CoGepedia - Recent changes [en]

Sequenced plant genomes

Jschnable — Wed, 16 May 2012 19:00:05 GMT

Planned, In-progress, and Private genome sequencing efforts (a partial list):

← Older revision		Revision as of 19:00, 16 May 2012
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	==Planned, In-progress, and Private genome sequencing efforts (a partial list)==		==Planned, In-progress, and Private genome sequencing efforts (a partial list)==
		+	*The genome of the dwarf birch tree ''Betula nana'' is currently being assembled by [http://www.sbcs.qmul.ac.uk/staff/richardbuggs.html Richard Buggs] at the university of London.
	*The sunflower genome project was just announced in early 2010. While it's far too early to predict when this genome will be released, it is still worth mentioning, because species within the sunflower genus (''Helianthus'') have genome sizes around 3000 megabases (sometimes substantially more) making this genome a candidate to steal from maize/corn the position of largest sequenced plant genome. More information [http://www.genomebc.ca/whatnew_press/press_releases/2010_press/documents/n100113_sunflower.pdf here] (warning this is a pdf formatted press release)		*The sunflower genome project was just announced in early 2010. While it's far too early to predict when this genome will be released, it is still worth mentioning, because species within the sunflower genus (''Helianthus'') have genome sizes around 3000 megabases (sometimes substantially more) making this genome a candidate to steal from maize/corn the position of largest sequenced plant genome. More information [http://www.genomebc.ca/whatnew_press/press_releases/2010_press/documents/n100113_sunflower.pdf here] (warning this is a pdf formatted press release)
	*Bayer CropScience [http://www.bayercropscience.com/bcsweb/cropprotection.nsf/id/8AAD8BA3537C1DDBC125764A002DE77C announced] they have a complete genome sequence for canola (''Bassica napus'') as well as varieties of ''Brassica rapa'' and ''Brassica oleracea''. These aren't being released publicly, but from what I've heard they are open to collaborating with individual researchers who want access to the data.		*Bayer CropScience [http://www.bayercropscience.com/bcsweb/cropprotection.nsf/id/8AAD8BA3537C1DDBC125764A002DE77C announced] they have a complete genome sequence for canola (''Bassica napus'') as well as varieties of ''Brassica rapa'' and ''Brassica oleracea''. These aren't being released publicly, but from what I've heard they are open to collaborating with individual researchers who want access to the data.

Angisperm ancestral genome reconstruction

Elyons — Tue, 15 May 2012 11:48:24 GMT

Amborella to vitis:

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	===Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera===		===Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera===
-	[[File:Screen Shot 2012-05-13 at 6.22.08 PM.png\|thumb\|center\|400px\|Major colors correspond to the ancestral pre-hexaploid chromosomes. Color intensity represents the degree of [[fractionation]]. Regions without color either did not have a syntenic signal, or have a conflicting syntenic signal and was thus dropped from the reconstruction~~. Figure complements of Chunfang Zheng~~.]]	+	[[File:Screen Shot 2012-05-13 at 6.22.08 PM.png\|thumb\|center\|400px\|Major colors correspond to the ancestral pre-hexaploid chromosomes. Color intensity represents the degree of [[fractionation]]. Regions without color either did not have a syntenic signal, or have a conflicting syntenic signal and was thus dropped from the reconstruction.]]
-	[[File:Screen Shot 2012-05-13 at 6.25.23 PM.png\|thumb\|center\|400px\|Ancestral pre-hexaploid chromosome mapped to grape genome. Counts refer to number of genes in grape regions. Percentages reflect the relative number of genes in the more highly fractionated genomic region when compared to the least fractionated region. Numbers (1,2,3) refer to the least, medium, and most fractionated genomic region, respectively~~. Data generated by Chunfang Zheng~~.]]	+	[[File:Screen Shot 2012-05-13 at 6.25.23 PM.png\|thumb\|center\|400px\|Ancestral pre-hexaploid chromosome mapped to grape genome. Counts refer to number of genes in grape regions. Percentages reflect the relative number of genes in the more highly fractionated genomic region when compared to the least fractionated region. Numbers (1,2,3) refer to the least, medium, and most fractionated genomic region, respectively.]]

