From Comaiwiki

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===Recently published or in press===
 
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|In a [http://www.plantcell.org/ forthcoming 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
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|In the [http://www.plantcell.org/content/early/2014/01/23/tpc.113.120626.full.pdf+html 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.  
 
|In the [http://www.plantcell.org/content/early/2014/01/23/tpc.113.120626.full.pdf+html 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.  
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|Jennifer Monson-Miller et al. describe the Comai lab method for reduced complexity sequencing, called RESCAN. In collaboration with the Tai lab they demonstrate its use for mutation discovery in rice (BMC Genomics 2012, 13:72 [http://www.biomedcentral.com/1471-2164/13/72/abstract link to journal]). In collaboration with the Maloof and Chan labs the method was used for ultradense mapping of RIL lines made by dihaploid induction [http://www.pnas.org/content/109/11/4227.full?sid=634c4a17-db91-4faf-8039-a39bf008db2b Seymour et al., PNAS].  
 
|Jennifer Monson-Miller et al. describe the Comai lab method for reduced complexity sequencing, called RESCAN. In collaboration with the Tai lab they demonstrate its use for mutation discovery in rice (BMC Genomics 2012, 13:72 [http://www.biomedcentral.com/1471-2164/13/72/abstract link to journal]). In collaboration with the Maloof and Chan labs the method was used for ultradense mapping of RIL lines made by dihaploid induction [http://www.pnas.org/content/109/11/4227.full?sid=634c4a17-db91-4faf-8039-a39bf008db2b Seymour et al., PNAS].  
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|Why do certain plant varieties hybridize more easily with other species than others? Diana Burkart-Waco, Caroline Josefsson, et al. describe the mapping of quantitative trait loci determining the differential response to interspecific hybridization in Arabidopsis thaliana. The work, revealing a network of interacting loci, can be accessed freely in [http://www.plantphysiol.org/content/early/2011/12/01/pp.111.188706.long Plant Physiology].
 
 
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Revision as of 14:13, 15 March 2014


Logo.png

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!

Publications

Pubmed report

Recently published or in press

Maps5.png In a forthcoming 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.
Seed heatmap.png In the June issue of the Plant Cell Diana Burkart-Waco and colleagues examine the early transcriptomic consequences of interspecific crosses between Arabidopsis thaliana and Arabidopsis arenosa, finding that the incompatibility response includes disruption of endosperm development and activation of defense pathways, but, surprisingly, no identifiable role for widespread transposon activation.
Tetraploid tilling.png Helen Tsai and colleagues demonstrate that treating Arabidopsis thaliana Col-0 autotetraploid with EMS results in high density mutations. A 500-individual population allows searches of KOs with an efficiency comparable to that of very large tagging populations. The paper can be accessed freely in Plant Physiology. A copy of CAMBa2.0 can be downloaded here.
Rescan adapters.png Jennifer Monson-Miller et al. describe the Comai lab method for reduced complexity sequencing, called RESCAN. In collaboration with the Tai lab they demonstrate its use for mutation discovery in rice (BMC Genomics 2012, 13:72 link to journal). In collaboration with the Maloof and Chan labs the method was used for ultradense mapping of RIL lines made by dihaploid induction Seymour et al., PNAS.


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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