ICAR- Directorate of Cashew Research (DCR), Puttur, D.K., Karnataka, 574 202, India.
Bionivid Technology Private Limited, 209, 4th Cross Rd, B Channasandra, Kasturi Nagar, Bengaluru, Karnataka, 560 043, India.
Sci Rep. 2022 Oct 28;12(1):18187. doi: 10.1038/s41598-022-22600-7.
Cashew is the second most important tree nut crop in the global market. Cashew is a diploid and heterozygous species closely related to the mango and pistachio. Its improvement by conventional breeding is slow due to the long juvenile phase. Despite the economic importance, very little genomics/transcriptomics information is available for cashew. In this study, the Oxford nanopore reads and Illumina reads were used for de novo assembly of the cashew genome. The hybrid assembly yielded a 356.6 Mb genome corresponding to 85% of the estimated genome size (419 Mb). The BUSCO analysis showed 91.8% of genome completeness. Transcriptome mapping showed 92.75% transcripts aligned with the assembled genome. Gene predictions resulted in the identification of 31,263 genes coding for a total of 35,000 gene isoforms. About 46% (165 Mb) of the cashew genome comprised of repetitive sequences. Phylogenetic analyses of the cashew with nine species showed that it was closely related to Mangifera indica. Analysis of cashew genome revealed 3104 putative R-genes. The first draft assembly of the genome, transcriptome and R gene information generated in this study would be the foundation for understanding the molecular basis of economic traits and genomics-assisted breeding in cashew.
腰果是全球市场上第二重要的坚果树种。腰果是一种二倍体和杂合种，与芒果和开心果关系密切。由于幼年期长，其通过传统育种进行改良的速度较慢。尽管具有重要的经济意义，但有关腰果的基因组学/转录组学信息却非常有限。在这项研究中，我们使用 Oxford nanopore 读取和 Illumina 读取进行腰果基因组的从头组装。杂交组装生成了 356.6 Mb 的基因组，对应于估计基因组大小（419 Mb）的 85%。BUSCO 分析显示基因组完整度为 91.8%。转录组映射显示 92.75%的转录本与组装的基因组对齐。基因预测导致鉴定出 31263 个编码总共 35000 个基因亚型的基因。腰果基因组的约 46%（165 Mb）由重复序列组成。与九种物种的腰果进行的系统发育分析表明，它与 Mangifera indica 密切相关。对腰果基因组的分析揭示了 3104 个推定的 R 基因。本研究中首次生成的基因组、转录组和 R 基因信息的草案组装将为理解经济性状的分子基础和腰果的基因组辅助育种奠定基础。
