Illumina Genome Analyzer IIx sequencing; Cavendish banana roots inoculated with Fusarium oxysporum fsp cubense Race4
Hardened three-month-old tissue-cultured banana plants of cv. Grand Naine (AAA, 2n=33) and the wild banana genotype Pahang (AA, 2n=22) were both inoculated with Fusarium oxysporum f.sp. cubense (Foc) isolates II-5 (tropical race 4, TR4, sampled from Cavendish [AAA] banana in Indonesia, vegetative compatibility group [VCG] 1213) or Foc_R1 (race 1, sampled from cv. Maca [AAB], unknown VCG). Root samples were collected at 72 and 144 hours after inoculation as well as seven days after the inoculation. To obtain the widest transcriptome possible, RNA samples from each interaction were eventually pooled at equal ratio and used for cDNA synthesis.
cDNA libraries were constructed using the SMARTer PCR cDNA Synthesis Kit (Clontech, Saint-Quentin-en-Yvelines, France) according to the manufacturer's instructions, using 1 ug of DNase-treated total RNA. The cDNAs were sonicated to a 150- to 600-bp size range using the S2 Covaris instrument (Covaris, Inc., USA). Single end libraries were prepared using standard Illumina protocols (Illumina DNA sample kit). Each library was sequenced using the 76-base length read chemistry in a single flow cell on the Illumina GA IIx (Illumina, USA).