The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes

Abstract

Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value in red wine blending and nutrient-enriched foods developing. However, due to the lack of genome information, the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient. Here, the cultivar ‘Yan73’ was used for assembling the telomere-to-telomere (T2T) genome of teinturier grapes by combining the High Fidelity (HiFi), Hi-C and ultralong Oxford Nanopore Technologies (ONT) reads. Two haplotype genomes were assembled, at the sizes of 501.68 Mb and 493.38 Mb, respectively. In the haplotype 1 genome, the transposable elements (TEs) contained 32.77% of long terminal repeats (LTRs), while in the haplotype 2 genome, 31.53% of LTRs were detected in TEs. Furthermore, obvious inversions were identified in chromosome 18 between the two haplotypes. Transcriptome profiling suggested that the gene expression patterns in ‘Cabernet Sauvignon’ and ‘Yan73’ were diverse depending on tissues, developmental stages, and varieties. The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages, whereas the expression levels of numerous genes showed significant differences. Compared with other genes, the expression levels of VvMYBA1 and VvUFGT4 in all samples, VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of ‘Yan73’ were higher than those of ‘Cabernet Sauvignon’. Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of ‘Yan73’ haplotype 2 genome. The ‘Yan73’ T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.

Acknowledgements

This work was supported by grants from the Major Innovation Project of Shandong Province (2022CXGC010605), the National Natural Science Foundation of China (32002023 and 32172518), the Regional Joint Key Innovation Project of NSFC (U22A20491), and Shaanxi Key R&D Plan Project (2023-ZDLNY-21).

Author contributions

Y.F., Y.Z., K.C., and K.Z. conceived and designed the project. M.D., Z.L., W.W., S.C., and X.W. performed the genome assembly and gene annotation. K.Z., Z.L., and K.C. performed transcriptome analysis. H.Z., X.Z., P.Z., J.L., and W.J. assisted in grape culture and sample collection. X.G., M.T., Q.Z., and M.C. assisted in bioinformatics analyses and data visualization. K.Z., M.D., K.C., and Y.F. wrote and purified the manuscript.

Data availability

All the raw sequencing data generated for this project have been deposited in the National Genomics Data Center (NGDC) Genome Sequence Archive (GSA) (https://ngdc.cncb.ac.cn/gsa/) with BioProject number PRJCA018686, and in the NCBI Sequence Read Archive under project number PRJNA1000119. The assembly and annotation as well as the sequences of centromeres and heterozygous regions have been deposited in Zenodo.

Conflict of interest statement

The authors declare no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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