Large-scale phylogenomic roadmapping – sources of diversity in factors of resistance to fungicidal substances

Grzegorz Koczyk 1 Monika Urbaniak 2 Adam Dawidziuk 1 Delfina Popiel 1
1Functional Evolution of Biological Systems Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
2Plant-Microbe Interactions Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland

Broad inquiries into evolution of gene families in multiple, both closely related and divergent taxa resolve naturally into “phylogenomic roadmaps” — annotated resources documenting sources of extant diversity in a way that reconciles species and gene histories explicitly. These, by definition, will not provide a conclusive proof in favor of one or the other evolutionary scenarios. However, a large-scale reconciliation can show how some parts of the family`s history are better explained with or without recourse to horizontal transfer versus duplication, or determine which parts best reflect the common functional traits betrayed by tight genetic linkage into process-related clusters.

In an effort to facilitate the ongoing characterisation of sources of resistance to fungicidal substances in both “higher” and “lower” fungi, we analysed relationships between members of several gene families involved in either efflux (families of ATP-binding casette pumps) or detoxification (hydrolases involved in resorcylic acid lactone breakdown). Owing to a large-scale analysis of genomic neighborhoods of family members, we were able to document how inferred patterns of synteny reflect ties between the biosynthetic process of toxins and the likely capability to detoxify the compounds (lactonases). In an opposite vein, our findings trace both how ABCC family proteins of higher fungi evolved in conjunction with specific biosynthetic activities and how extensively duplicated ABCG family pumps remained coupled to the different primary metabolic or housekeeping activities that they protected in the past. For the first time, our analysis integrates over 20 available genomes of divergent “lower” fungi lineages, showing ancestral groups of diverging transporters in Dikarya, as well as documenting adaptation of transporter repertoire towards different ecological niches.

Research funded under the Polish National Science Centre SONATA/2011/03/D/NZ9/02061 and OPUS/2016/21/B/NZ9/01875 research grants.