RT Journal
A1 Shalev, Tal J.
A1 Gamal El-Dien, Omnia
A1 Yuen, Macaire M.S.
A1 Shengqiang, Shu
A1 Jackman, Shaun D.
A1 Warren, René L.
A1 Coombe, Lauren
A1 van der Merwe, Lise
A1 Stewart, Ada
A1 Boston, Lori B.
A1 Plott, Christopher
A1 Jenkins, Jerry
A1 He, Guifen
A1 Yan, Juying
A1 Yan, Mi
A1 Guo, Jie
A1 Breinholt, Jesse W.
A1 Neves, Leandro G.
A1 Grimwood, Jane
A1 Rieseberg, Loren H.
A1 Schmutz, Jeremy
A1 Birol, Inanc
A1 Kirst, Matias
A1 Yanchuk, Alvin D.
A1 Ritland, Carol
A1 Russell, John H.
A1 Bohlmann, Joerg
T1 The western redcedar genome reveals low genetic diversity in a self-compatible conifer
JF Genome Research 
JO Genome Research 
YR 2022 
FD October 01 
VO 32 
IS 10 
SP 1952 
OP 1964 
DO 10.1101/gr.276358.121 
UL http://genome.cshlp.org/content/32/10/1952.abstract 
AB 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.