Since the beginning of my PhD, my research projects have been focused on using RNA-Seq data to improve existing gene annotations for model organisms or create a solid first annotation draft for non-model species.
During my doctoral studies, I investigated the transcriptome of two plant species - M. truncatula and V. vinifera in search of unannotated genes and splicing variants. I dedicated particular attention to reconstruct and characterize in silico genes missing from the available reference genome due to assembly errors or natural variation between cultivars. In grape, this approach has led to the identification of hundreds of genes expressed during the maturation of the berry providing new possible avenues for identifying the genetic factors underlying the different features of grape berries in different varieties. My interests subsequently shifted towards annotating newly assembled plant genomes, such as that of the aubergine.
At the Earlham Institute, my responsibilities include the annotation of the multiple genome assemblies of Triticum species and varieties. While at this position, I started creating bioinformatics tools to generate a reliable RNA-Seq draft annotation from multiple sources and methods; this has led to the creation of the Mikado suite for evidence-based annotations.
Venturini L, Ferrarini A, et al. (2012), BMC Genomics 14 (1), DOI: 10.1186/1471-2164-14-41
The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome.
Da Silva C, Zamperin G, et al. (2013), The Plant Cell, doi: 10.1105/tpc.113.118810