*4.5. Expression Analyses of the TCP Genes and Search for miR319 Targets*

Expression data for *GhTCP* genes were obtained from transcriptome data. RNA-seq data were obtained from the NCBI Sequence Read Archive (SRA: PRJNA248163). The expression pattern of *GhTCP* genes was analyzed in leaves, roots, and stems of 2-week-old plants; petals, torus, pistils, stamens, and lower sepals dissected from whole mature flowers; ovules from −3, −1, 0, 1, 3, 5, 10, and 20 days after pollination; fibers from 5, 10, 20, and 25 days; and true leaves of seedlings treated with salt, PEG, and heat. Gene expression levels were calculated according to Fragments Per Kilobase Million (FPKM) values and the default empirical abundance threshold of FPKM > 1 was used to identify the expressed gene.

Degradome sequencing data were used to find miR319 that caused TCP transcript degradation (GEO: GSE69820). We matched the degraded fragments to the GhTCP gene sequences, identified the cDNA sequences expressed, and then calculated normalized expression numbers of each degraded site along every cDNA, blast with miR319 sequences. A t-plot figure was constructed to show the tag distributions. PairFinder software was used to identify the sliced targets for miRNAs.
