Difference between revisions of "IC4R006-Genome-2014-25064006"
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[[File:IC4R006-Genome-2014-25064006-2.png |center |thumb |10000px |'''''']] | [[File:IC4R006-Genome-2014-25064006-2.png |center |thumb |10000px |'''''']] | ||
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*The researchers derived 33,164 gene models, including potential gene models and 701 tRNA genes (Fig. 1). | *The researchers derived 33,164 gene models, including potential gene models and 701 tRNA genes (Fig. 1). | ||
*The researchers found that transposable elements (TEs)represented 104 Mb (i.e., 34.25%) in the O. glaberrima genome assembly (Fig. 1). | *The researchers found that transposable elements (TEs)represented 104 Mb (i.e., 34.25%) in the O. glaberrima genome assembly (Fig. 1). | ||
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[[File:IC4R006-Genome-2014-25064006-1.png |center |thumb |10000px |'''Figure 1 The O. glaberrima genome(CG14 v1). Concentric circles show structural,functional and evolutionary aspects of the genome: A, chromosome number; B, heat map view of genes; C, repeat (RNA and DNA TEs without MITEs) density in 200-kb windows(red, average +1 s.d.; blue, average −1 s.d.; | [[File:IC4R006-Genome-2014-25064006-1.png |center |thumb |10000px |'''Figure 1 The O. glaberrima genome(CG14 v1). Concentric circles show structural,functional and evolutionary aspects of the genome: A, chromosome number; B, heat map view of genes; C, repeat (RNA and DNA TEs without MITEs) density in 200-kb windows(red, average +1 s.d.; blue, average −1 s.d.; | ||
yellow, gene and repeat density between red and blue); and D paralogous relationships between O. glaberrima chromosomes.''']] | yellow, gene and repeat density between red and blue); and D paralogous relationships between O. glaberrima chromosomes.''']] | ||
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==Labs working on this Project== | ==Labs working on this Project== | ||
==Corresponding Author== | ==Corresponding Author== | ||
Revision as of 18:05, 23 June 2016
Contents
Project Title
- The genome sequence of African rice (Oryza glaberrima)and evidence for independent domestication
The Background of This Project
- The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection.
Plant Culture & Treatment
- The researchers sequenced the O. glaberrima genome (International Rice Germplasm Collection (IRGC) accession #96717, var. CG14) using a minimum tiling path (MTP) of 3,485 BAC clones selected from a BAC-based physical map aligned to the O. sativa ssp. japonica reference genome (RefSeq)10,11 with (i) a hybrid BAC pool (3,319 BACs) and whole genome shotgun approach using Roche/454GS-FLX Titanium sequencing technology for 11.5 chromosomes12 and(ii) a BAC-by-BAC (166 BACs) Sanger method for the short arm of chromosome 3 (Chr3S).
Research Findings
- The researchers evaluated the final assembly for accuracy and completeness using four previously Sanger-sequenced and finished BACs located on chromosomes 1 (1 BAC), 5 (1 BAC) and 6 (2 BACs). Overall, more than 98% of the query BAC sequences were detected and localized in the correct chromosomal locations (549,598 bp query/557,270 bp subject) with a sequence accuracy of 99.6%. The 7.7 kb of missing sequence was located across 23 sequence gaps in the pseudomolecules.The overall run statistics are summarized in Supplementary Table 1,The genome was assembled as outlined in Supplementary Figure 1
- The researchers derived 33,164 gene models, including potential gene models and 701 tRNA genes (Fig. 1).
- The researchers found that transposable elements (TEs)represented 104 Mb (i.e., 34.25%) in the O. glaberrima genome assembly (Fig. 1).
Figure 1 The O. glaberrima genome(CG14 v1). Concentric circles show structural,functional and evolutionary aspects of the genome: A, chromosome number; B, heat map view of genes; C, repeat (RNA and DNA TEs without MITEs) density in 200-kb windows(red, average +1 s.d.; blue, average −1 s.d.; yellow, gene and repeat density between red and blue); and D paralogous relationships between O. glaberrima chromosomes.
