International rice genome sequencing project irgsp the international rice genome sequencing project irgsp, a consortium of publicly funded laboratories, was established in 1997 to obtain a high. 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. Weedy rice samples were sequenced to an average 19. The agronomic importance of rice, its shared evolutionary history with major cereal crops, and its small genome size led to the generation of two draft sequences goff et al. For genomic comparison, public genomic sequence data were retrieved for a worldwide sample of 426 locally cultivated rice varieties and 53 wild rice accessions 3, 9, 10. In summary, here we present sub1like genes identified in wild rice species through genomewide sequence analysis. This study highlights the prevalence of functionally coupled disease resistance genes and. 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.
This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of oryza sativa and related oryza species. It is found in mopane or savanna woodland, savanna or fadama. The genome sequence of african rice oryza glaberrima and evidence for independent domestication. Oryza glaberrima, commonly known as african rice, is one of the two domesticated rice species. Dnabinding is atpdependent, however specific dna sequences that define origins of replication have not been identified. Oryza 200 genome project has released the genome sequence data of 208 accessions from 19 wild and 2 cultivated oryza species collected in the national institute of genetics japan and a part from other institutions for comparison. Interestingly, african rice is not of the same origin as asian rice oryza sativa l. Diverse genetic mechanisms underlie worldwide convergent. Jan 22, 2018 genome assemblies of domesticated and wild rice relatives reveal salient features of genome evolution across the genus oryza, especially rapid species diversification and turnover of. Rice chloroplast genome variation architecture and. You are encouraged use these data to advance your research on. Oryza barthii is an annual, clumpforming grass with erect to semierect culms that form new roots at the lower nodes.
We are releasing a draft genome sequence for rice from 9311 19, which is a cultivar. In particular, the wholegenome dna sequence of a cultivated rice, oryza sativa ssp. The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by wholegenome shotgun sequencing. Oryza repeat database rice genome annotation project. Pdf the genome sequence of african rice oryza glaberrima and. Mar 26, 2020 weedy rice samples were sequenced to an average 19.
Using reference genomes spanning the oryza species tree, we. Oryza minuta, a tetraploid wild relative of cultivated rice family poaceae, possesses a bbcc genome and contains genes that confer resistance to bacterial blight bb and whitebacked wbph and brown bph plant hoppers. The name oryza barthii was for some time wrongly used for the perennial o. All accession has sequence information of illumination. Origins and geographic diversification of african rice oryza. The assembled sequence covers 93% of the 420megabase genome. Download table summary of genome assembly and annotation of the six. Tools sequence analysis tools accessed from the genome context view menu use the current genomic region as input. Genome assemblies of domesticated and wild rice relatives reveal salient features of genome evolution across the genus oryza, especially rapid species diversification and turnover of.
For genomic comparison, public genomic sequence data were retrieved for a worldwide sample of 426 locally. Oryza glumaepatula chr 3s oryza granulata chr 3s oryza longistaminata chr 3s oryza meridionalis chr 3s oryza minutabb chr 3s oryza minutacc chr 3s oryza nivara chr 3s oryza officinalis chr 3s oryza punctata. It belongs to the aa genome group and has 12 chromosomes and a nuclear genome size of 411 mb flow cytometry. Aagenome sequences for oryza nivara, oryza glaberrima, oryza barthii, oryza. This shows the sequence data of 208 accessions from 19 wild and 2 cultivated oryza species. The international rice genome sequencing project irgsp consortium was launched in. Our chromosomal location, phylogenetic, and gene structure. The genus oryza has become a model for the study of plant genome structure, function, and evolution. Global characterization of the root transcriptome of a wild.
In this study, we sampled all 53 singlecopy genes together with 16 intergenic genomic regions to determine overall extent of genome divergence between rice and aa genome oryza species by using the japonica genome sequence as a reference. International rice genome sequencing project irgsp the international rice genome sequencing project irgsp, a consortium of publicly funded laboratories, was established in 1997 to obtain a high quality, mapbased sequence of the rice genome using the cultivar nipponbare of oryza sativa ssp. Rap id, separate keywords with a space to find results with all of the keywords. Probably the wild progenitor of cultivated african rice oryza glaberrima. It belongs to the aa genome group and has 12 chromosomes and a nuclear genome size. Dec 15, 2010 oryza longistaminata, an aa genome type 2 n 24, originates from africa and is closely related to asian cultivated rice o.
Phylogenetic relationships and genome divergence among the aa. We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in china, oryza sativa l. The genome sequence of african rice oryza glaberrima and evidence. Oryza minuta, a tetraploid wild relative of cultivated rice family poaceae, possesses a bbcc genome and contains genes that confer resistance to bacterial blight bb and whitebacked wbph and. It contains various valuable traits with respect to tolerance to biotic and abiotic stress, qtls with agronomically important traits and high ability to use nitrogen efficiently nue. The download site also contains the annotation data in gff format. The donor parent, w0009, has been characterized as having the characteristic morphology of the african wild rice, as well as tolerance to multiple bioticabiotic stresses according. Asian rice oryza sativa is among the worlds most important crops. The genomics of oryza species provides insights into rice. In this study, we developed a set of rice chromosome segment substitution lines harboring o. Digenomeseq is an in vitro nucleasedigested whole genome sequencing to profile genome wide nuclease offtarget effects in cells. All accession has sequence information of illumination short reads 100150 bp of over x10 depth and is linked by the dra registration number shown in the table. A recent reduction of african rice cultivation is also evident. The study of domestication provides insights about where and how major cultural transitions to agriculture have arisen.
