Fig. 3: Transcriptomic analysis of strain YIM 93972 wild type and non-differentiating mutants.
From: Cellular differentiation into hyphae and spores in halophilic archaea
a Schematic workflow for transcriptomic analysis. We collected cultures representative for aerial hyphae (AH) and substrate hyphae (SH) from wild-type colony, and the morphological mutants. Two transitional (T) and three bald (B) colonies were chosen for the mutants. Each sample included 3 technical repetitions. Total 16 culture plates were randomly pooled for W-SH and W-AH sample, respectively. Total 32 culture plates were randomly pooled for each mutant sample. b Spearman’s correlation coefficients for transcriptomic profiling of 21 samples. The x and y axes represent the log2-transformed gene intensities in each two-sample comparison. c Heat maps of differentially expressed genes. Red indicates upregulated genes; blue, downregulated genes. Statistical differences between two groups were analyzed using two-tailed unpaired t-tests. P < 0.05 was considered statistically significant. d The expression clusters of total differentially expressed genes. All dysregulated genes were clustered into different expression groups according to the fold change based on the gene expression value at the mRNA level in different samples by Mfuzz (v2.58.0)75. e Functional classification of dysregulated genes according to COG functional categories. The COG categories are listed as follows. J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; B: Chromatin structure and dynamics; D: Cell cycle control, cell division, chromosome partitioning; V: Defense mechanisms; T: Signal transduction mechanisms; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; U: Intracellular trafficking, secretion, and vesicular transport; O: Posttranslational modification, protein turnover, chaperones; C: Energy production and conversion; G: Carbohydrate transport and metabolism; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown.
