IC4R003-Genome-2005-16100779 - Revision history

Guangyi: /* Project Title */

2016-06-26T04:51:27Z

‎Project Title

Guangyi at 07:32, 22 June 2016

2016-06-22T07:32:13Z

Guangyi: /* Plant Culture & Treatment */

2016-06-22T07:14:11Z

‎Plant Culture & Treatment

Guangyi: /* Research Findings */

2016-06-22T06:54:24Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-22T06:47:40Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-22T06:44:38Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-22T06:42:24Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-22T06:38:36Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-22T06:38:07Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-22T06:35:42Z

‎Research Findings

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 ==Project Title==
-'''The map-based sequence of the rice genome'''
+*The map-based sequence of the rice genome
 <br>

@@ Line 5: / Line 5: @@
 ==The Background of This Project==
 *Rice (Oryza sativa L.) is the most important food crop in the world and feeds over half of the global population. As the first step in a systematic and complete functional characterization of the rice genome, the International Rice Genome Sequencing Project(IRGSP) has generated and analysed a highly accurate finished sequence of the rice genome that is anchored to the genetic map.The researchers analysis has revealed several salient features of the rice genome.
+<br>
 ==Plant Culture & Treatment==
 *The IRGSP sequenced the genome of a single inbred cultivar, Oryza sativa ssp. japonica cv. Nipponbare, and adopted a hierarchical cloneby-clone method using bacterial and P1 artificial chromosome clones(BACs and PACs, respectively).
 *The researchers masked the pseudomolecules for repetitive sequences and used the ab initio gene finder FGENESH to identify only non-transposable-element-related genes.
+<br>
 ==Research Findings==
 *Providing evidence for a genome size of 389 Mb. This size estimation is ,260 Mb larger than the fully sequenced dicot plant model Arabidopsis thaliana. The researchers generated 370 Mb of finished sequence, representing 95% coverage of the genome and virtually all of the euchromatic regions.Ninety-seven percent of the BAC/PACs and gap sequences (3,360)have been submitted as finished quality in the PLN division of GenBank/DDBJ/EMBL. These and the remaining draft-sequenced clones were used to construct pseudomolecules representing the 12 chromosomes of rice (Fig. 1).
@@ Line 21: / Line 21: @@
 <br>
 [[File:IC4R003-Genome-2005-16100779-4.png |center |thumb |10000px |''''''Table 3.Transposons in the rice genome'''''']]
+<br>
 ==Labs working on this Project==
 *National Institute of Agrobiological Sciences/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 2-1-2 Kannondai,Tsukuba, Ibaraki 305-8602, Japan.
@@ Line 54: / Line 54: @@
 *Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan.
 *Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.
+<br>
 ==Corresponding Author==
 *'''Takuji Sasaki''' (tsasaki@nias.affrc.go.jp).

@@ Line 7: / Line 7: @@
 ==Plant Culture & Treatment==
 ==Research Findings==
 *Providing evidence for a genome size of 389 Mb. This size estimation is ,260 Mb larger than the fully sequenced dicot plant model Arabidopsis thaliana. The researchers generated 370 Mb of finished sequence, representing 95% coverage of the genome and virtually all of the euchromatic regions.Ninety-seven percent of the BAC/PACs and gap sequences (3,360)have been submitted as finished quality in the PLN division of GenBank/DDBJ/EMBL. These and the remaining draft-sequenced clones were used to construct pseudomolecules representing the 12 chromosomes of rice (Fig. 1).

@@ Line 17: / Line 17: @@
 *A total of 37,544 non-transposable-element-related protein-coding sequences were detected, compared with ,28,000–29,000 in Arabidopsis, with a lower gene density of one gene per 9.9 kb in rice. A total of 2,859 genes seem to be unique to rice and the other cereals, some of which might differentiate monocot and dicot lineages.The rice genome is populated by representatives from all known transposon superfamilies, including elements that cannot be easily classified into either class I or II (ref. 40). Previous estimates of the transposon content in the rice genome range from 10 to 25% (refs 21,40). However, the increased availability of transposon query sequences and the use of profile hidden Markov models allow the identification of more divergent elements41 and indicate that the transposon content of the O. sativa ssp. japonica genome is at least 35% (Table 3).
 <br>
-[[File:IC4R003-Genome-2005-16100779-3.png |center |thumb |10000px |''''''Table 3.Transposons in the rice genome'''''']]
+[[File:IC4R003-Genome-2005-16100779-4.png |center |thumb |10000px |''''''Table 3.Transposons in the rice genome'''''']]
 ==Labs working on this Project==

@@ Line 9: / Line 9: @@
 ==Research Findings==
 *Providing evidence for a genome size of 389 Mb. This size estimation is ,260 Mb larger than the fully sequenced dicot plant model Arabidopsis thaliana. The researchers generated 370 Mb of finished sequence, representing 95% coverage of the genome and virtually all of the euchromatic regions.Ninety-seven percent of the BAC/PACs and gap sequences (3,360)have been submitted as finished quality in the PLN division of GenBank/DDBJ/EMBL. These and the remaining draft-sequenced clones were used to construct pseudomolecules representing the 12 chromosomes of rice (Fig. 1).
 <br>
 [[File:IC4R003-Genome-2005-16100779-1.png |center |thumb |10000px |''''''Figure 1.Maps of the twelve rice chromosomes.''' ''']]
 <br>
 [[File:IC4R003-Genome-2005-16100779-2.png |center |thumb |10000px |''''''Table 2.Size of each chromosome based on sequence data and estimated gaps'''''']]
@@ Line 18: / Line 16: @@
 <br>
 *A total of 37,544 non-transposable-element-related protein-coding sequences were detected, compared with ,28,000–29,000 in Arabidopsis, with a lower gene density of one gene per 9.9 kb in rice. A total of 2,859 genes seem to be unique to rice and the other cereals, some of which might differentiate monocot and dicot lineages.The rice genome is populated by representatives from all known transposon superfamilies, including elements that cannot be easily classified into either class I or II (ref. 40). Previous estimates of the transposon content in the rice genome range from 10 to 25% (refs 21,40). However, the increased availability of transposon query sequences and the use of profile hidden Markov models allow the identification of more divergent elements41 and indicate that the transposon content of the O. sativa ssp. japonica genome is at least 35% (Table 3).
 <br>
 [[File:IC4R003-Genome-2005-16100779-3.png |center |thumb |10000px |''''''Table 3.Transposons in the rice genome'''''']]