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Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [degradome]

ABSTRACT: The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.

ORGANISM(S): Oryza rufipogon

PROVIDER: GSE39307 | GEO | 2012/08/10

SECONDARY ACCESSION(S): PRJNA170713

REPOSITORIES: GEO

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Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [small RNA]

Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.

2012-08-10 | GSE39308 | GEO

Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [small RNA]

2012-08-10 | E-GEOD-39308 | biostudies-arrayexpress

Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [degradome]

Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication. The 5' end of the 3' degraded mRNAs with polyA tails were collected and generated from seedlings at four-leaves stage of O.rufipogon by degradome highthoughput sequecing using Illumina GAII

2012-08-10 | E-GEOD-39307 | biostudies-arrayexpress

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [Degradome]

Project description:MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. Analysis of sRNA datasets revealed a surprisingly higher abundance of 22nt sRNAs originating from a loci on Chromosome 2 in wild rice species. This locus codes for a 22 nt miRNA named as miR397. Studies in Arabidopsis and O. sativa japonica nipponbare have shown that miR397 targets a group of proteins called laccases, which are involved in secondary metabolite (lignin) production. The expression of these targets also differs across the species shown through RNA-Seq analysis. Although a functional significance of this interaction between the miRNA and laccase has not been understood. In the current study we attempt to explain the functional relevance of the miRNA in domestication of rice.

2020-09-30 | GSE118702 | GEO

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [ncRNA-seq]

2018-04-25 | GSE111440 | GEO

Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [RNA-seq]

2018-04-25 | GSE111438 | GEO

Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice

Project description:Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. Three of these genes regulate the plant architecture in O. rufipogon and are closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene. Therefore, we refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Furthermore, a similar but independent 113-kb deletion was detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, coupled with the loss of a tandem repeat of zinc-finger genes, drove the parallel domestication of plant architecture in Asian and African rice.

2018-07-04 | GSE116423 | GEO

Gene expression level of six rice lineages

Project description:Towards understanding gene expression variation among related rice lineages on a genome-wide scale, we sought to assess global gene expression in the heading-stage panicle using a whole genome oligonucleotide microarray designed to represent 36,926 annotated indica genes. Using a loop-design, we interrogated gene expression patterns in six related rice lineages, including O. sativa (two Asian cultivars indica and japonica), O. nivara (Asian annual wild rice), O. rufipogon (Asian perennial wild rice) and O. glaberrima (African cultivated rice). Series_sample_order: Sample 1-12 Slide A; Sample 13-24 Slide B

2008-06-10 | E-GEOD-11712 | biostudies-arrayexpress

Single-base resolution DNA methylomes of rice and functional roles of DNA methylation

Project description:To examine the rice genome methylation landscape and assess its functional significance, we generated the first single-base resolution genome methylation maps for Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. The methylation level of rice genomes is four times higher than that of Arabidopsis. Methylation in the promoter and gene body regions have similar patterns and effects on gene expression as those in Arabidopsis but different from a previous study on rice chromosomes 4 and 10. Most interestingly, we discovered for the first time that methylation in gene transcriptional termination regions can significantly repress gene expression, and the effect is even stronger than promoter methylation, which opens a new direction in the study of epigenetic regulation of gene expressions. Through integrated analysis of genetic, methylome and expression variation between cultivated and wild rice, we found that the genetic factor reflected by DNA variations may be the major determinant for methylation patterns at the whole-genome level and that methylation variation can only account for limited expression variation of genes between cultivated and wild rice.

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The COG1-OsSERL2 complex senses cold to trigger signaling network for chilling tolerance in japonica rice

Project description:Improvement of chilling tolerance is a key strategy to face potential menace from abnormal temperature in rice production, which depends on the signaling network triggered by receptors. However, little is known about the QTL genes encoding membrane complexes for sensing cold. Here, Chilling-tolerance in Gengdao/japonica rice 1 (COG1) was isolated from a chromosome segment substitution line containing a QTL (qCS11-jap) for chilling sensitivity. The major gene COG1 was found to confer chilling tolerance in japonica rice. In natural rice populations, only the haplogroup1 encoded a functional COG1. Evolutionary analysis showed that COG1 originated from Chinese O. Rufipogon and was fixed in japonica rice during domestication. COG1, a membrane-localized LRR-RLP, targeted and activated the kinase OsSERL2 in a cold-induced manner, promoting chilling tolerance. Furthermore, the cold signal transmitted by COG1-OsSERL2 activates OsMAPK3 in the cytoplasm. Our findings reveal a cold-sensing complex, which mediates signaling network for the chilling defense in rice.

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