From Comaiwiki

(NEW VERSION – all previous content has been broken down and moved to pages linked from this one)
 
(45 intermediate revisions by 2 users not shown)
Line 1: Line 1:
__NOTOC__
+
<!--<div style="margin:auto;"> [[File:MainPageBanner.jpg|800px]] </div>-->
 
+
{|style="margin:auto; text-align:center;"
[[image:logo.png|600px|]]
+
|colspan="4" style="padding:0px;"| [[File:MainPageBanner.jpg|815px]]
 
+
==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|Polyploidy]], [[Heterosis]], [[Centromeres]], [[Poplar]] and [[TILLING]]
+
 
+
==News==
+
 
+
[[LabNews|Click here for Comai Lab News!]]
+
 
+
[[image:alex_seed1.png| align="center"|500px|]]
+
 
+
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 [https://www.flickr.com/photos/102709054@N05/sets/72157645902090243/ 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==
+
 
+
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=PubMed&term=Comai+L%5BAU%5D+(plant+OR+TILLING) Pubmed report]
+
 
+
===Recently published or in press===
+
{| align="center" border="1" cellpadding="5" cellspacing="2"
+
|[[image:nucl.png| align="center"|300px|]]
+
|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.
+
 
|-
 
|-
{| align="center" border="1" cellpadding="5" cellspacing="2"  
+
|style="background:#EA4F20<!--Flame-->; width: 200px; padding-top: 50px; padding-bottom: 50px;"|[[Research|<span style="color:black; font-size:16pt;">Research</span>]]
|[[image:are.png| align="center"|300px|]]
+
|style="background:#EFCA34<!--Saffron-->; width: 200px; padding-top: 50px; padding-bottom: 50px;"|[[People|<span style="color:black; font-size:16pt;">People</span>]]
|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 [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117293 PLoS One] how paternally expressed genes (PEG) are frequently misregulated during interspecific hybridization.
+
|style="background:#AAD129<!--Arabidopsis-->; width: 200px; padding-top: 50px; padding-bottom: 50px;"|[[Data methods|<span style="color:black; font-size:16pt;">Data</span>]]
 +
|style="background:#48917b<!--Wintergreen-->; width: 200px; padding-top: 50px; padding-bottom: 50px;"|[[Contact|<span style="color:black; font-size:16pt;">Contact</span>]]
 
|-
 
|-
{| align="center" border="1" cellpadding="5" cellspacing="2"
+
|style="background:#ED8F33<!--Cadmium-->; width: 200px; padding-top: 50px; padding-bottom: 50px;"|[[Publications|<span style="color:black; font-size:16pt;">Publications</span>]]
|[[image:dlotus1.png| align="center"|300px|]]
+
|style="background:#CBCE21<!--Lemon-->; width: 200px; padding-top: 50px; padding-bottom: 50px;"|[[LabNews|<span style="color:black; font-size:16pt;">News</span>]]
|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 [http://www.sciencemag.org/content/346/6209/646.short paper in Science] describing a small RNA-based sex determination mechanism encoded by the Y chromosome of persimmon. Download a reprint of the [http://comailab.genomecenter.ucdavis.edu/images/b/b2/Akagi-Science.pdf article] and of [http://comailab.genomecenter.ucdavis.edu/index.php/File:Akagi_sup.pdf the supplementary data].
+
|style="background:#70AD34<!--Palm-->; width: 200px; padding-top: 50px; padding-bottom: 50px;"|[[Resources|<span style="color:black; font-size:16pt;">Resources</span>]]
|-
+
|style="background:#1E759E<!--Lapis-->; width: 200px; padding-top: 50px; padding-bottom: 50px;"|[[Job Openings|<span style="color:black; font-size:16pt;">Job Openings</span>]]
{| align="center"  border="1" cellpadding="5" cellspacing="2"
+
|[[image:toolbox.png| align="center"|300px|]]
+
|On Halloween 2014, Ravi et al. published a set of methods in [http://www.nature.com/ncomms/2014/141031/ncomms6334/full/ncomms6334.html Nature Communications] covering multiple uses of the CENH3-based haploid induction system. Download a reprint of  [http://comailab.genomecenter.ucdavis.edu/images/e/ef/Ravi2014.pdf this article].
+
|-
+
{| align="center"  border="1" cellpadding="5" cellspacing="2"
+
|[[image:maps5.png| align="center"|300px|]]
+
|In the [http://www.plantcell.org/content/26/4/1382.long 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
+
|-
+
|[[image:homoeo_pairing.png| align="center"|300px|]]
+
|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.
+
|-
+
|[[image:seed_heatmap.png| align="center"|300px|]]
+
|In a [http://www.plantcell.org/content/25/6/2037.full paper in 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.
+
|}
+
 
+
<!--===TILLING workshops===
+
A [http://tilling.ucdavis.edu/index.php/TILLING_workshop TILLING training workshop] was held Aug 24 and 25 2009, Aug 23 and 24 2010, and August 22 and 23 2011. There is no workshop planned for 2013. We may resume our free workshop program if funding allows. Future workshop might include RESCAN and mutation discovery by exome capture.-->
+
 
+
===Video tutorials on analysis of high throughput sequence data and on multiplexing===
+
 
+
{| align="center"  border="1" cellpadding="5" cellspacing="2"
+
|[[image:barcoded_adapter.png‎|300px|The Y adapter for Illumina sequencing]]
+
|We offer [http://comailab.genomecenter.ucdavis.edu/index.php/Video 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.
 

Latest revision as of 00:59, 1 April 2019

MainPageBanner.jpg
Research People Data Contact
Publications News Resources Job Openings
Personal tools