Comparative genomics

Species radiations are a striking feature of evolution and may be responsible for much of life’s diversity. Yet understanding the evolution of species radiations remains a central problem in biology. Advances in genomics, however, are revolutionizing evolutionary biology through the rapid development of novel sequencing approaches and computational tools. We are focusing on the application of these to non-model systems, providing new opportunities to discover the genetic and genomic bases of phenotypic diversity.

This goal is particularly relevant for extending molecular understanding to woody plant species, including many of the world’s most important fruit and nut crops, in which functional manipulation and traditional genetics remain very challenging or impractical. Variability in economically and ecologically important traits across a panel of related woody species that result from a species radiation provides the opportunity to correlate functional variation with genetic changes, and to ask whether similar genes may have been involved when traits have evolved repeatedly within a group.

We are using the apple tribe (Maleae, Rosaceae) as a model system to investigate genome-scale changes associated with 1) rapid diversification and 2) genetic adaptation to whole genome duplication (WGD). The tribe is well-suited for exploration of both of these questions by resequencing approaches. First, quality genome sequences for species of Malus, Pyrus, and Prunus are available to serve as reference points; second, genomes are relatively small (1C=196-765mb); third, the tribe includes the diverse and economically important subtribe Malinae, whose rapid evolutionary radiation was apparently fueled by the evolution of a unique fruit type, the pome; fourth, WGD has been important at two phylogenetic scales, once at the origin of Maleae and later, within several large genera that have evolved multiple ploidy levels. In addition to shedding light on genomic aspects of two phenomena – rapid species radiations and polyploidy – that have played significant roles in plant evolution, we are generating genomic resources for an economically important group of species 

Our current goals in this project are to:

1. Generate and assemble quality genome sequence for species representing a broad range of genera in the apple tribe using several complementary approaches, including synthetic long reads. Characterize genome-level changes associated with rapid diversification, including patterns of duplicate gene fate and evolutionary rate covariation.

2. Characterize genome-level changes following genome doubling in closely related apple species M. ionensis and M. coronaria. Determine whether the patterns of adaptation we see in this long lived woody plant mirror what we have observed in other independent WGD adaptation events.

This project is funded by NSF and being pushed ahead by Jeffrey DaCosta whom I’m advising in collaboration with Sarah Mathews (Australian National University).

Maximum likelihood topology for Rosaceae. Each branch is a genus. A whole genome duplication leading to a base chromosome number of X=17 occurred after the split of Gillenia and Maleae (WGD, black branch). The pome evolved on the branch to Malinae (green branch), after the split first of Kageneckia/Lindleya and then of Vauquelinia from the rest of Maleae. Subsequently, there was a rapid origin of approximately 32 genera (note compressed branches, which are proportional to time). Genera with published genomes are marked by pink branches. Genera for which we aim ultimately to generate genome data are marked by blue branches. Figure by S. Mathews.