View source for IC4R007-Genome-2015-26358679

==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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==Plant Culture & Treatment==
*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-2015-26358679-1.png |center |thumb |10000px |'''Figure A.Assembly genome of O. longistaminata(Oryza_longistaminata_v1.0). Concentric circles show the structural, functional, and evolutionary aspects of the genome: a, chromosome number; b, heatmap view of repeats; c, density of genes; d, GC content; e, paralogous relationships between chromosomes
of O. longistaminata.''']]
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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 |'''''']]
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[[File:IC4R007-Genome-2015-26358679-s10.png |center |thumb |10000px |'''''']]
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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.'''''']]
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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.'''''']]
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*Gene family clustering analysis based on pair-wise genes among four rice species (O. longistaminata, O. sativa, O. glaberrima, and
O. brachyantha) shows that 13 238 gene families were identified in these four species (Figure 1C). The expansion or contraction of
gene families analysis using seven species (four rice species as described above as well as B. distachyon, P. heterocycla, and
Setaria italica) showed that 393 gene families contracted and 474 expanded in the genome of O. longistaminata (Figure 1D). 
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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==
*State Key Laboratory of Genetic Resources and Evolution, Kunming Instituteof Zoology, Chinese Academy of Sciences, Kunming 650223, China
*Food Crops Research Institute, Yunnan Academy of Agricultural Sciences,Kunming 650205, China
*University of Chinese Academy of Sciences, Beijing 100039, China
*Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
*BGI-Shenzhen, Shenzhen 518083, China
*Laboratory of Applied Genomics and Synthetic Biology, College of Life Science, Kunming University of Science and Technology, Kunming 650093, P. R. China
*Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences,Kunming 650201, China
*Arizona Genomics of Institute, School of Plant Sciences, University of Arizona,Tucson, AZ 85721, USA
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==Corresponding Author==
* '''Fengyi Hu''' (hfengyiyaas@aliyun.com) & '''Wen Wang'''(wwang@mail.kiz.ac.cn) & '''Rod A. Wing''' (rwing@ag.arizona.edu)
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