	===Mapping [[Amborella]] contings to eudicot genomes===		===Mapping [[Amborella]] contings to eudicot genomes===
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	====Amborella to vitis====		====Amborella to vitis====
-	[[File:Screen Shot 2012-05-13 at 6.42.41 PM.png\|thumb\|center\|800px\|]]	+	[[File:Screen Shot 2012-05-13 at 6.42.41 PM.png\|thumb\|center\|800px\|Syntenic dotplot may be regenerated at: http://genomevolution.org/r/4sct]]

	===Fractionation anomaly===		===Fractionation anomaly===
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	Of particular interest is the genome of Brassica rapa, which had a hexaploidy event much like the eudicots and shows a consistent genome-wide bias in fractionation:		Of particular interest is the genome of Brassica rapa, which had a hexaploidy event much like the eudicots and shows a consistent genome-wide bias in fractionation:
	* [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html The genome of the mesopolyploid crop species Brassica rapa]		* [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html The genome of the mesopolyploid crop species Brassica rapa]
-	[[File:Screen Shot 2012-05-13 at 6.56.33 PM.png\|thumb\|center\|~~600px~~\|Taken and used without permission from: http://www.nature.com/ng/journal/v43/n10/full/ng.919.html]]	+	[[File:Screen Shot 2012-05-13 at 6.56.33 PM.png\|thumb\|center\|400px\|Taken and used without permission from: http://www.nature.com/ng/journal/v43/n10/full/ng.919.html]]
		+
		+	Interestingly, a different pattern is observed with the pattern of fractionation following the eudicot [[paleohexaploidy]] event. In the two cases detailed above (amborella to peach and ambroella to grape), about have the derived genomic regions show a three-way separation in biased fractionation, and half of the genomic regions show that two the of ancestral regions have about the same degree of fractionation while the third region has the most losses.
		+
		+	[[File:Screen Shot 2012-05-13 at 6.43.05 PM.png\|thumb\|center\|800px\|Showing a case where the classical pattern of [[biased fractionation]] is broken: two ancestral regions of grape derived from the eurosid [[paleohexaploidy]] are equally fractionated while the third region is heavily fractionated]]
		+
		+	'''There have been no previous observationa of such a difference in fractionation rates within a polyploid genome.'''

File:Screen Shot 2012-05-13 at 6.43.05 PM.png

Elyons — Mon, 14 May 2012 02:08:12 GMT

uploaded "[[File:Screen Shot 2012-05-13 at 6.43.05 PM.png]]"

New page

Angisperm ancestral genome reconstruction

Elyons — Mon, 14 May 2012 02:05:31 GMT

Fractionation anomaly:

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	* [http://genome.cshlp.org/content/16/7/934.full Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes]		* [http://genome.cshlp.org/content/16/7/934.full Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes]
	* [http://www.pnas.org/content/108/10/4069.full Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss]		* [http://www.pnas.org/content/108/10/4069.full Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss]
-	* [http://w01.biomedcentral.com/1471-2164/13/S1/S8 A model for biased fractionation after whole genome duplication]]	+	* [http://w01.biomedcentral.com/1471-2164/13/S1/S8 A model for biased fractionation after whole genome duplication]
	Of particular interest is the genome of Brassica rapa, which had a hexaploidy event much like the eudicots and shows a consistent genome-wide bias in fractionation:		Of particular interest is the genome of Brassica rapa, which had a hexaploidy event much like the eudicots and shows a consistent genome-wide bias in fractionation:
	* [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html The genome of the mesopolyploid crop species Brassica rapa]		* [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html The genome of the mesopolyploid crop species Brassica rapa]
	[[File:Screen Shot 2012-05-13 at 6.56.33 PM.png\|thumb\|center\|600px\|Taken and used without permission from: http://www.nature.com/ng/journal/v43/n10/full/ng.919.html]]		[[File:Screen Shot 2012-05-13 at 6.56.33 PM.png\|thumb\|center\|600px\|Taken and used without permission from: http://www.nature.com/ng/journal/v43/n10/full/ng.919.html]]

