Chromosome-level genome and annotation data for parentally phased diploid Theobroma cacao clone 26

The genome and annotation data herein relates to the following publication. Please cite the current version of this manuscript if this data is useful to your work (https://www.biorxiv.org/content/10.1101/2024.05.26.595985v2).  Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback Diseases of Theobroma cacao disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTL). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome-level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide-binding site leucine-rich repeat class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates at informative QTLs. We identified structural variants within NLRs inherited from parentals. Our research provides the first diploid, fully scaffolded and parentally phased genome resource for Theobroma cacao L. and provides insights into the genetics underlying resistance and susceptibility to VSD.本数据集附带的基因组与注释数据关联如下发表成果。若本数据对你的研究有所助益，请引用本稿件的当前版本（https://www.biorxiv.org/content/10.1101/2024.05.26.595985v2）。 《栽培可可的亲本来源分型染色体为抗血管条纹坏死病的遗传结构解析提供新见解》 可可树（Theobroma cacao）病害会破坏可可豆供应链，对种植者造成经济损失。由可可丝核菌（Ceratobasidium theobromae）引起的血管条纹坏死病（Vascular streak dieback, VSD）是可可的一种新兴病害，目前仅分布于东南亚和美拉尼西亚地区。针对VSD的抗性已通过印度尼西亚苏拉威西岛与巴布亚新几内亚的大型后代试验开展验证，并已鉴定出具有参考价值的数量性状基因座（quantitative trait loci, QTL）。本研究以一株来自抗病与感病亲本杂交的VSD感病后代植株（克隆系26，clone 26）为材料，将其基因组组装至染色体水平，并区分了来自抗病或感病亲本的等位基因。对经亲本分型的基因组进行了所有预测基因的注释，并重点注释了核苷酸结合位点亮氨酸重复序列类（nucleotide-binding site leucine-rich repeat, NLR）抗病基因。研究发现，在具有参考价值的QTL区域存在NLR基因簇与其他潜在病害响应基因候选位点。本研究还鉴定了来自亲本的NLR基因内部的结构变异。本研究首次为可可树（Theobroma cacao L.）提供了二倍体、全支架组装且经亲本分型的基因组资源，并为解析可可抗/感VSD的遗传机制提供了新的见解。