Genomics Research
Origins of diversity in Carex (Cyperaceae) and the evolution of plant genomes with holocentric chromosomes.
Karyotypic evolution is a prominent feature in the diversification of many plants and animals yet the role that chromosomal changes play in the process of diversification is still debated. At the diploid level, chromosome fusion and/or fission are necessary components of chromosomal structural change associated with diversification. Yet the genomic features required for these events remain unknown. This project is exploring the nature of genomic structural change at the diploid level in the genus Carex, a group where chromosome fusion/fission events are common and associated with diversification of many of its 2000 species. A hypothesized mechanism of chromosome number change in this genus is agmatoploidy, changes in chromosome number without change in DNA amount through fission/fusion of holocentric chromosomes (chromosomes without localized centromeres). This collaborative project with Dr. Andrew McCubbin (Washington State University) and Dr. Richard Whitkus (Sonoma State University) is focusing on chromosomal innovations in Carex sections Lupulinae and Vesicariae, a well-defined group of approximately 50 species with chromosome number variation from n = 24 to 40. A bacterial artificial chromosome (BAC) library and expressed sequence tagged (EST) library are in the process of being generated, characterized, and used in physical and genetic linkage mapping studies to reveal the patterns of genome structural variation associated with agmatoploidy in Carex, and to explore the sequence and genic characteristics of chromosomal break points in the genome. Bioinformatics is an integral part of this project and as such BAC and EST library information are in the process of being databased and made available on the web to the wider scientific community.
Our specific goals for these studies are to:
* Explore the pattern of genome structural evolution in the Cyperales, a group of plants with holocentric (without defined centromere) chromosomes.
* Define the DNA sequence characteristics of chromosomal breakage points in the genome.
* Explore whether genetic changes are associated with genome structural evolution.
* Train undergraduate science majors and graduate students in modern genomics research applied to systematic and evolutionary questions; increase opportunities for research projects of graduate students; provide graduate students and post-doctoral investigator opportunity to train undergraduate students in genomic research activities; and provide opportunities and funds for students to present results at professional meetings.