Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

Abstract

To preserve their varietal attributes, established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with a very low haplotype switch-error rate (<0.025). The haplophase alignment identified > 25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as a reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated with abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and unveil the molecular bases of clonal phenotypic variation.

Acknowledgements

This work was supported by Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT): PICT2018-02381, MINCyT/ANPCyT (FONTAR)-CDTI IBEROGEN; CONICET (Bilateral PCB-II, CONICET-CSIC, MINECO BIO2017-86375-R, and the project PID2020-120183RB-I00 funded by MCIN/AEI/10.13039/501100011033), and the Max Planck Society. L.C. was supported by a CONICET travel grant for a short-term stay at the Max Planck (Tübingen). We are grateful to Ilja Bezrukov for answering bioinformatics question and Silvina van Houten for collaboration with field work. We thank Olivier Yobregat (Institut Français de la Vigne et du Vin, IFV) for providing plant material from Malbec parental cultivars. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797460. This study benefited from the networking activities and resources produced within the COST action Integrape (CA17111) and COST innovators grant Grapedia (IG17111).

Author contributions

L.C.: coordinated the project and wrote the article, produced and analyzed phenotypic, transcriptomic, and genomic data. P.C.B.: laboratory work for genomic sequencing and designed the bioinformatic pipelines for genome assembly and annotation, analyzed genomic data, and global data interpretation. C.M.: phenotypic and transcriptomic diversity analysis. L.B.: field and laboratory work for phenotypic diversity analysis. D.B. and C.S.: project design, provided insight, and access to the analyzed clonal accessions. W.T.: bioinformatic analysis, set-up, and maintenance of genome browse at IBAM-CONICET web-page. C.L.: laboratory work for genomic data obtention. S.G.T., J.I., and J.M.M.Z.: project design for genomic and transcriptomic experiments. C.R., J.I., and J.M.M.Z.: parental cultivars plant material and provided resources for whole DNA extractions. D.W.: resources, facilities, and advice for genomic laboratory work and bioinformatic analyses. D.L.: designed and coordinated the entire project and performed transcriptomic analysis. All authors read and improved this manuscript.

Data availability

Malbec-Mag and Malbec-Pru assemblies are available at the NCBI public repository under BioProjects: PRJNA1036636 and PRJNA1036637, respectively. All raw data is available at NCBI under BioProject: PRJNA1037531, including genomic Illumina short-reads obtained for cultivars Malbec, Prunelard, and Magdeleine, PacBio long reads for Malbec and a batch of 22 RNA-Seq from eight Malbec clones and replicates. Malbec annotated assemblies are also available for visualization and gene browse at two public repositories: IBAM-CONICET (http://ibam.mendoza-conicet.gob.ar/resources/genome-visualizer/) and Gramene (https://www.gramene.org/). A gene correspondence between Malbec-Pru and Malbec-Mag annotated genes, alongside with PN40024.v4 and VCost.v3 annotations is provided, therefore gene queries can be performed using any of the mentioned formats.

Conflict of interest statement

The authors declare no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research Journal online.

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