Genome Sequencing Studies in Rice - Revision history

Xysj1987: /* Projects List */

2016-06-21T01:43:00Z

‎Projects List

Xysj1987: /* Projects List */

2016-06-21T01:42:45Z

‎Projects List

Xysj2012: /* Projects List */

2016-06-20T10:32:33Z

‎Projects List

Xysj2012: /* Projects List */

2016-06-20T10:30:21Z

‎Projects List

Xysj2012: /* Projects List */

2016-06-20T10:29:55Z

‎Projects List

Xysj2012: /* Rice Genome Sequencing */

2016-06-20T10:23:21Z

‎Rice Genome Sequencing

Xysj2012: Created page with "==What is Genome Sequencing ?== '''Figure 1. Crop and plant genomes and their application. ''' * The basis of all biolo..."

2016-06-20T10:12:54Z

Created page with "==What is Genome Sequencing ?== right|thumb|470px|'''Figure 1. Crop and plant genomes and their application. ''' * The basis of all biolo..."

New page

==What is Genome Sequencing ?==
[[File: IC4R-Genome-overview-1.png|right|thumb|470px|'''Figure 1. Crop and plant genomes and their application. ''']]
* The basis of all biological life is the genetic code. Thus, access to the primary DNA sequence, i.e. the genome, and how genes are encoded within the genome, has become a fundamental resource in biology. <ref name="ref1" />Genome sequencing (also known as full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.<ref name="ref2" /> 

* The study of plant biology in the 21st century is, vastly different from that in the 20th century. One driver for this has been the use of Genome Sequencing to reveal the genetic blueprints for not one but dozens of plant species, as well as resolving genome differences in thousands of individuals at the population level. Genomics technology has advanced substantially since publication of the first plant genome sequence, that of Arabidopsis thaliana, in 2000. Plant genomics researchers have readily embraced new algorithms, technologies and approaches to generate genome, transcriptome and epigenome datasets for model and crop species that have permitted deep inferences into plant biology.<ref name="ref1" />
==Rice Genome Sequencing==

* Rice (Oryza sativa) has been cultivated for more than 9000 years and is a major food staple for over 50% of the human population. Using the approach taken by the Arabidopsis Genome Initiative, the genome of rice (Oryza sativa) was finally completely by the International Rice Genome Sequencing Project with a BAC-by-BAC method, yielding the only other plant genome sequence after Arabidopsis that is of 'finished quality' (International Rice Genome Sequencing Project 2005). 
* As the first crop genome sequenced, rice provides an excellent opportunity to illustrate the impact on plant biology and breeding of having access to a finished genome sequence for a species of major socio-economic importance. Using existing genetic and genomic resources and tools (mutants, genetic populations and transformation techniques [52,53]), rice researchers were rapidly able to integrate and apply genome sequence information to understand rice genome structure and evolution as well as to discover and mine genes, including those underlying complex traits of agricultural importance. Members of large gene families [such as transcription factors, peptide transporters, kinases, nucleotide binding leucine-rich repeats (NB-LRRs), microRNAs and germins] have been discovered through genome-wide surveys, enabling their cellular functions to be dissected and their roles in plant growth and development to be elucidated (e.g. 151 members of the rice NAC transcription family). 
* In another example, genome sequence enabled identification and positional cloning of genes responsible for traits selected during domestication, including the seed-shattering trait, led to the identification of molecular changes selected during domestication. This enabled, for the first time, the integration of major effect genes into a single map, thereby providing a foundation for breeders to link these easily recognizable landmarks to QTL studies and improve breeding programs.<ref name="ref3" /><ref name="ref4" /> 
[[File:IC4R-Genome-overview-2.png|center|thumb|1200px|]]

==Crop and plant genomes and their application==
* The Figure 1 gives the approximate timeline of when crop genomes were sequenced along with the underlying techniques and sequencing strategy used. Hybrid strategies which use BAC by BAC and WGS are indicated by the placement of a genome twice. Also note that the distinction between pure NGS and Hybrid sequencing is sometimes arbitrary as many genome projects rely on previously generated Sanger sequences. In addition, some major applications are marked by symbols: Grains for an improvement in grain quality, a flower for flowering time and a tomato for a tomato ripening trait.<ref name="ref4" /> 

