Abstract Detail

Comparative Genomics/Transcriptomics

Thomas, Shawn [1], Pires, Joseph [2].

Generating a target-enrichment bait set to explore polyploid and reticulate evolution in the tribe Brassiceae.

The tribe Brassiceae (~50 genera, ~250 species) is a monophyletic lineage within the Brassicaceae (Mustard) family. Evidence from previous studies show that the tribe shares an ancient hexaploidy and diverged from the rest of the Brassicaceae around 24mya. Furthermore, the tribe is rife with extensive hybridization and numerous polyploids leading to hypotheses of ancient reticulate evolution. NGS sequencing approaches such as targeted enrichment allows researchers to tackle these large-scale genome-level questions. Targeted enrichment specifically allows for the generation of hundreds to thousands of nuclear loci that can be generated relatively easily and applied at a phylogenetic scale. As part of my dissertation, I plan to develop a targeted enrichment bait set to explore reticulate evolution and polyploid evolution in the tribe Brassiceae. The major limitation of targeted enrichment tends to be the need for prior genomic resources. Fortunately, in the core group of the tribe Brassiceae there are a large number of economically important crop species (broccoli, cabbage, kale, canola, etc.) with substantial existing data. Thus, we will focus on generating data for early diverging lineages of the Brassiceae where data is sparser. Using genomes and transcriptomes within the tribe, we will identify single, duplicated and triplicated genes in the dataset. Then we plan to use a k- medoids clustering approach to identify the appropriate number of sequences to represent each locus. This targeted enrichment bait set will serve as the foundation for my dissertation research. With it I can generate the necessary data to explore patterns of duplicate gene retention and rigorously testing hypotheses of ancient reticulate evolution in the tribe.

1 - University Of Missouri, Division Of Biological Sciences, 1201 Rollins Street, 311 Bond Life Sciences Center, Columbia, MO, 65211, United States
2 - University Of Missouri, 371 Bond Life Sciences Center, 1201 Rollins Street, Columbia, MO, 65211, United States

Keywords:
Target Enrichment
polyploidy
genomics
Brassicaceae.

Presentation Type: Poster
Session: P, Comparative Genomics and Transcriptomics Posters
Location: Virtual/Virtual
Date: Monday, July 27th, 2020
Time: 5:00 PM Time and date to be determined
Number: PGT003
Abstract ID:600
Candidate for Awards:Genetics Section Poster Award