De novo assembly and characterization of the draft genome of the cashew (Anacardium occidentale L.)

Abstract

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.

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

“…The Cashew Microsatellite Database (CMDB) is an online relational database that stores the microsatellite repeats information mined from the recently sequenced cashew genome ( Savadi et al., 2022b ) and the shoot transcriptome ( Savadi et al., 2022a ), as well as the experimentally validated SSR markers. CMBD is available at https://www.cashewmicrosatellitesdatabase.in/ .…”

“…The whole-genome sequence (356 MB size, 92% BUSCO value) of cashew cv. Bhaskara generated by hybrid assembly of Illumina mate-pair reads and Oxford Nanopore reads at ICAR-DCR ( Savadi et al., 2022b ) and deposited in the National Centre for Biotechnology Information (NCBI) database (PRJNA766521) was used for the mining of genome-wide microsatellites/SSRs. The PolyMorphPredict software, which permits in silico mining of microsatellites and designs primers from genome and transcriptome data, was used to discover and characterize the composition and distributions of genome-wide SSRs ( Das et al., 2019 ).…”

“…Recently, the first draft genome of cashew cv. Bhaskara (356 Mb size with 92% BUSCO value) was generated through hybrid assembly of Illumina mate-pair reads and Oxford Nanopore reads and reported by our group ( Savadi et al., 2022b ). The availability of draft genome sequence prompts the discovery of a large set of SSRs at the genome level and make them easily accessible to researchers.…”