An evolutionary genomic tale of two rice species. O. glaberrima contains many important adaptive traits for cultivation in African soils and climates. There are only two species of cultivated rice in the world: Oryza glaberrima, or African rice, and Oryza sativa, or Asian rice.Native to sub-Saharan Africa, O. glaberrima is thought to have been domesticated from the wild ancestor Oryza barthii (formerly known as Oryza brevilugata) by peoples living in the floodplains at the bend of the Niger River some 2,000–3,000 years ago (1, 2). doi: 10.1371/journal.pgen.1007414. Nat Commun. Bot. Rice is the staple food for the world and two rice species are cultivated for food production. It incorporates the previously assembled chromosome 3 short arm (Chr3s) sequence and consists of 12 chromosome pseudomolecules and 1,939 unplaced scaffolds. The tool does not require any annotation data, and is able to correctly identify the gene even if this is spread on several genome contigs and contains mismatches and frameshifts. Front Plant Sci. Get the latest research from NIH: https://www.nih.gov/coronavirus. As an important model organism in monocot plants, Oryza sativa belongs to the Oryza genus. Data source Oryza Genome Evolution Project. Epub 2014 Apr 18. The Oryza genus contains 11 different genome types across 27 species, both diploid and polyploid, with a 3.6-fold difference in genome sizes (from around 300 Mb in the diploid FF genome of O. brachyantha to 1,283 Mb in the HHJJ polyploid genome of O. ridleyi, with the AA genome of cultivated rice falling in the 400Mb range). ; yellow, gene and repeat density between red and blue); and D paralogous relationships between, Plot of the composite likelihood ratio (CLR) across. Figure 5. Figure 4. Gene phylogenetic trees with other Gramene species. Plant Sci. 2019 Apr 29;70:639-665. doi: 10.1146/annurev-arplant-050718-100320. Li J, Zhou J, Zhang Y, Yang Y, Pu Q, Tao D. Front Plant Sci. Since that time, it has served as a reference genome for many rice genomic studies [ 27 ]. Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs. EMBL-EBI, Theobroma cacao Belizian Criollo B97-61/B2. COVID-19 is an emerging, rapidly evolving situation. 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. sativa (Asian rice). Rice (Oryza sativa L.), one of the most important staple foods, provides more than one-fifth of the calories consumed worldwide (Khush, 2003). Oryza_glaberrima_V1 Organism: Oryza glaberrima (African rice) Submitter: The Oryza Map Alignment Project (OMAP) Date: 2010/09/22 Assembly level: Scaffold Genome representation: full RefSeq category: representative genome GenBank assembly accession: GCA_000147395.2 (latest) RefSeq assembly accession: n/a IDs: 242461[UID] 1476248 [GenBank] doi: 10.1016/j.cub.2018.05.066. 2014 May;23(9):2210-27. doi: 10.1111/mec.12738. traits by finding commonalities and differences with O. sativa. ( a ) Orthologous gene relationship of…, NLM Figure 1. cultivars with improved yield and quality traits, that have been adopted Figure 5. Oryza sativa L. and Oryza glaberrima, the domestic rice varieties, are diploid species (2n = 24), with 22 wild relative species, and together, comprise four species complexes: the cultivated rice complex and six primary gene pool relatives; the officinalis complex of nine species with five diploid and four tetraploid: the meyeriana complex with two diploid species; the ridleyi complex with two tetraploid species; and two … We are pleased to announce the initial release of the Oryza glaberrima genome from the Arizona Genomics Institute and the Rounsley Lab. A previous reference genome was published but newer studies highlighted some missing parts. Epub 2018 Jul 5. African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. 2008;174:394–408. glaberrima reference genome and analysed through a combination of population genetic and phylogenetic approaches, details of which can be found in the Materials and methods. This The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication 1. New Insights Into the Nature of Interspecific Hybrid Sterility in Rice. The genome was assembled as outlined in Supplementary Figure 1and is composed of 5,309 scaffolds (scaffold N50, 217 kb) assembled into 12 pseudomolecules, result- ing in a total assembly size of 316 Mb (Supplementary Table 2). Download genes, cDNAs, ncRNA, proteins - FASTA - GFF3. Our whole-genome shotgun sequencing yielded a total of 206 317 153 bp of 437 642 sequence reads, which corresponds to about 0.6× coverage of 357 Mbp of the Og genome (Kim et al., 2008).Repeat elements accounted for 22.5% of the total nucleotides, which was significantly smaller than 29% observed in a … African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Background African rice, Oryza glaberrima , is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. 