Scanning electron microscopy (SEM) and transcriptome analyses during fibre development stages in G . hirsutum L. cv. MCU5 wild-type and its near isogenic fuzzless-lintless ( fl ) mutant. (A) SEM images (bar is 10 μM) of epidermal layer of −2 to 2 dpa ovules from the WT and fl mutant. (B) Fibre-bearing ovules of WT and fuzzless-lintless ovule of mutant at 10 dpa. (C) Number of differentially expressed transcripts (DETs) during fibre development stages in the fl mutant as compared to their respective stages in WT and inset represents the percentage of up- and down-regulated transcripts in the fl mutant (D) Venn diagrams showing the commonly up- and down-regulated transcripts among the fibre development stages in the fl mutant. Cluster analysis showing the down-regulation of transcripts related to transcription factors (E) and phytohormones (F) at 0 dpa and up-regulation of about 50% of those transcripts at 15 dpa. DETs with p value ≤ 0.01 and fold change ≥ 3 were included and presented in Additional file1.