Abstract
Hemizygous genes, which are present on only one of the two homologous chromosomes of diploid organisms, have been mainly studied in the context of sex chromosomes and sex-linked genes. However, these genes can also occur on the autosomes of diploid plants due to structural variants (SVs), such as a deletion/insertion of one allele, and this phenomenon largely unexplored in plants. Here, we investigated the genomic and epigenomic landscapes of hemizygous genes across 22 genomes with varying propagation histories: eleven clonal lineages, seven outcrossed samples, and four inbred and putatively homozygous genomes. We identified SVs leading to genic hemizygosity. As expected, very few genes (0.01 to 1.2%) were hemizygous in the homozygous genomes, representing negative controls. Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes, but consistently elevated for the clonal samples at 13.8% genes, likely reflecting heterozygous SV accumulation during clonal propagation. Compared to diploid genes, hemizygous genes were more often situated in centromeric than telomeric regions and experienced weaker purifying selection. They also had reduced levels of expression, averaging ~20% of the expression levels of diploid genes, violating the evolutionary model of dosage compensation. We also detected higher DNA methylation levels in hemizygous genes and transposable elements, which may contribute to their reduced expression. Finally, expression profiles showed that hemizygous genes were more specifically expressed in contexts related to fruit development, organ differentiation, and stress responses. Overall, hemizygous genes accumulate in clonally propagated lineages and display distinct genetic and epigenetic features compared to diploid genes, shedding unique insights into genetic studies and breeding programs of clonal crops.
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Claims 12
Claim · model-written summary
Structural variants leading to genic hemizygosity were identified in the crop genomes.
Verbatim
e0“We identified SVs leading to genic hemizygosity”
t0“crops”
Claim · model-written summary
Very few genes (0.01 to 1.2%) were hemizygous in the inbred, putatively homozygous genomes used as negative controls.
Verbatim
e0“very few genes (0.01 to 1.2%) were hemizygous in the homozygous genomes”
t0“crops”
Claim · model-written summary
Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes.
Verbatim
e0“Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes”
t0“crops”
Claim · model-written summary
Hemizygosity was more elevated in clonal samples (13.8% of genes) than in outcrossed lineages.
Verbatim
e0“Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes, but consistently elevated for the clonal samples at 13.8% genes”
t0“crops”
Claim · model-written summary
The elevated hemizygosity in clonal samples likely reflects accumulation of heterozygous structural variants during clonal propagation.
Verbatim
e0“likely reflecting heterozygous SV accumulation during clonal propagation”
t0“crops”
Claim · model-written summary
Hemizygous genes were situated more often in centromeric than telomeric regions than diploid genes were.
Verbatim
e0“Compared to diploid genes, hemizygous genes were more often situated in centromeric than telomeric regions”
t0“crops”
Claim · model-written summary
Hemizygous genes experienced weaker purifying selection than diploid genes.
Verbatim
e0“Compared to diploid genes, hemizygous genes were more often situated in centromeric than telomeric regions and experienced weaker purifying selection”
t0“crops”
Claim · model-written summary
Hemizygous genes had reduced expression, averaging about 20% of the expression levels of diploid genes.
Verbatim
e0“They also had reduced levels of expression, averaging ~20% of the expression levels of diploid genes”
t0“crops”
Claim · model-written summary
The reduced expression of hemizygous genes violates the evolutionary model of dosage compensation.
Verbatim
e0“violating the evolutionary model of dosage compensation”
t0“crops”
Claim · model-written summary
Higher DNA methylation levels were detected in hemizygous genes.
Verbatim
e0“We also detected higher DNA methylation levels in hemizygous genes”
t0“crops”
Claim · model-written summary
The higher DNA methylation may contribute to the reduced expression of hemizygous genes.
Verbatim
e0“higher DNA methylation levels in hemizygous genes and transposable elements, which may contribute to their reduced expression”
t0“crops”
Claim · model-written summary
Hemizygous genes were more specifically expressed in contexts related to fruit development, organ differentiation and stress responses.
Verbatim
e0“hemizygous genes were more specifically expressed in contexts related to fruit development, organ differentiation, and stress responses”
t0“crops”