The genome was assembled as outlined in supplementary figure 1 and is composed of 5,309 scaffolds scaffold n50, 217 kb assembled into 12 pseudomolecules, resulting in a total assembly size of 316. We have created the oryza repeat database to assist in. These oryza genome resources provide insights into rice evolutionary genomics and are valuable for the improvement of rice and conservation of wild rice germplasm. We first analyzed the combined data matrix comprising of gene and intergenic region sequences to estimate. Our chromosomal location, phylogenetic, and gene structure analyses have revealed that the sub1 locus is conserved in the long arm of chr 9 in most oryza species with aa, bb and ffgenomes. Frontiers the complete chloroplast genome of wild rice. It contains various valuable traits with respect to.
The species in the genus oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. It is now rarely sold in west african markets, having been replaced by asian strains. The agronomic importance of rice, its shared evolutionary history with major cereal crops, and its small genome size led to the. Origin recognition complex subunit 1 oryza barthii. The ultimate goal of the international oryza map alignment project is to create a basic and translational research platform that can provide immediate access to virtually any region of the collective oryza genome both genomically i. Oryza longistaminata, an aa genome type 2 n 24, originates from africa and is closely related to asian cultivated rice o. Digenomesequencing genomewide profiling of offtarget effects. Genomes of domesticated and wild rice relatives highlight.
Because they are a source of resistance to, or tolerance of. Involved in chromatin condensation and control of cell cycle. Aligning the putative protein sequence of olong01m100278 to its homologs in o. In this study, we sampled all 53 singlecopy genes together with 16 intergenic genomic regions to determine overall extent of genome divergence between rice and aa genome oryza species by using.
Oryza glumipatula is a wild rice from south america, one of the rice species included in the omap project. There are several options for downloading rice genome annotation data from the rice genome annotation project annotation database. Mingsheng chen, klaus mayer, steve rounsley, rod wing and colleagues report the genome sequence of african rice oryza glaberrima, a different species than asian rice. Alternative splicing involving retention of the th intron in oryza nhx1 transcripts is more ancient in origin compared to the 5. All accession has sequence information of illumina short reads 100150 bp of over x10 depth of each genome length.
Required for the import of protein into the nucleus and also for rna export. Details oryza barthii ensembl genomes 45 ensembl plants. Pdf genome sequences of oryza species researchgate. Using genomewide computational scans, based on mapping matepaired bes from each oryza species to the refseq, all putative major sites of genome alteration. The species in the genus oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of. In summary, here we present sub1like genes identified in wild rice species through genome wide sequence analysis.
Construction of rice chromosome segment substitution lines. Apr 05, 2002 the genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole genome shotgun sequencing. Oryza glaberrima african rice is a cultivated grain distinct from its better known cousin oryza sativa asian rice. The cultivation of rice in africa dates back more than 3,000 years. Oryza barthii, also called barths rice, wild rice, or african wild rice, is a grass in the rice genus oryza. The rice genome consists of repetitive dna sequence intermixed with coding sequence. Oct 18, 2016 chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Nipponbare, was revealed in 2004 by the activity of an international research consortium. Aegilops tauschii wheat d genome triticum urartu wheat a genome progenitor organelles. Diverse genetic mechanisms underlie worldwide convergent rice. The rise and fall of african rice cultivation revealed by. Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Script to search for simple sequence repeats in fastaformatted dna sequences by s. Oryza sativa indica is one of the two most commonly cultivated subspecies of rice along with o.
Component of the origin recognition complex orc that binds origins of replication. Nov 18, 2014 asian rice oryza sativa is among the worlds most important crops. These species are native to quite different environments. Assembling the genome of the african wild rice oryza. Frontiers distinct evolutionary origins of intron retention. Global characterization of the root transcriptome of a. The download site is available for those who wish to download the annotation data as an entire set or by chromosome. African rice was independently domesticated 3000 years ago in the niger river delta from its still extant progenitor, oryza barthii.
It belongs to the aa genome group and has 12 chromosomes with a nuclear genome size of 464 mb flow cytometry. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic. It was first domesticated and grown in west africa around 2,0003,000 years ago. Digenomeseq is an in vitro nucleasedigested wholegenome sequencing to profile genomewide nuclease offtarget effects in cells. The genome sequence of african rice oryza glaberrima. Oryza glumaepatula chr 3s oryza granulata chr 3s oryza longistaminata chr 3s oryza meridionalis chr 3s oryza minutabb chr 3s oryza minutacc. The genome of indica is very similar to that of japonica, which is generally restricted to temperate climes such as japan.
African rice was independently domesticated 3000 years ago in the. Summary of genome assembly and annotation of the six aa. Here we present a highquality assembly and annotation of the o. Foxtail millet setaria maize zea oats avena pearl millet pennisetum rice oryza rye secale sorghum sorghum wheat triticum wild rice zizania other oryza. Oryza barthii is the aa genome progenitor of the west african cultivated rice, o. These species are native to quite different environments, representing four continents. Phylogenetic relationships and genome divergence among the. The genome sequence of african rice oryza glaberrima and. Oryza rufipogon chr 3s oryza rufipogon fpc map oryza sativa indica. These prepublication data are being released under guidelines of the fort lauderdale agreement, which reaffirms the balance between fair use i. Mar 11, 2020 based on sequence comparisons, we predict that this splicing event is likely absent in nhx1 transcripts of oryza bb and ff genome types and possibly other oryza genome types as well. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of o. A draft sequence of the rice genome oryza sativa l. Evolutionary analysis of the sub1 locus across the oryza.
972 1552 410 1316 830 955 1342 179 253 1456 167 1032 1133 1153 880 1600 471 1386 361 1259 1569 444 101 1134 1066 371 773 191 715 730 209 758 1051 777 207 634 310 400