Oryza Sativa Genome Research Articles

Analyses of Old "Prokaryotic" Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa.

During evolution, various processes such as duplication, divergence, recombination, and many other events leads to the evolution of new genes with novel functions. These evolutionary events, thus significantly impact the evolution of cellular, physiological, morphological, and other phenotypic trait of organisms. While evolving, eukaryotes have acquired large number of genes from the earlier prokaryotes. This work is focused upon identification of old “prokaryotic” proteins in Arabidopsis and Oryza sativa genome, further highlighting their possible role(s) in the two genomes. Our results suggest that with respect to their genome size, the fraction of old “prokaryotic” proteins is higher in Arabidopsis than in Oryza sativa. The large fractions of such proteins encoding genes were found to be localized in various endo-symbiotic organelles. The domain architecture of the old “prokaryotic” proteins revealed similar distribution in both Arabidopsis and Oryza sativa genomes showing their conserved evolution. In Oryza sativa, the old “prokaryotic” proteins were more involved in developmental processes, might be due to constant man-made selection pressure for better agronomic traits/productivity. While in Arabidopsis, these proteins were involved in metabolic functions. Overall, the analysis indicates the distinct pattern of evolution of old “prokaryotic” proteins in Arabidopsis and Oryza sativa.

Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition

Oryza meyeriana (O. meyeriana), with a GG genome type (2n = 24), accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. It is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq and obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (japonica-type Nipponbare and indica-type 93–11) genomes revealed that 13% of the O. meyeriana contigs had not been detected in O. sativa. Many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. There are two kinds of rice bacterial blight-resistant genes (Xa1 and Xa26) differentially or specifically expressed in O. meyeriana. The 4 Xa1 contigs were all only expressed in root, while three of Xa26 contigs have the highest expression level in leaves, two of Xa26 contigs have the highest expression profile in stems and one of Xa26 contigs was expressed dominantly in roots. The transcriptomic database of O. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease resistance in O. meyeriana.

Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor.

Sorghum bicolor is one of the most important crops for food and bioethanol production. Its small diploid genome and resistance to environmental stress make sorghum an attractive model for studying the functional genomics of the Saccharinae and other C4 grasses. We analyzed the domain-based functional annotation of the cDNAs using the gene ontology (GO) categories for molecular function to characterize all the genes cloned in the full-length cDNA library of sorghum. The sorghum cDNA library successfully captured a wide range of cDNA-encoded proteins with various functions. To characterize the protein function of newly identified cDNAs, a search of their deduced domains and comparative analyses in the Oryza sativa and Zea mays genomes were carried out. Furthermore, genes on the sense strand corresponding to antisense transcripts were classified based on the GO of molecular function. To add more information about these genes, we have analyzed the expression profiles using RNA-Seq of three tissues (spikelet, seed and stem) during the starch-filling phase. We performed functional analysis of tissue-specific genes and expression analysis of genes of starch biosynthesis enzymes. This functional analysis of sorghum full-length cDNAs and the transcriptome information will facilitate further analysis of the Saccharinae and grass families.

Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants.

BackgroundSimple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest.MethodsHere, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea.ResultsWe explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics.ConclusionsThe present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2031-1) contains supplementary material, which is available to authorized users.

Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing.

Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling Assembly genes with their corresponding full-length cDNA. We applied our pipeline to additional organisms and identified numerous unannotated genes, demonstrating that Tiling Assembly is an organism-independent tool for genome annotation.

Patatin-related phospholipase A, pPLAIIIα, modulates the longitudinal growth of vegetative tissues and seeds in rice.

Patatin-related phospholipase A (pPLA) hydrolyses glycerolipids to produce fatty acids and lysoglycerolipids. The Oryza sativa genome has 21 putative pPLAs that are grouped into five subfamilies. Overexpression of OspPLAIIIα resulted in a dwarf phenotype with decreased length of rice stems, roots, leaves, seeds, panicles, and seeds, whereas OspPLAIIIα-knockout plants had longer panicles and seeds. OspPLAIIIα-overexpressing plants were less sensitive than wild-type and knockout plants to gibberellin-promoted seedling elongation. OspPLAIIIα overexpression and knockout had an opposite effect on the expression of the growth repressor SLENDER1 in the gibberellin signalling process. OspPLAIIIα-overexpressing plants had decreased mechanical strength and cellulose content, but exhibited increases in the expression of several cellulose synthase genes. These results indicate that OspPLAIIIα plays a role in rice vegetative and reproductive growth and that the constitutive, high activity of OspPLAIIIα suppresses cell elongation. The decreased gibberellin response in overexpressing plants is probably a result of the decreased ability to make cellulose for anisotropic cell expansion.

Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination.

The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of Arabidopsis thaliana and Oryza sativa genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated via the regulation of gene expression. The in silico expression analysis of the SAGA components in Arabidopsis and O. sativa clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA subunits in Arabidopsis. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.

Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.).

MicroRNAs (miRNAs) are small endogenous RNAs of ~22 nucleotides that have been shown to play regulatory role by negatively affecting the expression of genes at the post-transcriptional level. Information of miRNAs on some important crops like soybean, Arabidopsis, and rice, etc. are available, but no study on heat-responsive novel miRNAs has yet been reported in wheat (Triticum aestivum L.). In the present investigation, a popular wheat cultivar HD2985 was used in small RNA library construction and Illumina HiSeq 2000 was used to perform high-throughput sequencing of the library after cluster generation; 110,896,604 and 87,743,861 reads were generated in the control (22 °C) and heat-treated (42 °C for 2 h) samples, respectively. Forty-four precursor and mature miRNAs were found in T. aestivum from miRBase v 19. The frequencies of the miRNA families varied from 2 (tae-miR1117) to 60,672 (tae-miR159b). We identify 1052 and 902 mature miRNA sequences in HD2985 control and HS-treated samples by mapping on reference draft genome of T. aestivum. Maximum identified miRNAs were located on IWGSC_CSS_3B_scaff (chromosome 3B). We could identify 53 and 46 mature miRNA in the control and HS samples and more than 516 target genes by mapping on the reference genome of Oryza sativa, Zea mays, and Sorghum bicolor. Using different pipelines and plant-specific criteria, 37 novel miRNAs were identified in the control and treated samples. Six novel miRNA were validated using qRT-PCR to be heat-responsive. A negative correlation was, however, observed between the expression of novel miRNAs and their targets. Target prediction and pathway analysis revealed their involvement in the heat stress tolerance. These novel miRNAs are new additions to miRNA database of wheat, and the regulatory network will be made use of in deciphering the mechanism of thermotolerance in wheat.

Determination of window size and identification of suitable method for prediction of donor splice sites in rice (Oryza sativa) genome

Accurate prediction of the gene structure depends upon the accurate prediction of splice sites. The conserved feature in splicing junction has been successfully used for the prediction of eukaryotic splice sites. In eukaryotes, though the di-nucleotide GT is conserved at 5′ splice sites, the pattern surrounding the conserved di-nucleotide varies from species to species. Most of the work related to splice site analysis has been extensively done in Homo sapiens and Arabidopsis thaliana. However, such works are yet to be fully explored in Oryza sativa and other species of grass family. In this study, statistical techniques have been applied to discriminate the real splice sites from pseudo splice sites in rice, maize and barley genomes and based on this a suitable window size is determined for the prediction of donor splice sites. Depending upon the determined window size, appropriate methods for predicting donor splice sites in rice have been considered and compared in terms of prediction accuracy. The results revealed that a window size of 9 base pair (3 bp at the exon end and 6 bp at the intron start including the conserved di-nucleotide GT at the beginning of intron) is an effective window size in all the three species of grass family for the prediction of donor splice sites. Further, the Maximum Entropy Model based method is found as best among the short sequence based prediction methods for donor splice sites with the 9 base pair window size.

Mutation of Oryza sativa CORONATINE INSENSITIVE 1b (OsCOI1b) delays leaf senescence.

