Additional file 1 of Heat-responsive microRNAs participate in regulating the pollen fertility stability of CMS-D2 restorer line under high-temperature stress

Additional file 1: Fig. S1. Evaluation of small RNA sequencing (sRNA-Seq) data quality. (a) Pearson correlation analysis between samples in the sequencing libraries. (b) Three-dimensional principle component analysis (PCA) factorial map showing the largest components of variance. PCA analysis was performed using the “vegan” package of R software based on normalized read counts of all miRNAs obtained from sRNA-Seq. Fig. S2. Classification statistics of repetitive sequences in total and unique data of 12 sRNA-seq libraries. Fig. S3. Rfam sequence category in total and unique data of 12 sRNA-seq libraries. Fig. S4. Statistics of different types of miRNAs identified in each sample and their base preference analysis. (A, B) Number of pre-miRNAs (A) and unique miRNAs (B) in different categories in each sample. (C, D) The first base preference of mature miRNAs in ‘gp1_3’ (C) and ‘gp4’ (D) categories. (E, F) Base preference in different positions of mature miRNAs in ‘gp1_3’ (E) and ‘gp4’ (F) categories. Fig. S5. Analysis of miRNA family and conservation. (A) Family analysis of identified miRNAs. (B) Statistics on the frequency of the identified miRNAs in other species. Fig. S6. Number of all expressed miRNAs and DEMs on different chromosomes of upland cotton. The X-axis represents different chromosomes; the Y-axis and the numbers above each bar represent the miRNA numbers on each chromosome. Fig. S7. GO functional classification of all DEGs. The X-axis indicates the GO categories, and the Y-axis indicates the number of DEGs. Fig. S8. T-plots of miRNAs in categories 1–4 verified by degradome sequencing. (A) T-plot showing that gra-miR157a cleaves the Ghir_A05G033800.1 transcript at the 101st nucleotide position. (B) T-plot showing that PC-5p-4140_1526 cleaves the Ghir_D01G002960.1 transcript at the 707th nucleotide position. (C) T-plot showing that gra-MIR477-p5_2ss19CT20AG cleaves the MSTRG.26509.1 transcript at the 178th nucleotide position. (D) T-plot showing that ghr-miR7505 cleaves the Ghir_D05G035640.1 transcript at the 770th nucleotide position.