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The genes most important to adaptation are often elusive in eukaryotes, including plant pathogenic fungi. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. There was also a strong overrepresentation of transcription factors among positively selected genes. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests.

Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes.

However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. Tests based on the d N /d S statistic are used to identify positive selection of nonsynonymous polymorphisms.

Download Software Yvert Et Tellier 2011 Pdf