we have tested different amounts of starting material as well as different tissue disruption methods, TissueLyser II from QIAGEN® or mortar and pestle (data not shown). In our hands, the best amount of starting material for a good quality RNA and DNA, accomplishing the requirements for RNA sequencing (RNAseq) and Whole Genome Bisulphite Sequencing analysis (WGBS), was 300 galls and 1000 RCs per biological replicate at 3 dpi and 250 galls and 500 RCs at 14 dpi. The best extraction method was using a mortar and a pestle as shown in Portillo et al. (2006).

issue disruption is performed in a mortar and pestle with a buffer containing 2-mercaptoethanol and homogenized using a QIAshredder® spin column (QIAGEN®). After the homogenization procedure, the lysate is transferred to an AllPrep® DNA Mini spin column (QIAGEN®) and centrifuged.