Complex cellular differentiation in a haloarchaeon

Purpose: The goals of this study are to describe the morphological diversity of a novel archaea. Methods: The aerial and substrate hyphae of wild strain, and the substrate hyphae of mutated strains were generated by deep sequencing, in triplicate, using Illumina HiSeq2000 system. Results: Using an optimized data analysis workflow, we mapped about 1.7-4.4 million sequence reads per sample to wild and mutated hyphae samples by Bowti2 and RSeQC. Approximately half of the transcripts showed differential expression between the aerial and substrate hyphae, with a fold change ≥2.0 and p adjust <0.05. Conclusions: Our study represents the first detailed analysis of wild and mutated hyphae transcriptomes, with biologic replicates, generated by RNA-seq technology. For wild aerial and substrate hyphae, 10^7 viable spores of YIM 93972 were spread on a layer of 0.20 μm BioTrace NT Nitrocellulose Transfer Membrane (Pall China, Beijing, China) covered on an ISP 4 medium containing 25% NaCl and 2% agar in 85 mm diameter Petri dish. The plates were cultured at 37 °C for 14 days. Totally, 96 culture plates were prepared, which were split into 6 groups as biological replicates. The aerial hyphae grown on nitrocellulose membrane, and the substrate hyphae below nitrocellulose membrane were recovered by scraping with a plain spatula, respectively. For two transitional and three bald mutants, the equal amounts of broken hyphae were spread on the same plates as described above. Totally 192 culture plates were prepared for each mutant strain, which were split into 6 groups as biological replicates. The substrate hyphae were recovered at 21 days. Totally, 6 pooled hyphae were collected for each strain, half of them were used for transcriptomic analysis.