The complete reference genome for grapevine (Vitis viniferaL.) genetics and breeding

Abstract

Grapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome consisted of thousands of fragments with missing centromeres and telomeres, which limited the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the pinot noir cultivar (PN40024) using the PacBio HiFi long reads. The T2T reference genome (PN_T2T) was 69 Mb longer with 9026 more genes identified than the 12X.v2 version (Canaguier et al., 2017). We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though the PN40024 sample had been selfed for nine generations, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation-reduction process and protein phosphorylation. The fully annotated complete reference genome, therefore, provides important resources for grapevine genetics and breeding.

Chromosome-scale genome assembly ofCamellia crapnellianaprovides insights into the fatty acid biosynthesis

“…4a, b). Our results showed that the occurrence of two polyploidization events in the C. crapnelliana genome, including the ancient WGT (γ) event that occurred in grape and eudicots 60,61 , the other WGD (β) event shared with A. chinensis and other Theaceae species 11,54,84 (Fig. 4a, b).…”

“…The protein-coding genes of nine representative species were selected for gene family analysis using OrthoFinder v2.5.4 73 oleifera 26 (CON), Olea europaea 57,74 (OEU), Vitis vinifera 60,61 (VVI), and C. crapnelliana (CCRA). A total of 107 single-copy orthologues were obtained, and they were aligned using MAFFT v7.505 75 , and then ProTest v3.4.2 76 was used to find the best model of amino acid replacement in the single-copy alignments.…”

CentIER: accurate centromere identification for plant genomes with sequence specificity information

“…A. chinensis (Han et al, 2023), http://182.92.183.62/; C. limon (Bao et al, 2023), https://ngdc.cncb.ac.cn/search/?dbId=gwh&q=GWHCBFQ00000000.1; E. rufpilus (Wang et al, 2023), http://sugarcane.zhangjisenlab.cn/SugarcaneDB/#/downloads; O. sativa (Song et al, 2021), http://rice.hzau.edu.cn/cgi-bin/rice_rs3/download_ext; V. vinifera (Shi et al, 2023), https://zenodo.org/record/7751391#.ZBgVmcJBy3A; Z. mays (Chen et al, 2023), https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA751841.…”

“…The wet-experiment-based method utilizes centromere-specific proteins (CenH3 in plants) to perform Chromatin Immunoprecipitation Sequencing (ChIP-seq) and maps centromeric reads to the assembly for identification, which is costly and time-consuming (Liu et al, 2023;Marques et al, 2015). The bioinformatics method detects all tandem repeat monomers (TRs) in the whole genome first, and performs the identification by assuming the centromeric TRs are the most abundant among all TRs of a genome (Shi et al, 2023). For example, quarTeT can be used for identifying centromeric repeats (Lin et al, 2023).…”

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

“…PN40024) obtained after several rounds of selfing of the cultivar Helfensteiner, the result of Pinot noir and Schiava grossa outcross 1,2 . The PN40024 reference genome has been a key tool for the study of grapevine molecular biology and genetics and both the reference assembly and annotation have been continuously improved [2][3][4] .…”