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Abstract:
Plant ecology in the future will benefit from the efficient use of next-generation sequencing methods. This includes the identification of genes and markers of potential ecological importance. Here we review how next-generation sequencing approaches have been used to genetically characterise the North American tobacco species Nicotiana attenuata. We first describe transcriptome sequencing on the GS FLX Titanium platform. We then explain how we have designed an AGILENT 44k transcriptomic array to study transcriptomic changes elicited by ecologically relevant biotic and abiotic interactions in N. attenuata. Virus-induced gene silencing and stable transformation that have been used to manipulate gene expression in N. attenuata are then reviewed. Overall, we have demonstrated next-generation sequencing to be a valuable tool to identify genetic loci for ecologically relevant traits. Our approaches can be used in non-model organisms to identify candidate genes of ecological relevance, and to confirm their ecological function. Future studies of non-model organisms need to not only characterise gene expression changes under different environments, but manipulate gene expression to falsify hypotheses about the function of genes and their ecological role.
