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(Recently published or in press)
(Video tutorials on analysis of high throughput sequence data and on multiplexing)
 
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==Research==
 
==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.  
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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.
  
Click on the research links below to find out more.
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[[POLYPLOIDY|Polyploidy]], [[Heterosis]], [[Potato]], [[Centromeres]], [[Poplar]], [[Persimmon]] Sex chromosomes, and [[TILLING]]
  
[[POLYPLOIDY|Polyploidy]], [[Heterosis]], [[Centromeres]], [[Poplar]] and [[TILLING]]
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==Job openings==
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We do not have any opening at this time.
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(posted November 2016)
  
 
==News==
 
==News==
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[[LabNews|Click here for Comai Lab News!]]
 
[[LabNews|Click here for Comai Lab News!]]
  
[[image:alex_seed1.png| align="center"|500px|]]
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[[image:alex_seed1.png| align="center"|250px|]]
  
 
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.
 
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.
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===Recently published or in press===
 
===Recently published or in press===
 
{| align="center"  border="1" cellpadding="5" cellspacing="2"  
 
{| align="center"  border="1" cellpadding="5" cellspacing="2"  
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|[[image:shamoni_chip.png| align="center"|100px|]]
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|CENH3 from other species can can complement the cenh3-1 mutant of A. thaliana. The complemented plants look normal until crossed to the wild type, when they become haploid inducers. Maheshwari et al. show that a diverged CENH3 recognizes the same sequences as the endogenous one.  This is surprising and inconsistent with expectations that CENH3 would coevolve with DNA targets. In addition, the authors describe the main active CEN repeat of A. thaliana. [http://genome.cshlp.org/content/early/2016/12/20/gr.214619.116?cited-by=yes&legid=genome;gr.214619.116v1 Article] .
 
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|[[image:leaf.png| align="center"|300px|]]
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|[[image:polyploid_persimmon.png| align="center"|100px|]]
|In a paper soon to be 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.
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|What happens when a dioecious species with X and Y chromosomes becomes polyploid? Cultivated persimmon does just that, managing to turn males into monoecious plants via epigenetic regulation of the sex determination gene MEGI. Epigenetic regulation provides flexibility for a polyploid with sex chromosomes. [http://www.plantcell.org/content/28/12/2905.abstract Article].  
 
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|[[image:frag.png| align="center"|300px|]]
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||[[image:align_cenh3.png| align="center"|100px|]]
|In a [http://elifesciences.org/content/early/2015/05/15/eLife.06516 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.
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|In [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005494 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.
 
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|[[image:nucl.png| align="center"|300px|]]
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|[[image:leaf.png| align="center"|100px|]]
|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.  
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|In [http://www.plantcell.org/content/27/9/2370.full?sid=94ff4db9-637d-41ed-acb6-4d2a6a3e9c10 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.
 
|-
 
|-
{| align="center"  border="1" cellpadding="5" cellspacing="2"
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|[[image:frag.png| align="center"|100px|]]
|[[image:are.png| align="center"|300px|]]
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|In a [http://elifesciences.org/content/early/2015/05/15/eLife.06516 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.
|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.  
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{| align="center"  border="1" cellpadding="5" cellspacing="2"
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|[[image:nucl.png| align="center"|100px|]]
|[[image:dlotus1.png| align="center"|300px|]]
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|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.  
|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].  
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{| align="center"  border="1" cellpadding="5" cellspacing="2"
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|[[image:are.png| align="center"|100px|]]
|[[image:toolbox.png| align="center"|300px|]]
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|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.  
|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]. This is a Simon Chan legacy paper.
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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.-->
 
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===
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===Video tutorials===
  
 
{| align="center"  border="1" cellpadding="5" cellspacing="2"  
 
{| align="center"  border="1" cellpadding="5" cellspacing="2"  
|[[image:barcoded_adapter.png‎|300px|The Y adapter for Illumina sequencing]]
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|[[image:bis_image.png‎|100px|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.
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|Luca Comai teaches Genetics BIS101 at UC Davis. In this flipped course he uses a number of  [https://www.youtube.com/playlist?list=PLxFj8OUe0SBBj3dzyXF-EoH4kK7tQLaLK short videos he made]. Some are prettier than others.
 +
|-
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|[[image:barcoded_adapter.png‎|100px|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. Although dated, these provide an interesting prospective on the evolution of Illumina sequencing.  
 
|}
 
|}
  
 
===Funding sources===
 
===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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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.

Latest revision as of 10:08, 3 April 2017


Logo.png

[edit] 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, Potato, Centromeres, Poplar, Persimmon Sex chromosomes, and TILLING

[edit] Job openings

We do not have any opening at this time.

(posted November 2016)

[edit] News

Click here for Comai Lab News!

Alex seed1.png

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.

[edit] Publications

Pubmed report

[edit] Recently published or in press

Shamoni chip.png CENH3 from other species can can complement the cenh3-1 mutant of A. thaliana. The complemented plants look normal until crossed to the wild type, when they become haploid inducers. Maheshwari et al. show that a diverged CENH3 recognizes the same sequences as the endogenous one. This is surprising and inconsistent with expectations that CENH3 would coevolve with DNA targets. In addition, the authors describe the main active CEN repeat of A. thaliana. Article .
Polyploid persimmon.png What happens when a dioecious species with X and Y chromosomes becomes polyploid? Cultivated persimmon does just that, managing to turn males into monoecious plants via epigenetic regulation of the sex determination gene MEGI. Epigenetic regulation provides flexibility for a polyploid with sex chromosomes. Article.
Align cenh3.png 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.
Leaf.png 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.
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 (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.
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.


[edit] Video tutorials

The Y adapter for Illumina sequencing Luca Comai teaches Genetics BIS101 at UC Davis. In this flipped course he uses a number of short videos he made. Some are prettier than others.
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. Although dated, these provide an interesting prospective on the evolution of Illumina sequencing.

[edit] Funding sources

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.

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