Decoding Phytophthora meadii (McRae): the first genomic insights into the arecanut fruit rot pathogen

Phytophthora meadii is an oomycetic pathogen that is destructive to economically important tropical crops. The impact of crop loss in arecanut plantations caused by this phytopathogen is increasing every year. Hence, the study integrated short and long-read sequencing technologies to provide the first genomic insights on the highly virulent P. meadii P19 isolate from the arecanut fruit rot disease hotspot region. The assembled genome consists of 439 scaffolds and is 58.74 Mb long. Additionally, the mycelial transcriptome of P. meadii P19 isolate was sequenced and assembled into 28,522 transcripts using Trinity. These transcripts were then clustered into 20,964 representative sequences with CD-HIT, which served as transcriptomic evidence for gene prediction. Using extensive bioinformatics resources, we present here the following genomic features predicted from the assembled genome: (i) protein-coding and non-coding genes, (ii) RxLR and CRN effectors, (iii) gene dense and sparse regions, (iv) carbohydrate-active enzymes, (v) gene orthologous groups, (vi) genes under positive selection, and (viii) evidence for horizontal gene transfer. The high-coverage reference genome will undoubtedly benefit researchers in exploring and manipulating the pathogenic characteristics of P. meadii.