Integrated analysis of transcriptome, small RNA, and degradome sequencing provides insights into mango anthracnose resistance

Mango anthracnose is a major biotic stress that limits mango production worldwide. An integrated transcriptome, small RNA (sRNA), and degradome sequencing analysis was conducted to determine the complex molecular mechanisms of mango anthracnose resistance. The transcriptome sequencing of 12 samples from a mango anthracnose resistant genotype under control and stress conditions on the 3rd and 5th day post inoculation identified 3,462 and 8,341 differentially expressed genes (DEGs), respectively, which were mainly involved in transcription factor activity, defense response, an obsolete oxidation - reduction process, and flavonoid biosynthetic processes. The sRNA sequencing of the samples identified 372 known and 104 novel miRNAs. A total of 81 differentially expressed miRNAs were identified, of which three were differentially expressed at both the 3rd and 5th day post-inoculation (dpi), including ath-MIR166e-p5_1ss15AC, mtr-miR156e, and csi-miR3954_L + 1_2ss17CG21CT. According to degradome sequencing, 2,274 targets were predicted for 341 miRNAs. The combined analysis of transcriptome and sRNA sequencing identified 257 miRNA-mRNA interaction pairs. In these pairs, csi-miR3954_L + 1_2ss17CG21CT was up-regulated at both the 3rd and 5th dpi under stress, which could cleave multiple sites of an NAC gene (LOC123212502) that was down-regulated under stress. Overall, these miRNAs and genes provide a molecular foundation for the miRNA-mediated response to mango anthracnose stress and can be regarded as promising candidates for mango improvement.