2007;100:951–957. Most cultivated varieties of Oryza sativa and Oryza glaberrima , however, have lost the ability to form long awns. Additional annotations generated by the Gramene and Ensembl Plants Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. Please enable it to take advantage of the complete set of features! In short, we wanted to 1) confirm the genetic bottleneck in African rice as a result of domestication; 2) identify which alleles have been driven to (near) fixation as a result of artificial selection; 3) discover population … the japonica genome was expanding relative to indica. See this image and copyright information in PMC. Both species have same genome AA (Chang 1976, Morinaga et al. and diseases and for its tolerance of drought and infertile soils. Population structure analysis of 94 O. barthii accessions. Mapping to the genome of multiple sequence-based feature sets using. What can I find? RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF. PLoS Genet. For complete certainty, a genetic test can be used. Figure 3. Interspecific crosses between African and Asian rice have produced drought). glaberrima, thus we hypothesize that Trinidad rice has a higher proportion of the Oryza glaberrima genome. There are, however, exceptions, and it can be hard to distinguish from Asian rice. The complex history of the domestication of rice. Concentric circles show structural, functional and evolutionary…, Figure 2. Despite its use, the long life cycle of Nipponbare makes it time-consuming for most genetic analyses. The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. Asian cultivated rice (Oryza sativa) and African cultivated rice (Oryza glaberrima) originated from the wild rice species Oryza rufipogon and Oryza barthii, respectively.The genomes of both cultivated species have undergone profound changes during domestication. Oryza glaberrima is the African cultivated rice species, domesticated from its wild ancestor by farmers living in Inland Delta of Niger River. 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. Short sequence variants. Oryza is a genus of plants in the grass family. From a scientific perspective the genome of O. glaberrima provides insight into the genetic basis of domestication and other traits by finding commonalities and differences with O. sativa. Figure 4. By analyzing whole genome re-sequencing data from 282 individuals of domesticated African rice Oryza glaberrimaand its progenitor O. barthii, we hypothesize a non-centric (i.e. Choi JY, Zaidem M, Gutaker R, Dorph K, Singh RK, Purugganan MD. Abstract. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. Homologues, gene trees, and whole genome alignments across multiple species. 1957).  |  2020 Sep 16;13(1):66. doi: 10.1186/s12284-020-00424-1. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. African rice is a tall rice plant, usually under 120 cm but up to five meters for floating varieties, which may also branch and root from higher stem nodes. eCollection 2019 Mar. 38 39 Keywords 40 African rice, Genome Wide Association Study, flowering … Figure 2. What can I find? Nat Genet. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Mussurova S, Al-Bader N, Zuccolo A, Wing RA. O. glaberrima is a west African species of cultivated rice that was domesticated independently of Asian rice (O. sativa ssp. [1] Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.Hiroaki S, Hiroshi I, Tsuyoshi T, Hisataka N, Hiroshi M, Masaki F, Michie S, Kanako K, Ari K, Masao H et al: Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysisThe Plant Journal 2011, 66(5):796-805. Population structure analysis of 94…. Fage, J.D. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. The O. glaberrima genome (CG14 v1). Harlan, J.R.) 409–452 (Mouton Publishers, 1976). The five wild and two domesticated A genome species, Oryza sativa and Oryza glaberrima, can be crossed relatively easily. O. glaberrima has not been as thor-oughly studied as O. sativa, there-fore, further genetic analysis on O. glaberrima is needed to resolve the unknown genetic and domestica-tion history of Trinidad rice. HHS NIH  |  It includes the major food crop rice (species Oryza sativa and Oryza glaberrima).Members of the genus grow as tall, wetland grasses, growing to 1–2 m tall; the genus includes both annual and perennial species. 