IC4R007-Genome-2015-26358679 - Revision history

Guangyi at 04:34, 26 June 2016

2016-06-26T04:34:49Z

2016-06-26T04:33:43Z

‎Research Findings

2016-06-26T04:33:22Z

‎Research Findings

2016-06-26T04:26:59Z

‎Research Findings

2016-06-26T04:19:03Z

‎Research Findings

2016-06-26T04:18:07Z

‎Research Findings

2016-06-26T04:15:09Z

‎Research Findings

2016-06-26T03:52:33Z

‎Plant Culture & Treatment

2016-06-26T03:32:14Z

‎Research Findings

2016-06-26T03:30:18Z

‎Research Findings

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 ==Project Title==
 *Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility
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 ==The Background of This Project==
 *Oryza longistaminata is an African wild rice species with AA genome type possessing special traits that are highly valued for improving cultivated rice, such as strong resistance to biotic and abiotic stresses (Song et al., 1995) for improving resistance of cultivars, rhizomatousness for perennial breeding (Glover et al., 2010), and self-incompatibility (SI) for new ways to produce hybrid seeds (Ghesquiere, 1986).Deciphering the genome of O. longistaminata will be the key to uncovering the mechanism of these hallmark traits and improving cultivated rice.
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 *The researchers assembled de novo a total length of �347 Mb of the reference genome of O. longistaminata (contig N50 12.5 kb; scaffold N50 363 kb) based on a large quantity of combined sequencing data (�396 3 Illumina short reads and �5.9 3 Roche GS FLX + long reads).
 *The researchers using the assembled genome to condeuct annotation.
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 ==Research Findings==
 *The researchers assembled scaffolds of O. longistaminata into 12 pseudo-chromosomes (Figure 1A) based on its syntenic relationship with Oryza glaberrima.

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 [[File:IC4R007-Genome-2015-26358679-1c.png |center |thumb |10000px |''''''Figure 1c.Clustering of gene families.'''''']]
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 ==Labs working on this Project==

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 [[File:IC4R007-Genome-2015-26358679-1c.png |center |thumb |10000px |''''''Figure 1c.Clustering of gene families.'''''']]
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-[[File:IC4R007-Genome-2015-26358679-1d.png |center |thumb |10000px |''''''Figure 1d.Expanded and contracted gene families.'''''']]
+[[File:IC4R007-Genome-2015-26358679-1e.png |center |thumb |10000px |''''''Figure 1d.Expanded and contracted gene families.'''''']]
 ==Labs working on this Project==

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 [[File:IC4R007-Genome-2015-26358679-f3.png |center |thumb |10000px |''''''Figure B.Divergence time between O. longistaminata and other species.'''''']]
 ==Labs working on this Project==

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 *Divergent times analysis among six Gramineae species, including O. sativa ssp. japonica, O. glaberrima, O. longistaminata, O. brachyantha, Phyllostachys heterocycla, and Brachypodium distachyon (Figure 1B) indicates that the genus Oryza shared a common ancestor �15.2 million years ago (MYA), with O. longistaminata having potentially diverged from O. glaberrima.
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-[[File:IC4R007-Genome-2015-26358679-f3.png |center |thumb |10000px |''''''Figure B.Divergence time between O. longistaminata and other species.(C) Clustering of gene families'''''']]
+[[File:IC4R007-Genome-2015-26358679-f3.png |center |thumb |10000px |''''''Figure B.Divergence time between O. longistaminata and other species.'''''']]
 ==Labs working on this Project==

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 [[File:IC4R007-Genome-2015-26358679-sf7.png |center |thumb |10000px |''''''Supplemental Figure 7.Distribution of divergence rate of each type( de novo method & homology-based method ) of transposable elements (TEs) in O. longistaminata.'''''']]
 ==Labs working on this Project==

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 *The transposable elements (TEs) annotation results show that 48.73% of the genome assembly were TEs (Supplemental Tables 9 and 10, and Supplemental Figure 7), which is a markedly higher percentage than previously found in O. glaberrima (34.25%), Oryza brachyantha (29.2%), and Oryza sativa (34.8%)
 [[File:IC4R007-Genome-2015-26358679-s9.png |center |thumb |10000px |'''''']]
 [[File:IC4R007-Genome-2015-26358679-s10.png |center |thumb |10000px |'''''']]
-[[File:IC4R007-Genome-2015-26358679-sf7.png |center |thumb |10000px |''''''Supplemental Figure 7.Distribution of divergence rate of each type( de novo method & homology-based method ) of transposable elements (TEs) in O. longistaminata'''.''']]
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 ==Labs working on this Project==