Biased fractionation

Elyons — Mon, 14 May 2012 02:05:04 GMT

New page

[[File:Screen Shot 2012-05-13 at 7.00.36 PM.png|thumb|800px|right|Biased fractionation between [[syntenic regions]] in the genome of Arabidopsis thaliana derived from its most recent [[whole genome duplication]] event. Results may be regenerated http://genomevolution.org/r/4s9n]]

'''Biased fractionation''': the process of [[fractionation]] of gene content following [[whole genome duplications]] where one homeologous chromosome is targeted for more gene loss events than the partner chromosome(s).

Please see these papers:
* [http://genome.cshlp.org/content/16/7/934.full Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes]
* [http://www.pnas.org/content/108/10/4069.full Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss]
* [http://w01.biomedcentral.com/1471-2164/13/S1/S8 A model for biased fractionation after whole genome duplication]
* [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html The genome of the mesopolyploid crop species Brassica rapa]

File:Screen Shot 2012-05-13 at 7.00.36 PM.png

Elyons — Mon, 14 May 2012 02:01:11 GMT

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-	+	http://genomevolution.org/r/4s9n

File:Screen Shot 2012-05-13 at 7.00.36 PM.png

Elyons — Mon, 14 May 2012 02:00:59 GMT

uploaded "[[File:Screen Shot 2012-05-13 at 7.00.36 PM.png]]"

New page

Syntenic block

Elyons — Mon, 14 May 2012 01:58:45 GMT

Redirected page to Synteny

New page

#redirect: [[synteny]]

Angisperm ancestral genome reconstruction

Elyons — Mon, 14 May 2012 01:58:24 GMT

Results:

← Older revision		Revision as of 01:58, 14 May 2012
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	====Amborella to vitis====		====Amborella to vitis====
	[[File:CompleteAmborellaColoredByVitis.png\|thumb\|center\|800px]]		[[File:CompleteAmborellaColoredByVitis.png\|thumb\|center\|800px]]
		+
		+	===Overlaying ancestral chromosomes and syntenic dotplots===
		+
		+	====Amborella to cacao====
		+	[[File:Screen Shot 2012-05-13 at 6.42.30 PM.png\|thumb\|center\|800px\|Syntenic dotplot may be regenerated: http://genomevolution.org/r/4s8k]]
		+
		+	====Amborella to vitis====
		+	[[File:Screen Shot 2012-05-13 at 6.42.41 PM.png\|thumb\|center\|800px\|]]
		+
		+	===Fractionation anomaly===
		+	[[File:Screen Shot 2012-05-13 at 6.42.59 PM.png\|thumb\|center\|800px]]
		+	The [[syntenic path assembly]] algorithm orders contigs by:
		+	# Determining the chromosome to which maps best based on highest the highest scoring [[syntenic block]]
		+	# Placing them starting with the contig that maps closest to the end of the chromosome (end determined by how the data is stored)
		+	# Orienting them based on whether the syntenic block maps in the positive or negative direction
		+
		+	As such, if there is a strong [[biased fractionation]] effect, then most of the contigs should map to the least fractionated syntenic region. Previous work on duplicated angiosperm genomes have shown that there is a consistent and genome-wide effect of biased fractionation:
		+	* [http://genome.cshlp.org/content/16/7/934.full Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes]
		+	* [http://www.pnas.org/content/108/10/4069.full Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss]
		+	* [http://w01.biomedcentral.com/1471-2164/13/S1/S8 A model for biased fractionation after whole genome duplication]]
		+	Of particular interest is the genome of Brassica rapa, which had a hexaploidy event much like the eudicots and shows a consistent genome-wide bias in fractionation:
		+	* [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html The genome of the mesopolyploid crop species Brassica rapa]
		+	[[File:Screen Shot 2012-05-13 at 6.56.33 PM.png\|thumb\|center\|600px\|Taken and used without permission from: http://www.nature.com/ng/journal/v43/n10/full/ng.919.html]]

