Genome-wide identification and analysis of subtilisin-like proteases in cassava (Manihot esculenta) reveals developmental and stress-responsive expression patterns

Abstract Subtilisin-like proteases (SBTs) participate in peptide maturation, plant development, and stress signaling. Despite the agronomic importance of cassava, the composition, evolutionary history, organ expression, and drought responsiveness of its SBT family remain unresolved. A genome-wide search based on the Peptidase_S8 profile identified 75 cassava SBT genes. Protein properties, chromosomal distribution, exon-intron structure, phylogenetic relationships, and duplication patterns were examined. Public RNA-seq datasets from 11 organs and drought-treated leaves were subsequently re-analyzed. Eight candidates were further assessed by qRT-PCR in detached leaves after 0, 6, and 12 h of dehydration. The 75 MeSBT genes were distributed across 17 chromosomes and separated into six phylogenetic clades. Twenty genes were intronless, and 27 duplication events comprised 11 tandem, one segmental, and 15 whole-genome duplications. Among the 46 MeSBT genes with detectable transcripts in at least one of the 11 organs and tissues, 23 had FPKM values ≥ 10 in at least one sample. MeSBT21 showed high transcript abundance in seven organs, whereas MeSBT62 and MeSBT75 exceeded 100 FPKM in the petiole, stem, and storage root. Descriptive comparison of drought and control RNA-seq expression estimates assigned 43 genes to the category with at least a twofold increase and 21 to the category with transcript abundance at or below half of the control, while 11 did not meet either magnitude criterion. Detached-leaf qRT-PCR detected concordant response directions for the induced genes MeSBT29 , MeSBT59 , MeSBT21 , and MeSBT62 and the repressed genes MeSBT03 , MeSBT75 , MeSBT65 , and MeSBT36 . This study addresses the cassava-specific knowledge gap in SBT family organization and identifies experimentally supported, drought-responsive candidates. These genes provide defined targets for whole-plant genetic and biochemical studies of cassava adaptation to water deficit.