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.
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(posted November 2016)
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.
Recently published or in press
|In a paper published in Plos Genetics the Britt Lab (Sundaram Kuppu et al.) and the Comai lab report a simple non-transgenic approach to the production of haploid inducers. Any of multiple changes in the conserved region of centromeric histone H3 is sufficient to yield a haploid inducer phenotype. This illustrates how simple variation at this locus can result in postzygotic incompatibility. This is a Simon Chan legacy paper.|
|In a paper published in the Plant Cell Isabelle Henry and collaborators from the Groover lab report the characterization of a mutant population of poplar produced by crossing Populus deltoides with irradiated pollen of P. nigra. The resulting F1 population of ~500 interspecific hybrids (soon to grow to ~800) provides in average 10 deletions and 3 insertions for every gene. The great phenotypic variation displayed will enable both the study of dosage-dependent regulation and the identification of dosage QTL in many traits.|
|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.|
|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 (2015) 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.|
|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.|
|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.|
|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.|
Video tutorials on analysis of high throughput sequence data and on multiplexing
|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.|
Our research is funded by the Department of Energy grant 201118510 (Creation of High-Precision Characterization of Novel Poplar Biomass Germplasm), by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation through Grant GBMF3068 (Chan legacy research), by a subaward from CSIRO of a Gates foundation grant, by National Science Foundation grants 1457230 (NSF-IOS), 1444612 (NSF-PGRP) and 1354564 (NSF-EAGER), and by industry grants. 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.