==Projects List==

{|class="wikitable sortable" style="width:100%;text-align:center"
|-
!Project Title
!Species
!Published years
!RiceWiki Project ID
|-
|'''A Draft Sequence of the Rice Genome ( ''Oryza sativa'' L. ssp. ''indica'' ) '''
|''Oryza sativa'' L. ssp. ''indica''
|2002
|[[IC4R001-Genome-2002-11935017]]
|-
|'''A Draft Sequence of the Rice Genome (''Oryza sativa'' L. ssp.''japonica'')'''
|''Oryza sativa'' L. ssp. ''Japnoica''
|2002
|[[IC4R002-Genome-2002-11935018]]
|-
|'''The map-based sequence of the rice genome'''
|''Oryza sativa'' L. ssp. ''Japnoica''
|2005
|[[IC4R003-Genome-2005-16100779]]
|-
|'''Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution'''
|''Oryza brachyantha''
|2013
|[[IC4R004-Genome-2013-23481403]]
|-
|'''Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data'''
|''Oryza sativa'' L. ssp. ''Japnoica''
|2013
|[[IC4R005-Genome-2013-24280374]]
|-
|'''The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication'''
|''Oryza glaberrima''
|2014
|[[IC4R006-Genome-2014-25064006]]
|-
|'''Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility'''
|''Oryza longistaminata''
|2015
|[[IC4R007-Genome-2015-26358679]]
|-
|'''Indica rice genome assembly, annotation and mining of blast disease resistance genes'''
|''Oryza sativa'' L. ssp. ''indica''
|2016
|[[IC4R008-Genome-2016-26984283]]
|-
|'''Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice'''
|''Oryza sativa'' L. ssp. ''indica''
|2014
|[[IC4R009-Genome-2014-24578372]]
|}

==References==
<references>
<ref name="ref1">Hamilton, John P., and C. Robin Buell. "Advances in plant genome sequencing." The Plant Journal 70.1 (2012): 177-190.
</ref>
<ref name="ref2">https://en.wikipedia.org/wiki/Whole_genome_sequencing
</ref>
<ref name="ref3">Feuillet, Catherine, et al. "Crop genome sequencing: lessons and rationales." Trends in plant science 16.2 (2011): 77-88.
</ref>
<ref name="ref4">Bolger, Marie E., et al. "Plant genome sequencing—applications for crop improvement." Current opinion in biotechnology 26 (2014): 31-37.
</ref>
</references>

@@ Line 9: / Line 9: @@
 * As the first crop genome sequenced, rice provides an excellent opportunity to illustrate the impact on plant biology and breeding of having access to a finished genome sequence for a species of major socio-economic importance. Using existing genetic and genomic resources and tools (mutants, genetic populations and transformation techniques [52,53]), rice researchers were rapidly able to integrate and apply genome sequence information to understand rice genome structure and evolution as well as to discover and mine genes, including those underlying complex traits of agricultural importance. Members of large gene families [such as transcription factors, peptide transporters, kinases, nucleotide binding leucine-rich repeats (NB-LRRs), microRNAs and germins] have been discovered through genome-wide surveys, enabling their cellular functions to be dissected and their roles in plant growth and development to be elucidated (e.g. 151 members of the rice NAC transcription family). <br><br>
 * In another example, genome sequence enabled identification and positional cloning of genes responsible for traits selected during domestication, including the seed-shattering trait, led to the identification of molecular changes selected during domestication. This enabled, for the first time, the integration of major effect genes into a single map, thereby providing a foundation for breeders to link these easily recognizable landmarks to QTL studies and improve breeding programs.<ref name="ref3" /><ref name="ref4" /> <br><br>
-[[File:IC4R-Genome-overview-2.png|center|thumb|1200px|]]
+[[File:IC4R-Genome-overview-2.png|center|thumb|1000px|]]
 ==Crop and plant genomes and their application==

