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The western redcedar genome reveals low genetic diversity in a self-compatible conifer

Journal Article · · Genome Research
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  1. Univ. of British Columbia, Vancouver, BC (Canada)
  2. Univ. of British Columbia, Vancouver, BC (Canada); Alexandria Univ., Ibrahimia, Alexandria (Egypt)
  3. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
  4. Michael Smith Genome Sciences Centre, Vancouver, BC (Canada)
  5. British Columbia Ministry of Forests, Victoria, BC (Canada)
  6. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  7. Rapid Genomics, Gainesville, FL (United States); Intermountain Precision Genomics, St. George, Utah (United States)
  8. Rapid Genomics, Gainesville, FL (United States)
  9. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  10. Univ. of Florida, Gainesville, FL (United States)
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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.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1994347
Journal Information:
Genome Research, Journal Name: Genome Research Journal Issue: 10 Vol. 32; ISSN 1088-9051
Publisher:
Cold Spring Harbor Laboratory PressCopyright Statement
Country of Publication:
United States
Language:
English

References (3)

Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome dataset January 2021
Western redcedar single nucleotide polymorphism (SNP) genotyping data for genomic selection and population genetics dataset January 2022
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics collection January 2020

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