File:Screen Shot 2012-05-13 at 6.56.33 PM.png

Elyons — Mon, 14 May 2012 01:57:16 GMT

uploaded "[[File:Screen Shot 2012-05-13 at 6.56.33 PM.png]]" Taken and used without permission from: http://www.nature.com/ng/journal/v43/n10/full/ng.919.html

New page

SynMap's

Elyons — Mon, 14 May 2012 01:39:31 GMT

Redirected page to SynMap

New page

#REDIRECT: [[SynMap]]

Angisperm ancestral genome reconstruction

Elyons — Mon, 14 May 2012 01:39:09 GMT

Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera:

← Older revision		Revision as of 01:39, 14 May 2012
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	===Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera===		===Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera===
-	[[File:Screen Shot 2012-05-13 at 6.22.08 PM.png\|thumb\|center\|400px\|~~Figure complements of Chunfang Zheng.~~ Major colors correspond to the ancestral pre-hexaploid chromosomes. Color intensity represents the degree of [[fractionation]]. Regions without color either did not have a syntenic signal, or have a conflicting syntenic signal and was thus dropped from the reconstruction.]]	+	[[File:Screen Shot 2012-05-13 at 6.22.08 PM.png\|thumb\|center\|400px\|Major colors correspond to the ancestral pre-hexaploid chromosomes. Color intensity represents the degree of [[fractionation]]. Regions without color either did not have a syntenic signal, or have a conflicting syntenic signal and was thus dropped from the reconstruction. Figure complements of Chunfang Zheng.]]
-	[[File:Screen Shot 2012-05-13 at 6.25.23 PM.png\|thumb\|center\|400px\|Ancestral pre-hexaploid chromosome mapped to grape genome. Counts refer to number of genes in grape regions. Percentages reflect the relative number of genes in the more highly fractionated genomic region when compared to the least fractionated region. Numbers (1,2,3) refer to the least, medium, and most fractionated genomic region, respectively.)]]	+	[[File:Screen Shot 2012-05-13 at 6.25.23 PM.png\|thumb\|center\|400px\|Ancestral pre-hexaploid chromosome mapped to grape genome. Counts refer to number of genes in grape regions. Percentages reflect the relative number of genes in the more highly fractionated genomic region when compared to the least fractionated region. Numbers (1,2,3) refer to the least, medium, and most fractionated genomic region, respectively. Data generated by Chunfang Zheng.]]
		+
		+	===Mapping [[Amborella]] contings to eudicot genomes===
		+	# Colored by ancestral pre-hexaploid chromosomes and degree of fractionation
		+	# Ordered by [[SynMap's]] [[syntenic path assembly]] algorithm
		+
		+
		+
		+	====Amborella to peach====
		+	[[File:CompleteAmborellaColoredByPeach.png\|thumb\|center\|800px]]
		+
		+	====Amborella to cacao====
		+	[[File:CompleteAmborellaColoredByCacao.png\|thumb\|center\|800px]]
		+
		+	====Amborella to vitis====
		+	[[File:CompleteAmborellaColoredByVitis.png\|thumb\|center\|800px]]

File:CompleteAmborellaColoredByVitis.png

Elyons — Mon, 14 May 2012 01:38:43 GMT

uploaded "[[File:CompleteAmborellaColoredByVitis.png]]"

New page

Angisperm ancestral genome reconstruction

Elyons — Mon, 14 May 2012 01:30:47 GMT

Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera:

← Older revision		Revision as of 01:30, 14 May 2012
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	===Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera===		===Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera===
-	[[File:Screen Shot 2012-05-13 at 6.22.08 PM.png\|thumb\|center\|~~800px~~\|Figure complements of ]]	+	[[File:Screen Shot 2012-05-13 at 6.22.08 PM.png\|thumb\|center\|400px\|Figure complements of Chunfang Zheng. Major colors correspond to the ancestral pre-hexaploid chromosomes. Color intensity represents the degree of [[fractionation]]. Regions without color either did not have a syntenic signal, or have a conflicting syntenic signal and was thus dropped from the reconstruction.]]
		+	[[File:Screen Shot 2012-05-13 at 6.25.23 PM.png\|thumb\|center\|400px\|Ancestral pre-hexaploid chromosome mapped to grape genome. Counts refer to number of genes in grape regions. Percentages reflect the relative number of genes in the more highly fractionated genomic region when compared to the least fractionated region. Numbers (1,2,3) refer to the least, medium, and most fractionated genomic region, respectively.)]]

