Plant Science

Phylogenetic analysis of disease resistance genes in the potato genome

Plants have a sophisticated defence system to protect against attacks by pathogens including bacteria, viruses, nematodes, insects, filamentous fungi and oocytes. The publication in 2011 of the first potato genome sequence by an international consortium, including scientists based at the James Hutton Institute, provided the opportunity to identify and classify all the R (resistance) genes belonging to the main type, NB-LRR, which contain a nucleotide-binding domain (NB-ARC) and a leucine-rich repeat (LRR). Working in collaboration with genomics scientists and bioinformaticians at the James Hutton Institute, BioSS produced a multiple alignment of these 438 NB-LRR genes using a hidden Markov model approach, and modelled their evolution from a single ancestral R gene, allowing for variation in the amino acid substitution rates along the sequences. The estimated phylogenetic tree shows the evolutionary history of duplication events and sequence divergence that has resulted in groups of highly similar genes with different functions. The model of protein evolution used in the Maximum Likelihood tree estimation was optimized using the model selection protocol in the TOPALi package, developed by BioSS, which allows joint estimation of the tree and the evolutionary model. The locations, i.e. the physical map positions, were established for 370 of the predicted NB-LRR genes across the 12 potato chromosomes and the genes were found to be clustered spatially into 63 groups. The NB-LRR group functions can now be studied by plant pathologists to better understand their roles in plant defence.

phylogeny tree detail Detail from the full phylogenetic tree which portrays the estimated relationships between the NB-LRR genes, using colour to indicate groups of particular interest.

Further details from: Frank Wright and Katrin MacKenzie

Article date 2013

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