Jasmonic acid (JA) functions in plant development, including senescence and immunity. Arabidopsis thaliana CORONATINE INSENSITIVE 1 encodes a JA receptor and functions in the JA-responsive signaling pathway. The Arabidopsis genome harbors a single COI gene, but the rice (Oryza sativa) genome harbors three COI homologs, OsCOI1a, OsCOI1b, and OsCOI2. Thus, it remains unclear whether each OsCOI has distinct, additive, synergistic, or redundant functions in development. Here, we use the oscoi1b-1 knockout mutants to show that OsCOI1b mainly affects leaf senescence under senescence-promoting conditions. oscoi1b-1 mutants stayed green during dark-induced and natural senescence, with substantial retention of chlorophylls and photosynthetic capacity. Furthermore, several senescence-associated genes were downregulated in oscoi1b-1 mutants, including homologs of Arabidopsis thaliana ETHYLENE INSENSITIVE 3 and ORESARA 1, important regulators of leaf senescence. These results suggest that crosstalk between JA signaling and ethylene signaling affects leaf senescence. The Arabidopsis coi1-1 plants containing 35S:OsCOI1a or 35S:OsCOI1b rescued the delayed leaf senescence during dark incubation, suggesting that both OsCOI1a and OsCOI1b are required for promoting leaf senescence in rice. oscoi1b-1 mutants showed significant decreases in spikelet fertility and grain weight, leading to severe reduction of grain yield, indicating that OsCOI1-mediated JA signaling affects spikelet fertility and grain filling.

A strategy for genome-wide identification of gene based polymorphisms in rice reveals non-synonymous variation and functional genotypic markers.

The genetic diversity of plants has traditionally been employed to improve crop plants to suit human needs, and in the future feed the increasing population and protect crops from environmental stresses and climate change. Genome-wide sequencing is a reality and can be used to make association to crop traits to be utilized by high-throughput marker based selection methods. This study describes a strategy of using next generation sequencing (NGS) data from the rice genome to make comparisons to the high-quality reference genome, identify functional polymorphisms within genes that might result in function changes and be used to study correlations to traits and employed in genetic mapping. We analyzed the NGS data of Oryza sativa ssp indica cv. G4 covering 241 Mb with ∼20X coverage and compared to the reference genome of Oryza sativa ssp. japonica to describe the genome-wide distribution of gene-based single nucleotide polymorphisms (SNPs). The analysis shows that the 63% covered genome consists of 1.6 million SNPs with 6.9 SNPs/Kb, and including 80,146 insertions and 92,655 deletions (INDELs) genome-wide. There are a total of 1,139,801 intergenic SNPs, 295,136 SNPs in intronic/non-coding regions, 195,098 in coding regions, 23,242 SNPs at the five-prime (5′) UTR regions and 22,686 SNPs at the three-prime (3′) UTR region. SNP variation was found in 40,761 gene loci, which include 75,262 synonymous and 119,836 non-synonymous changes, and functional reading frame changes through 3,886 inducing STOP-codon (isSNP) and 729 preventing STOP-codon (psSNP) variation. There are quickly evolving 194 high SNP hotspot genes (>100 SNPs/gene), and 1,513 out of 2,458 transcription factors displaying 2,294 non-synonymous SNPs that can be a major source of phenotypic diversity within the species. All data is searchable at https://plantstress-pereira.uark.edu/oryza2. We envision that this strategy will be useful for the identification of genes for crop traits and molecular breeding of rice cultivars.

Polyamine Oxidase 7 is a Terminal Catabolism-Type Enzyme in Oryza sativa and is Specifically Expressed in Anthers

Polyamine oxidase (PAO), which requires FAD as a cofactor, functions in polyamine catabolism. Plant PAOs are classified into two groups based on their reaction modes. The terminal catabolism (TC) reaction always produces 1,3-diaminopropane (DAP), H2O2, and the respective aldehydes, while the back-conversion (BC) reaction produces spermidine (Spd) from tetraamines, spermine (Spm) and thermospermine (T-Spm) and/or putrescine from Spd, along with 3-aminopropanal and H2O2. The Oryza sativa genome contains seven PAO-encoded genes termed OsPAO1-OsPAO7. To date, we have characterized four OsPAO genes. The products of these genes, i.e. OsPAO1, OsPAO3, OsPAO4 and OsPAO5, catalyze BC-type reactions. Whereas OsPAO1 remains in the cytoplasm, the other three PAOs localize to peroxisomes. Here, we examined OsPAO7 and its gene product. OsPAO7 shows high identity to maize ZmPAO1, the best characterized plant PAO having TC-type activity. OsPAO7 seems to remain in a peripheral layer of the plant cell with the aid of its predicted signal peptide and transmembrane domain. Recombinant OsPAO7 prefers Spm and Spd as substrates, and it produces DAP from both substrates in a time-dependent manner, indicating that OsPAO7 is the first TC-type enzyme identified in O. sativa. The results clearly show that two types of PAOs co-exist in O. sativa. Furthermore, OsPAO7 is specifically expressed in anthers, with an expressional peak at the bicellular pollen stage. The physiological function of OsPAO7 in anthers is discussed.