File:Screen Shot 2012-05-13 at 6.25.23 PM.png

Elyons — Mon, 14 May 2012 01:25:54 GMT

uploaded "[[File:Screen Shot 2012-05-13 at 6.25.23 PM.png]]"

New page

Angisperm ancestral genome reconstruction

Elyons — Mon, 14 May 2012 01:23:59 GMT

Results:

← Older revision		Revision as of 01:23, 14 May 2012
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	== Results ==		== Results ==
	'''Warning''': The results published here do not constitute a peer-reviewed publication. These results are a combination of work-in-progress, research notes, and various hypotheses. As such, please do not republish them, reference them, or use them as a basis for truth. However, please feel free to contact any of the researchers involved with this project if you have any questions or would like to discuss any ideas. Most of them are friendly.		'''Warning''': The results published here do not constitute a peer-reviewed publication. These results are a combination of work-in-progress, research notes, and various hypotheses. As such, please do not republish them, reference them, or use them as a basis for truth. However, please feel free to contact any of the researchers involved with this project if you have any questions or would like to discuss any ideas. Most of them are friendly.
		+
		+	===Mapping the seven hypothesized ancestral chromosomes of the pre-hexaploid onto the genome of Vitis vinifera===
		+	[[File:Screen Shot 2012-05-13 at 6.22.08 PM.png\|thumb\|center\|800px\|Figure complements of ]]

File:Screen Shot 2012-05-13 at 6.22.08 PM.png

Elyons — Mon, 14 May 2012 01:22:40 GMT

uploaded "[[File:Screen Shot 2012-05-13 at 6.22.08 PM.png]]" Mapping of ancestral regions the chromosomes of Vitis.

New page

Angisperm ancestral genome reconstruction

Elyons — Mon, 14 May 2012 01:21:34 GMT

Results:

← Older revision		Revision as of 01:21, 14 May 2012
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	== Overview ==		== Overview ==

-	Zheng and Sankoff have developed and continue to refine a mathematical framework for reconstructing ancestral genome states of various angiosperm lineages using [[syntenic blocks]] identified by [[SynMap]], an interactive tool for the pairwise comparison of whole genomes development by Tang and Lyons. This problem is complicated by [[whole genome duplications]], a common occurrence in angiosperm lineages.	+	Zheng and Sankoff have developed and continue to refine a mathematical framework for reconstructing ancestral genome states of various angiosperm lineages using [[syntenic blocks]] identified by [[SynMap]], an interactive tool for the pairwise comparison of whole genomes development by Tang and Lyons. This problem is complicated by [[whole genome duplications]], a common occurrence in angiosperm lineages, followed by [[fractionation]] of duplicated gene content.

-	Of particular interest are:	+	Of particular interest are the ancestral genomes of:
-	# the ancestral ~~genome~~ of ~~the eudicots~~ which have undergone a [[paleohexaploidy]]	+	# Eudicots which have undergone a [[paleohexaploidy]]
-	#	+	## [http://www.springerlink.com/content/71656277268rx541/ OMG! Orthologs in Multiple Genomes – Competing Graph-Theoretical Formulations]]
		+	## [http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6182649&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6182649 Ancient angiosperm hexaploidy meets ancestral eudicot gene order]
		+	# Monocots
		+	## Not possible to solve with the current taxonomic sampling of monocot genomes (currently, only grass genomes are available and of sufficient quality)
		+	## Anticipated high-quality genomes that may help:
		+	### Banana: http://www.musagenomics.org/
		+	### Duckweed: http://lemna.rutgers.edu/
		+	# Angiosperms
		+	## Of current research interest by this team
		+
		+	== Results ==
		+	'''Warning''': The results published here do not constitute a peer-reviewed publication. These results are a combination of work-in-progress, research notes, and various hypotheses. As such, please do not republish them, reference them, or use them as a basis for truth. However, please feel free to contact any of the researchers involved with this project if you have any questions or would like to discuss any ideas. Most of them are friendly.

