College of Biological Sciences
This group has recently assembled 188 nitrogen-fixing rhizobial genomes de novo from Illumina reads and 12 from Pacific Biosciences sequencing technology to better understand the genomic variation and structural variation within the species of Ensifer meliloti and E. medicae and related genomes. Two publications during 2018 used this dataset. One describes structural variation among the PacBio-sequenced strains and the other presents an association mapping study (GWAS) that explored the genetic architecture of bacterial traits and identified genes underlying variation in interaction with the host plant. Ongoing work describes variation in repeat diversity in these genomes and develops neural networks to improve genome assemblies. The researchers have also used the sequencing data for several select-and-resequence evolution experiments, the first paper of which was published during 2018.
The group is extending their select and resequence method to a root parasite, Aphanomyces, for which they anticipate sequencing 3 - 8 genomes, as well as pooled DNA sequencing from several experiments. They have recently received sequencing data from ~ 350 more E. meliloti and E. medicae strains. They are collaborating with other labs to assemble genomes and conduct analyses to understand population structure at both global and local population levels, to identify genomic variation involved in local adaptation, and to conduct additional select & resequence experiments.
Finally, the researchers have three RNA-seq projects:
- An analysis of both host and symbiont expression patterns from an Ensifer / Medicago experiment.
- An investigation of the genomic basis of local adaptation in common ragweed (Ambrosia artemisiifolia) using population genomic approaches. This project is using a combination of environmental association analyses and transcriptome-wide association analysis.
- Using cacao transcriptomes to advance basic cacao biology and breeding resources.
This group's research was featured on the MSI website in July 2019: Evaluating Species Distribution Models.