2020 Sep 23;11:579980. doi: 10.3389/fpls.2020.579980. Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. 12 chromosomes and an estimated size of ~358 Mb. The cultivation of rice in Africa dates back more than 3,000 years. eCollection 2020. In 2005 the Nipponbare genome was sequenced and annotated to a high-quality level (International Rice Genome Sequencing and Sasaki 2005). Ann Bot. Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. Clipboard, Search History, and several other advanced features are temporarily unavailable. © EMBL-EBI Similar to Asian rice, African rice is a diploid A-type genome, having 12 chromosomes and an estimated size of ~358 Mb. its better known cousin Oryza Dong L, Liu S, Kyaing MS, Xu P, Tharreau D, Deng W, Li X, Bi Y, Zeng L, Li J, Zhou J, Tao D, Yang Q. 2017), however, some of the 14 non-A genome Oryza species dating from the divergence of Oryza … Get the latest public health information from CDC: https://www.coronavirus.gov. 2020 Sep 8;11(1):4488. doi: 10.1038/s41467-020-18329-4. African rice was independently domesticated ~3000 years ago in the They were independently domesticated from divergent progenitor wild species in different geographic locations, South Asia and West Africa, respectively [2] . 2007 Nov;100(5):951-7. doi: 10.1093/aob/mcm128. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. Project funding: National Science Foundation Plant Genome Research Program (#082224) awarded to R. Wing, S. Rounsley and Y. Yu. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima). Identification of the domestication center…. Our analyses showed genetic structure within O. glaberrimathat has a geographical association. The O. glaberrima genome (CG14…. Since its domestication in the inner Niger delta ca. However, these studies could rarely identify the precise natures of specific DNA sequence changes, because it was usually not clear whether the changes occurred in the indica or japonica lineage. Similar to Asian rice, African rice is a diploid A-type genome, having & Oliver, R.A.) 43–58 (Cambridge University Press, 1970). Figure 1. The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717. From a scientific perspective the genome of O. glaberrima Sequence comparisons of OsSh1 and Sh4 . 2020 Sep 23;11:555572. doi: 10.3389/fpls.2020.555572. The current assembly is Oryza_glaberrima_AGI1.1. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. 2020 Aug 7;11:1190. doi: 10.3389/fpls.2020.01190. The genus Oryza probably originated within a relatively short time scale about 15 million years ago (MYA), which includes 23 species categorized into 10 genomic types (AA, BB, BBCC, CC, CCDD, EE, FF, GG, HHJJ, and HHKK) (Aggarwal et al., 1997; Ge et al., 1999; Khush, 2003… Oryza glaberrima (African rice) is a cultivated grain distinct from Identification of various repeat features by programs such as glaberrima originated and is cultivated in West Africa. ; blue, average −1 s.d. Cubry P, Pidon H, Ta KN, Tranchant-Dubreuil C, Thuillet AC, Holzinger M, Adam H, Kam H, Chrestin H, Ghesquière A, François O, Sabot F, Vigouroux Y, Albar L, Jouannic S. Rice (N Y). eCollection 2020. This organ is thought to aid in seed dispersal and prevent predation by animals. Oryza glaberrima genome sequence as a resource for breeding based on genomics Our whole‐genome shotgun sequencing yielded a total of 206 317 153 bp of 437 642 sequence reads, which corresponds to about 0.6× coverage of 357 Mbp of the Og genome (Kim et al., 2008). Identification of candidate regions of artificial selection during O. glaberrima domestication. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error, 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. The complex geography of domestication of the African rice Oryza glaberrima. Construct DNA fingerprint/BAC-end sequence physical maps from 11 deep coverage BAC libraries that represent the 11 wild genomes of Oryza (830,000 fingerprints; 1,659,000 BAC ends) align the 11 physical maps with the sequenced reference subspecies japonica and indica. Since its domestication in the inner Niger delta ca. Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquière A, Santoni S, David J, Glémin S. Mol Ecol. While lacking many of the agronomic and quality traits found in Asian This site needs JavaScript to work properly. Scipio is used for the retrieval of the genome sequence corresponding to a protein query. Identification of the domestication center of O. glaberrima . 2018 Jul 23;28(14):2274-2282.e6. USA.gov. Oryza sativa originated in Asia but is widely grown.O. multiregional) domestication origin for African rice. Portères, R. in Papers in African Prehistory (eds. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events … Hybrid sterility between Oryza sativa and O. glaberrima is a main reproduction barrier when transferring the favorable alleles from O. glaberrima to O. sativa and it happens due to allelic interaction at sterility loci. Generally, African rice has small, pear-shaped grain, reddish bran and green to black hulls, straight, simply-branched panicles, and short, rounded ligules. The authors declare no competing financial interests. Abrouk M, Ahmed HI, Cubry P, Å imoníková D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Čížková J, Hřibová E, Doležel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG. What can I find? Identification of candidate regions of…. -. Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima. food. 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.). by many African countries to meet the growing need for rice as a staple We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes. 2019 Mar 7;15(3):e1007414. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. Vaughan DA, Lu BR, Tomooka N. The evolving story of rice evolution. A long awn is one of the distinct morphological features of wild rice species. Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). Front Plant Sci. Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie K, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y. Curr Biol. International audienceThe African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Niger River Delta from its still extant progenitor, Oryza barthii. Oryza glaberrima genome sequence as a resource for breeding based on genomics. 36 within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might 37 be useful to the rice breeding community. Littlefield, D.C. Rice and Slaves: Ethnicity and the Slave Trade in Colonial South Carolina (University of Illinois Press, 1991). Ann. Annu Rev Plant Biol. project include: Ensembl Plants release 49 - November 2020 However, little is known about the genetic basis of quantitative traits and adaptive variation of … japonica and indica) about 3,500 years ago. eCollection 2020. Figure 3. There are two distinct cultivated species in the genus Oryza that both belong to the AA genome with diploid level (2n = 24), O. sativa (Asian rice) and O. glaberrima (African rice). More about the Ensembl Plants microarray annotation strategy. African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. The A genome diversified roughly 3 Ma (Brozynska et al. Portères, R. in Origins of African Plant Domestication (ed. Several studies indicated that it has extremely narrow genetic diversity compared to both its wild progenitor, Oryza barthii and the Asian rice, Oryza sativa which can mainly be attributed to a severe domestication bottleneck. provides insight into the genetic basis of domestication and other Variation effect prediction with sequence ontology. 2014 Sep;46(9):931-2. doi: 10.1038/ng.3071. Sequence comparisons of OsSh1 and…. Epub 2007 Jul 6.  |  Neutral alleles at each locus have the potential to overcome the … eScholarship, California Digital Library, University of California, Sweeney M, McCouch S. The complex history of the domestication of rice. rice, O. glaberrima is significant for its resistance to many pests Still extant progenitor, Oryza barthii the cultivation of rice sativa ), O. glaberrima genome and analyses. Nipponbare genome was published but newer studies highlighted some missing parts Prehistory ( eds, the long life cycle Nipponbare! 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Library, University of California, Sweeney M, McCouch S. the complex geography domestication. By Analysis of 246 New Genomes BP, African rice is a West African species of rice... 11 oryza glaberrima genome 1 ):4488. doi: 10.1186/s12284-020-00424-1 however, exceptions, and Dust,.! Sasaki 2005 ) test can be hard to distinguish from Asian rice two rice species are cultivated for food.!
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