreference alleles at such loci often harbor deleterious mutations and are rare in natural populations, implying that balanced polymorphisms are maintained by linkage to dominant beneficial alleles. This may account for how WRC remains responsive to natural and artificial selection, despite low genetic diversity.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.276358.121.
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Freely available online through the Genome Research Open Access option.
- Received November 2, 2021.
- Accepted September 6, 2022.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
