Towards a Better Genome Annotation of Different Musa Cultivars Using mRNA Seq and Proteomics Data: The Search for Allelic Variants Related to Drought

After assembling the genomic reads, the next step is the structural and functional annotation of genes. Even with the current annotation tools many structural annotations in Musa contain errors. Our group is engaged to correct annotations of gene families potentially involved in response to drought. We use RNA-Seq and proteomics data to confirm or correct the actual gene structure. Based on mRNAseq, we have revised the structural annotation of 53 drought related gene families containing 384 different revised members. Circumstantial evidence suggests that the Musa balbisiana (B) genome confers greater drought tolerance than the Musa acuminata (A) genome. Hence the genetic constitution may affect the stress response. We used proteomics to detect B specific allelic variants that are correlated to drought. From gel-electrophoresis we already published drought related B specific proteins in an ABB Bluggoe variety (Henry et.al.2011, Carpentier et.al.2011, Delanghe et.al.2010). Though they can only be distinguished if they differ in a manner that affects gel migration. Using a LCMSMS approach peptides can be distinguished if they differ in mass. This gives a much higher resolution and throughput. Using this approach, we were able to detected 7281 peptides correlated to the B allele whereof 337 could be correlated to a higher abundance after stress. We conclude that both methods are complementary, that mRNAseq is extremely useful to correct the structural annotation due to higher gene coverage and that proteomics is more powerful for a better functional annotation due to the higher correlation to the phenotype.