IC4R002-Genome-2002-11935018 - Revision history

Guangyi at 14:46, 30 June 2016

2016-06-30T14:46:32Z

Guangyi: /* Plant Culture & Treatment */

2016-06-30T14:43:34Z

‎Plant Culture & Treatment

Guangyi: /* Plant Culture & Treatment */

2016-06-30T14:33:29Z

‎Plant Culture & Treatment

Guangyi: /* Research Findings */

2016-06-30T13:53:28Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-30T13:40:26Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-30T13:37:47Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-30T13:24:15Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-30T13:17:36Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-30T13:15:00Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-30T13:04:55Z

‎Research Findings

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 *Contigs of nonrice origin were identified by sequence homology to known bacteria, high GC content, lack of homology to rice BAC end sequences, and/or depth of coverage. Sequence analysis identified 6 Mbp as originating from two related bacterial species(Xanthomonadales), likely representing endophytes present in the plant material used for DNA isolation.
 *Syd(Syngenta draft sequence;data access information is available at www.tmri.org) data were compared to almost 1 million bases of IRGSP’s completed rice genome sequence to determine coverage and quality.
+*Timelogic’s Decypher FrameSearch algorithm was used to detect and guide the correction of frameshifts caused by indels. For each predicted gene,the fraction of the length with homology to known genes, predicted genes from other species, Prosite motifs (25), or Pfam domains (26) was used as a confidence score.
 ==Research Findings==
 *Translated HMLgenes300 were classified with the software package INTERPRO (27,28). INTERPRO output was filtered to create sets of the longest protein domain for each associated protein, and domains were categorized using Gene Ontology (GO) software(29). The results of these classifications are shown in Fig. 1; about 44% of Hgenes, 32% of Mgenes, and 5% of Lgenes were classified, respectively. Most of the classified proteins fall into the categories of metabolism and cell communication/signal transduction.

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 ==Plant Culture & Treatment==
 *Contigs of nonrice origin were identified by sequence homology to known bacteria, high GC content, lack of homology to rice BAC end sequences, and/or depth of coverage. Sequence analysis identified 6 Mbp as originating from two related bacterial species(Xanthomonadales), likely representing endophytes present in the plant material used for DNA isolation.
 ==Research Findings==

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 ==Plant Culture & Treatment==
 ==Research Findings==

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 expression of the meristem identity genes to floral meristems, where they promote the patterned expression of floral organ identity genes AP2, AP3, PI, and AG, which are also affected by the regulatory genes ANT, UFO, and SUP (102, 103).''']]
 <br>
-*ctional differences within similar genes.The level of synteny among cereals was determined by comparing anchored rice genomic sequence to mapped sequence from other cereals. Related regions of the rice and maize genomes were aligned (Fig. 4).
+*The level of synteny among cereals was determined by comparing anchored rice genomic sequence to mapped sequence from other cereals. Related regions of the rice and maize genomes were aligned (Fig. 4).
 [[File:IC4R002-Genome-2002-11935018-f4.png |center |thumb |10000px |'''Fig. 4. Rice-maize synteny. Maize markers were mapped to the rice genome in silico. Maize map and sequence information were derived from MaizeDB (610 markers) and GenBank, respectively. Maize chromosomes are indicated along the vertical black lines; positions of specific markers and bins are defined by horizontal lines. Rice chromosomes are represented by numbered, colored rectangles. Significant homology (at least 80% identity, over 100 continuous base pairs, between a maize chromosomal region and a particular rice region) is indicated by a colored rectangle to the right of the maize chromosome. For a more detailed version of this map, see Web site link 24.''']]
 ==Labs working on this Project==

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 expression of the meristem identity genes to floral meristems, where they promote the patterned expression of floral organ identity genes AP2, AP3, PI, and AG, which are also affected by the regulatory genes ANT, UFO, and SUP (102, 103).''']]
 <br>
 [[File:IC4R002-Genome-2002-11935018-f4.png |center |thumb |10000px |'''Fig. 4. Rice-maize synteny. Maize markers were mapped to the rice genome in silico. Maize map and sequence information were derived from MaizeDB (610 markers) and GenBank, respectively. Maize chromosomes are indicated along the vertical black lines; positions of specific markers and bins are defined by horizontal lines. Rice chromosomes are represented by numbered, colored rectangles. Significant homology (at least 80% identity, over 100 continuous base pairs, between a maize chromosomal region and a particular rice region) is indicated by a colored rectangle to the right of the maize chromosome. For a more detailed version of this map, see Web site link 24.''']]

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 HMLgenes300 translations.The expectation values range from E , 2180(high homology) to E . 26 (low homology) and are depicted in intervals spanning 10 exponents(e.g., , 2180, 2180 to 2171, 2170 to 2161, etc.)''']]
 <br>
-*Flowering in Arabidopsis is initiated by flowering-time genes that activate floral meristem identity genes, leading to the patterned expression of floral organ identity genes (Fig. 3). Rice contains single-copy homologs of the Arabidopsis flowering-time
+*Flowering in Arabidopsis is initiated by flowering-time genes that activate floral meristem identity genes, leading to the patterned expression of floral organ identity genes (Fig. 3). Rice contains single-copy homologs of the Arabidopsis flowering-time genes GI, CO, LD, and FCA.
 <br>
 [[File:IC4R002-Genome-2002-11935018-f3.png |center |thumb |10000px |'''Fig. 3. Flowering-time and flower development genes in the rice genome. A simplified model shows the predicted genetic network regulating flowering time and flower development in Arabidopsis, with gene names color-coded to indicate clearidentification of an ortholog in the rice genome (red) or no clear identification(white). In Arabidopsis there are three genetic pathways that control flowering time (100, 101). The long-day pathway
 represented by GI and CO and the autonomous pathway represented by LD, FCA, and FLC are likely integrated through FT and AGL20 to promote activation of meristem identity genes LFY, AP1, and CAL.The vernalization pathway, represented by FRI, feeds into the autonomous pathway upstream of FLC. The GA pathway,represented by GA1, leads to the activation of LFY. TFL serves to restrict the
 expression of the meristem identity genes to floral meristems, where they promote the patterned expression of floral organ identity genes AP2, AP3, PI, and AG, which are also affected by the regulatory genes ANT, UFO, and SUP (102, 103).''']]
 ==Labs working on this Project==

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 [[File:IC4R002-Genome-2002-11935018-f1.png |center |thumb |10000px |'''Fig. 1. Rice gene prediction classifications. HMLgenes300 were classified with Interpro and GO software (27–29); the categories generated are shown.''']]
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-*Eighty-five percent of Arabidopsis predicted proteins (21,590 of 25,554) were significantly homologous to HMLgenes300
+*Eighty-five percent of Arabidopsis predicted proteins (21,590 of 25,554) were significantly homologous to HMLgenes300 predicted proteins; of these, 2565 show very strong conservation between Arabidopsis and rice (Fig. 2).
 <br>
 [[File:IC4R002-Genome-2002-11935018-f2.png |center |thumb |10000px |'''Fig. 2. Similarity of 25,554 Arabidopsis proteins and best rice homologs. Predicted Arabidopsis proteins (October 2001, ftp.tigr.org) were compared (BLASTP E value # –6) with