Abstract
The tetraploid table grape Kyoho, a cultivar of major global economic importance, has long presented a challenge in understanding its genetic architecture and the regulatory landscapes between its different ancestral genomes. Here, we assemble a haplotype-resolved, near-complete reference genome (480.32-489.47 Mb, contig N50 17.5-23.3 Mb, with a total of only 11 gaps) to investigate regulatory dynamics through integrative multiomic analyses during fruit development. Comparative evolutionary genomics classifies Kyoho as a segmental allotetraploid with a complex mosaic genome, composed of ∼71% V. vinifera (Vv) and ∼29% V. labrusca (Vl) ancestry. A total of 67.3% of genes are shared among the four haplotypic genomes with 9.8% haplotype specific genes. Transcriptomic analysis revealed that among 17,750 pairs of ancestral alleles exhibiting directional bias, only 4,086 (23.4%) maintained a consistent ancestral dominance direction across all tissues. Similarly, comparisons of DNA methylation profiles showed no significant differences between genome ancestries Vl (0.009∼0.676): Vv (0.010∼0.670). However, alternative splicing (AS) analyses demonstrated that allele-specific splicing changes were correlated with ancestral origin across tissues (Vl: 1,529 vs. Vv: 2,052). Integrative omics identified 2,307 differentially expressed ancestral alleles that showed no significant genomic variants or methylation bias but exhibited AS bias. These genes include key regulators of fruit ripening, including ZEP, PIN, DOG1and MYB. Overall, this work delivers a landmark genomic resource and characterizes its regulatory architecture, facilitating functional genomic studies and guiding precision polyploid breeding in grapes.
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Claims 9
Claim · model-written summary
A haplotype-resolved near-complete reference genome of Kyoho was assembled at 480.32-489.47 Mb.
Verbatim
e0“The tetraploid table grape Kyoho”
e1“Here, we assemble a haplotype-resolved, near-complete reference genome (480.32-489.47 Mb, contig N50 17.5-23.3 Mb, with a total of only 11 gaps)”
Claim · model-written summary
Kyoho is a segmental allotetraploid with about 71% V. vinifera and 29% V. labrusca ancestry.
Verbatim
e0“The tetraploid table grape Kyoho”
e1“composed of ∼71% V. vinifera (Vv) and ∼29% V. labrusca (Vl) ancestry”
Claim · model-written summary
A total of 67.3% of genes are shared among the four haplotypic genomes.
Verbatim
e0“The tetraploid table grape Kyoho”
e1“A total of 67.3% of genes are shared among the four haplotypic genomes”
Claim · model-written summary
Kyoho has 9.8% haplotype-specific genes.
Verbatim
e0“The tetraploid table grape Kyoho”
e1“with 9.8% haplotype specific genes”
Claim · model-written summary
Only 23.4% of 17,750 ancestral allele pairs with directional bias kept a consistent ancestral dominance direction across all tissues.
Verbatim
e0“The tetraploid table grape Kyoho”
e1“among 17,750 pairs of ancestral alleles exhibiting directional bias, only 4,086 (23.4%) maintained a consistent ancestral dominance direction across all tissues”
Claim · model-written summary
DNA methylation profiles did not differ significantly between genome ancestries Vl and Vv.
Verbatim
e0“The tetraploid table grape Kyoho”
e1“comparisons of DNA methylation profiles showed no significant differences between genome ancestries Vl (0.009∼0.676): Vv (0.010∼0.670)”
Claim · model-written summary
Allele-specific splicing changes were correlated with ancestral origin across tissues (Vl: 1,529 vs. Vv: 2,052).
- Taxon
- Kyohoe0
- Organ / stage
- across tissuese1
- Outcome
- allele-specific splicing changese1
- Value
- Vl: 1,529 vs. Vv: 2,052e1
Not reportedDirection
Verbatim
e0“The tetraploid table grape Kyoho”
e1“alternative splicing (AS) analyses demonstrated that allele-specific splicing changes were correlated with ancestral origin across tissues (Vl: 1,529 vs. Vv: 2,052)”
Claim · model-written summary
Integrative omics identified 2,307 differentially expressed ancestral alleles with AS bias but no genomic variant or methylation bias.
Verbatim
e0“The tetraploid table grape Kyoho”
e1“Integrative omics identified 2,307 differentially expressed ancestral alleles that showed no significant genomic variants or methylation bias but exhibited AS bias”
Claim · model-written summary
The AS-biased genes include key regulators of fruit ripening, such as ZEP, PIN, DOG1 and MYB.
Verbatim
e0“The tetraploid table grape Kyoho”
e1“These genes include key regulators of fruit ripening, including ZEP, PIN, DOG1and MYB”