Syntenic blocks

Elyons — Mon, 14 May 2012 01:08:27 GMT

Redirected page to Synteny

New page

#REDIRECT: [[synteny]]

Synteny

Elyons — Mon, 14 May 2012 01:08:05 GMT

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	[[Image:Gevo-synteny.png\|thumb\|600px\|right\|Syntenic comparison of two regions from the genome of Arabidopsis thaliana using [[GEvo]]. This genome underwent a whole genome duplication event which created a copy of every genomic region. Over evolutionary time, many of the duplicated genes were lost by a process known as [[fractionation]]. However, many duplicated genes have been retained in duplicate and their collinear arrangement in the genome is evidence for synteny. Results can be regenerated at: http://tinyurl.com/noul6b]]		[[Image:Gevo-synteny.png\|thumb\|600px\|right\|Syntenic comparison of two regions from the genome of Arabidopsis thaliana using [[GEvo]]. This genome underwent a whole genome duplication event which created a copy of every genomic region. Over evolutionary time, many of the duplicated genes were lost by a process known as [[fractionation]]. However, many duplicated genes have been retained in duplicate and their collinear arrangement in the genome is evidence for synteny. Results can be regenerated at: http://tinyurl.com/noul6b]]

-	Synteny is a valid deduction that two or more genomic regions are derived from a single ancestral genomic region. Syntenic region can be from different organisms and are derived from speciation, or from the same genome and are derived from genome duplication events (such as [[polyploidy]]). ~~Synteny~~ is ~~detected~~ through evidence based on collinearity of genomic content such as genes. If two regions have obvious collinear features, they are syntenous. However, many noncollinear regions may be logically rearranged (e.g. through inversions) into a common ancestor, and thus be syntenous.	+	'''Synteny''' is a valid deduction that two or more genomic regions are derived from a single ancestral genomic region. Syntenic region can be from different organisms and are derived from speciation, or from the same genome and are derived from genome duplication events (such as [[polyploidy]]). One method for inferring synteny is through evidence based on collinearity of genomic content such as genes. If two regions have obvious collinear [[genomic features]], they are syntenous. However, many noncollinear regions may be logically rearranged (e.g. through inversions) into a common ancestor, and thus be syntenous.
		+
		+	'''Syntenic block''': This term refers to a set of syntenic genomic regions and is usually comprised of syntenic gene sets. Syntenic blocks are of interest to researchers as a unit of evolutionary history that may be used for additional studies such as:
		+	# genome evolution
		+	# ancestral genome reconstruction
		+	# gene family evolution
		+	# origin of gene family duplicates

Whole genome duplications

Elyons — Mon, 14 May 2012 01:04:11 GMT

Redirected page to Whole genome duplication

New page

#REDIRECT: [[whole genome duplication]]

Angisperm ancestral genome reconstruction

Elyons — Mon, 14 May 2012 01:03:42 GMT

Created page with 'Collaboration of: * Chunfang Zheng * David Sankoff * Haibao Tang * Eric Lyons == Overview == Zheng and Sankoff have developed and continue to refine a mathematical framework fo...'

New page

Collaboration of:
* Chunfang Zheng
* David Sankoff
* Haibao Tang
* Eric Lyons

== Overview ==

Zheng and Sankoff have developed and continue to refine a mathematical framework for reconstructing ancestral genome states of various angiosperm lineages using [[syntenic blocks]] identified by [[SynMap]], an interactive tool for the pairwise comparison of whole genomes development by Tang and Lyons. This problem is complicated by [[whole genome duplications]], a common occurrence in angiosperm lineages.

Of particular interest are:
# the ancestral genome of the eudicots which have undergone a [[paleohexaploidy]]
#