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Research

The Comai Lab is in the Department of Plant Biology and the UC Davis Genome Center. We study how hybridization, chromosome number and type affect gene regulation, development and genome evolution. Our model systems are Arabidopsis thaliana, rice, poplar and tomato. With collaborators, we are continuing the work of our colleague Simon Chan investigating the role of Centromeric Histone 3 in centromere function. We are developing improved methods for TILLING to efficiently discover mutations in plant genes.

Click on the research links below to find out more.

Polyploidy, Heterosis, Centromeres, Poplar and TILLING

News

Click here for Comai Lab News!

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Wish you could have a good pic of the "weed"? Alex Kozik and the Comai lab are producing public domain pictures of A. thaliana. See the stunning series at this FLICKR site. Free to the world: no IP, no strings, no charge. Download and use them. Special thanks to Brett Pike for plant growth.

Publications

Pubmed report

Recently published or in press

Frag.png In a paper in eLife published in May 2105 Han Tan and colleagues report that when Arabidopsis with weakened centromeres is crossed to the wild type, i.e. a plant with normal centromeres, the resulting embryos undergo chromothripsis, the cut-and-reassembly process leading to highly rearranged chromosomes. Because weakened centromeres can occur naturally, this process may contribute to the evolution of new chromosomes types. Additionally, this process can be manipulated genetically to provide a high frequency of haploids, a genetic type that accelerates plant breeding. Last, this provides an experimentally tractable system to study complex rearrangements associated with human diseases. This is a Simon Chan legacy paper.
Nucl.png Genome elimination mediated by the chimeric "GFP-tailswap" CENH3 is a promising tool for the production of haploids (see the Centromeres page). But, what is the significance of natural variation in CENH3? Shamoni Maheshwari et al. describe in PLoS Genetics (in press) how wide variation in CENH3 is compatible with its essential function, but epigenetically different centromeres do not function well when brought together in a hybrid embryo. This is a Simon Chan legacy paper.
Are.png Parental gene imprinting has been postulated to play a major role in postzygotic incompatibility. What happens to imprinted genes when two different species are mated? Diana Burkart-Waco et al. describe in PLoS One how paternally expressed genes (PEG) are frequently misregulated during interspecific hybridization.
Dlotus1.png Certain plant species, such as spinach, pistachio, papaya, hemp, hop, and persimmon, have a dioecious habit: male and female individuals bear unisexual flowers whose sex is determined by specialized chromosomes, most often X and Y. The genes responsible were unknown, until now. On Halloween 2014, Takashi Akagi, Isabelle Henry, Ryutaro Tao and LC published a paper in Science describing a small RNA-based sex determination mechanism encoded by the Y chromosome of persimmon. Download a reprint of the article and of the supplementary data.
Toolbox.png On Halloween 2014, Ravi et al. published a set of methods in Nature Communications covering multiple uses of the CENH3-based haploid induction system. Download a reprint of this article. This is a Simon Chan legacy paper.
Maps5.png In the April 2014 issue of the Plant Cell, Isabelle Henry and colleagues describe a method to find mutations in the exome of rice and wheat. The method entails sequence capture and analysis through the MAPS pipeline. The work was in collaboration with the lab of Tom Tai and Jorge Dubcosvky
Homoeo pairing.png In the January 2014 issue of the Plant Cell, Isabelle Henry and colleagues describe BOY_NAMED_SUE, a genetic locus required for regular meiosis in the allopolyploid Arabidopsis suecica. Isabelle used Illumina sequencing to identify genomic changes consistent with intragenomic recombination. These changes are only found in synthetic A. suecica.


Video tutorials on analysis of high throughput sequence data and on multiplexing

The Y adapter for Illumina sequencing We offer instructional video tutorials on manipulating and analyzing datasets from next-generation sequencing, as well as on sample multiplexing. The target audience is biologists who might use these techniques but would like to perform some of the analysis themselves.

Funding sources

Our research is funded by the Department of Energy grant 201118510 (Creation of High-Precision Characterization of Novel Poplar Biomass Germplasm) and by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation through Grant GBMF3068 (Chan research). Recent previous support was from National Science Foundation Plant Genome grant DBI-0733857 (Functional Genomics of Polyploids), NSF Plant Genome award DBI-0822383, (TRPGR: Efficient identification of induced mutations in crop species by ultra-high-throughput DNA sequencing), and National Institutes of Health R01 GM076103-01A1 (Dosage dependent regulation in hybridization) to LC.

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