Complete genome sequence of the mango bacterial dry rot pathogen Sphingomonas carotinifaciens strain NY01

Mango bacterial dry rot has become an increasingly serious issue in the mango-producing regions of Guangdong, China, leading to dry and necrotic leaves and branches. Previous studies have shown that the pathogenic bacterium, strain NY01 was identifed as Sphingomonas sanguinis by morphological observation and 16S rRNA sequencing analysis. In order to further understand the pathogenic physiological and pathogenic mechanism of the pathogen, the whole genome sequence of the pathogen was analyzed on the PacBio RSII platform.The complete genome of strain NY01 consists of one chromosome (3,280,800 bp) and three plasmids (275,887 bp, 143,601 bp, and 37,326 bp), 59 transfer RNA (tRNA) sequences, and 12 rRNA sequences. The genome was found to comprise 3593 coding genes, of which 3426 were annotated with biological functions across various databases. Comparative genomic analysis found that the NY01 strain clustered closely together with Sphingomonas carotinifaciens DSM 27347 2020 (GCF_009789535.1), exhibiting an average nucleotide identity (ANI) of 97.18%, indicating a strong evolutionary relationship. This finding contrasts with prior 16S rRNA sequencing results, highlighting that 16S rRNA sequence analysis for genus identification of Sphingomonas should be regarded as a preliminary assessment and requires validation through whole genome sequencing. This conclusion serves as a caution for future identifications of Sphingomonas species. This study clarified the taxonomic status of the pathogenic bacteria and explored pathogenic factors, which can serve as a theoretical basis for understanding the occurrence and progression of the disease, as well as for implementing effective prevention and control measures.