Computational prediction of submergence responsive microRNA and their binding position within the genome of Oryza sativa.

Background: MicroRNAs (miRNAs) are small noncoding RNAs which play crucial role in response to the adverse biotic and abiotic stress conditions at the post transcriptional level. The functions of the miRNAs are generally based on complementarity to their target region. Results: We used the online tool psRNA Target for the identification of submergence responsive miRNA using the gene expression profile related to the submergence condition. We wrote a perl script for the prediction of miRNA target gene. The position based feature of the script increases the overall specificity of the program. Our perl script performed well on the genomic data of Oryza sativa and produced significant results with their positions. These results were analyzed on the basis of complementarity and the statistical scores are used to find out the most probable binding regions. These predicted binding regions are aligned with their respective miRNAs to find out the consensus sequence. We scored the alignment using a position dependent, mismatch penalty system. We also identified the rate of conservation of bases at a particular position for all the predicted binding regions and it was found that all the predicted binding regions maintain above 70% rate of conservation of bases. Conclusion: Our approach provides a novel framework for screening the genome of Oryza sativa. It can be broadly applied to identify complementarity specific miRNA targets computationally by doing a little modification of the script depending on the type of the miRNA.

Genes for iron–sulphur cluster assembly are targets of abiotic stress in rice, Oryza sativa

Iron-sulphur (Fe-S) cluster assembly occurs in chloroplasts, mitochondria and cytosol, involving dozens of genes in higher plants. In this study, we have identified 41 putative Fe-S cluster assembly genes in rice (Oryza sativa) genome, and the expression of all genes was verified. To investigate the role of Fe-S cluster assembly as a metabolic pathway, we applied abiotic stresses to rice seedlings and analysed Fe-S cluster assembly gene expression by qRT-PCR. Our data showed that genes for Fe-S cluster assembly in chloroplasts of leaves are particularly sensitive to heavy metal treatments, and that Fe-S cluster assembly genes in roots were up-regulated in response to iron toxicity, oxidative stress and some heavy metal assault. The effect of each stress treatment on the Fe-S cluster assembly machinery demonstrated an unexpected tissue or organelle specificity, suggesting that the physiological relevance of the Fe-S cluster assembly is more complex than thought. Furthermore, our results may reveal potential candidate genes for molecular breeding of rice.

Genomewide Variation in an Introgression Line of Rice-Zizania Revealed by Whole-Genome re-Sequencing

BackgroundHybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies.Methodology/Principal FindingsIn this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizania latifolia Griseb. in general, 131 millions 90 base pair (bp) paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs) and 17,839 homozygous insertions/deletions (indels) were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs) was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q) RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35.Conclusions/SignificanceOur results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a sexually incompatible species may represent a potent means to generate novel genetic diversities, and which may have played relevant roles in plant evolution and can be manipulated for crop improvements.

Unique and Conserved MicroRNAs in Wheat Chromosome 5D Revealed by Next-Generation Sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow-sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat.

Analysis of rice Snf2 family proteins and their potential roles in epigenetic regulation

Snf2 family proteins are ATP-dependent chromatin remodeling factors that control many aspects of DNA events such as transcription, replication, homologous recombination and DNA repair. In animals several members in this family have been revealed to control gene expression in concert with other epigenetic mechanisms including histone modification, histone variants and DNA methylation. Their function in regulating genome expression in plant has hardly been disclosed before except in Arabidopsis. Here we identified 40 members of this family in the rice (Oryza Sativa) genome and constructed a phylogenetic tree together with Arabidopsis 41 Snf2 proteins. Sequence alignment of the Snf2 helicase regions revealed conserved motifs and blocks in most proteins. Expression profile analysis indicates that many rice Snf2 family genes show a tissue-specific expression pattern and some of them respond to abiotic stresses including drought, salt and cold. The results provide a basis for further analysis of their roles in epigenetic regulation to control rice development.

