Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development

RNA-seq analysis of developmental stages from the filamenous ascomycete Sordaria macrospora. Using laser capture microdissection, we separated protoperithecia (young fruiting bodies) from the surrounding hyphae. RNA isolation and amplification from 150 protoperithecia yields enough material for RNA-seq analysis. The resulting data were compared to RNA-seq data from whole mycelial exctracts (total vegetative and total sexual mycelium) to characterize the genome-wide spatial distribution of gene expression during sexual development. We analyzed total vegetative mycelium, total sexual mycelium, and protoperithecia from the wild type as well as protoperithecia from the sterile mutant pro1. Additionally, we used the RNA-seq information to improve the predicted S. macrospora gene models, and annotated UTRs for more than 50 % of the genes. 8 samples were sequenced (2 independent biological replicates for the four conditions "wt sex: SM2, SM7", "wt veg: SM1, SM6", "wt proto: SM4, SM5", "pro1 proto: SM8, SM9", each on one Illumina/Solexa lane (GAII or HiSeq, single reads of 36 or 100 bases))