@@ Line 52: / Line 52: @@
 |2013
 |Rice
-|[[IC4R005-Genome-2013-24280374]]
+|'''[[IC4R005-Genome-2013-24280374]]'''
 |-
 |'''The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication'''

@@ Line 28: / Line 28: @@
 |2002
 |Science
-|[[IC4R001-Genome-2002-11935017]]
+|'''[[IC4R001-Genome-2002-11935017]]'''
 |-
 |'''A Draft Sequence of the Rice Genome (''Oryza sativa'' L. ssp.''japonica'')'''
@@ Line 34: / Line 34: @@
 |2002
 |Science
-|[[IC4R002-Genome-2002-11935018]]
+|'''[[IC4R002-Genome-2002-11935018]]'''
 |-
 |'''The map-based sequence of the rice genome'''
@@ Line 40: / Line 40: @@
 |2005
 |Nature
-|[[IC4R003-Genome-2005-16100779]]
+|'''[[IC4R003-Genome-2005-16100779]]'''
 |-
 |'''Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution'''
@@ Line 46: / Line 46: @@
 |2013
 |Nature Communications
-|[[IC4R004-Genome-2013-23481403]]
+|'''[[IC4R004-Genome-2013-23481403]]'''
 |-
 |'''Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data'''
@@ Line 58: / Line 58: @@
 |2014
 |Nature Genetics
-|[[IC4R006-Genome-2014-25064006]]
+|'''[[IC4R006-Genome-2014-25064006]]'''
 |-
 |'''Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility'''
@@ Line 64: / Line 64: @@
 |2015
 |Molecular Plant
-|[[IC4R007-Genome-2015-26358679]]
+|'''[[IC4R007-Genome-2015-26358679]]'''
 |-
 |'''Indica rice genome assembly, annotation and mining of blast disease resistance genes'''
@@ Line 70: / Line 70: @@
 |2016
 |BMC Genomics
-|[[IC4R008-Genome-2016-26984283]]
+|'''[[IC4R008-Genome-2016-26984283]]'''
 |-
 |'''Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice'''
@@ Line 76: / Line 76: @@
 |2014
 |DNA Research
-|[[IC4R009-Genome-2014-24578372]]
+|'''[[IC4R009-Genome-2014-24578372]]'''
 |}

@@ Line 51: / Line 51: @@
 |''Oryza sativa'' L. ssp. ''Japnoica''
 |2013
+|Rice
 |[[IC4R005-Genome-2013-24280374]]
 |-
@@ Line 57: / Line 57: @@
 |''Oryza glaberrima''
 |2014
 |[[IC4R006-Genome-2014-25064006]]
 |-
@@ Line 62: / Line 63: @@
 |''Oryza longistaminata''
 |2015
 |[[IC4R007-Genome-2015-26358679]]
 |-
@@ Line 67: / Line 69: @@
 |''Oryza sativa'' L. ssp. ''indica''
 |2016
 |[[IC4R008-Genome-2016-26984283]]
 |-
@@ Line 72: / Line 75: @@
 |''Oryza sativa'' L. ssp. ''indica''
 |2014
 |[[IC4R009-Genome-2014-24578372]]
 |}

@@ Line 21: / Line 21: @@
 !Species
 !Published years
 !RiceWiki Project ID
 |-
@@ Line 31: / Line 32: @@
 |''Oryza sativa'' L. ssp. ''Japnoica''
 |2002
 |[[IC4R002-Genome-2002-11935018]]
 |-
@@ Line 36: / Line 38: @@
 |''Oryza sativa'' L. ssp. ''Japnoica''
 |2005
 |[[IC4R003-Genome-2005-16100779]]
 |-
@@ Line 41: / Line 44: @@
 |''Oryza brachyantha''
 |2013
 |[[IC4R004-Genome-2013-23481403]]
 |-
@@ Line 46: / Line 50: @@
 |''Oryza sativa'' L. ssp. ''Japnoica''
 |2013
 |[[IC4R005-Genome-2013-24280374]]
 |-