The evolution and diversification of plant microtubule‐associated proteins

Plant evolution is marked by major advances in structural characteristics that facilitated the highly successful colonization of dry land. Underlying these advances is the evolution of genes encoding specialized proteins that form novel microtubular arrays of the cytoskeleton. This review investigates the evolution of plant families of microtubule-associated proteins (MAPs) through the recently sequenced genomes of Arabidopsis thaliana, Oryza sativa, Selaginella moellendorffii, Physcomitrella patens, Volvox carteri and Chlamydomonas reinhardtii. The families of MAPs examined are AIR9, CLASP, CRIPT, MAP18, MOR1, TON, EB1, AtMAP70, SPR2, SPR1, WVD2 and MAP65 families (abbreviations are defined in the footnote to Table 1). Conjectures are made regarding the evolution of MAPs in plants in relation to the evolution of multicellularity, oriented cell division and vasculature. Angiosperms in particular have high numbers of proteins that are involved in promotion of helical growth or its suppression, and novel plant microtubular structures may have acted as a catalyst for the development of novel plant MAPs. Comparisons of plant MAP gene families with those of animals show that animals may have more flexibility in the structure of their microtubule cytoskeletons than plants, but with both plants and animals possessing many MAP splice variants.

High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences

In an effort to identify newly evolved genes in rice, we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr. We identified 28 functional O. sativa genes, which likely originated after O. sativa diverged from O. glaberrima. These genes account for around 1% (28/3,176) of all annotated genes on O. sativa’s Chr3s. Among the 28 new genes, two recently duplicated segments contained eight genes. Fourteen of the 28 new genes consist of chimeric gene structure derived from one or multiple parental genes and flanking targeting sequences. Although the majority of these 28 new genes were formed by single or segmental DNA-based gene duplication and recombination, we found two genes that were likely originated partially through exon shuffling. Sequence divergence tests between new genes and their putative progenitors indicated that new genes were most likely evolving under natural selection. We showed all 28 new genes appeared to be functional, as suggested by Ka/Ks analysis and the presence of RNA-seq, cDNA, expressed sequence tag, massively parallel signature sequencing, and/or small RNA data. The high rate of new gene origination and of chimeric gene formation in rice may demonstrate rice’s broad diversification, domestication, its environmental adaptation, and the role of new genes in rice speciation

Oryza sativa COI homologues restore jasmonate signal transduction in Arabidopsis coi1-1 mutants.

CORONATINE INSENSITIVE 1 (COI1) encodes an E3 ubiquitin ligase complex component that interacts with JAZ proteins and targets them for degradation in response to JA signaling. The Arabidopsis genome has a single copy of COI1, but the Oryza sativa genome has three closely related COI homologs. To examine the functions of the three OsCOIs, we used yeast two-hybrid assays to examine their interactions with JAZ proteins and found that OsCOIs interacted with OsJAZs and with JAZs, in a coronatine dependent manner. We also tested whether OsCOI1a and OsCOI1b could complement Arabidopsis coi1-1 mutants and found that overexpression of either gene in the coi1-1 mutant resulted in restoration of JA signal transduction and production of seeds, indicating successful complementation. Although OsCOI2 interacted with a few OsJAZs, we were not able to successfully complement the coi1-1 mutant with OsCOI2. Molecular modeling revealed that the three OsCOIs adopt 3D structures similar to COI1. Structural differences resulting from amino acid variations, especially among amino acid residues involved in the interaction with coronatine and JAZ proteins, were tested by mutation analysis. When His-391 in OsCOI2 was substituted with Tyr-391, OsCOI2 interacted with a wider range of JAZ proteins, including OsJAZ1, 2, 5∼9 and 11, and complemented coi1-1 mutants at a higher frequency than the other OsCOIs and COI1. These results indicate that the three OsCOIs are orthologues of COI1 and play key roles in JA signaling.