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Oryza punctata

Showkat Ahmad Ganie, Ananda Bhusan Debnath, Abubakar Mohammad Gumi, Tapan Kumar Mondal
BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. RESULT: All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species...
September 11, 2017: BMC Genomics
Sajjad Asaf, Muhammad Waqas, Abdul L Khan, Muhammad A Khan, Sang-Mo Kang, Qari M Imran, Raheem Shahzad, Saqib Bilal, Byung-Wook Yun, In-Jung Lee
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 white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites...
2017: Frontiers in Plant Science
Kshirod K Jena, Ma LaRue E Ballesfin, Ricky B Vinarao
This paper describes the development of monosomic alien addition and disomic introgression lines through a cross between autotetraploid indica rice and Oryza punctata toward tapping valuable traits for rice improvement. Oryza punctata is a distantly related wild Oryza species having BB genome with untapped genetic resources for rice improvement. Low crossability between the cultivated O. sativa and O. punctata restricts the success of transferring many desirable traits into cultivated rice. Artificially induced autotetraploids of an elite breeding line, IR31917-45-3-2, were produced and crossed with O...
October 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Koji Miyamoto, Masahiro Fujita, Matthew R Shenton, Shota Akashi, Chizu Sugawara, Arisa Sakai, Kiyotaka Horie, Morifumi Hasegawa, Hiroshi Kawaide, Wataru Mitsuhashi, Hideaki Nojiri, Hisakazu Yamane, Nori Kurata, Kazunori Okada, Tomonobu Toyomasu
Plants frequently possess operon-like gene clusters for specialized metabolism. Cultivated rice, Oryza sativa, produces antimicrobial diterpene phytoalexins represented by phytocassanes and momilactones, and the majority of their biosynthetic genes are clustered on chromosomes 2 and 4, respectively. These labdane-related diterpene phytoalexins are biosynthesized from geranylgeranyl diphosphate via ent-copalyl diphosphate or syn-copalyl diphosphate. The two gene clusters consist of genes encoding diterpene synthases and chemical-modification enzymes including P450s...
August 2016: Plant Journal: for Cell and Molecular Biology
Yu-Chia Hsu, Chang-Sheng Wang, Yann-Rong Lin, Yong-Pei Wu
Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups...
2016: Evolutionary Bioinformatics Online
Xin-Hui Zou, Yu-Su Du, Liang Tang, Xin-Wei Xu, Jeff J Doyle, Tao Sang, Song Ge
In the rice genus (Oryza), about one half of the species are allopolyploids. These species are not only important resources for rice breeding but also provide a unique opportunity for studying evolution of polyploid species. In the present study, we sequenced four biparentally inherited nuclear loci and three maternally inherited chloroplast fragments from all diploid and tetraploid species with the B- and C-genome types in this genus. We detected at least three independent origins of three BC-genome tetraploid species...
October 13, 2015: Scientific Reports
Ying Wu, Yue Sun, Xutong Wang, Xiuyun Lin, Shuai Sun, Kun Shen, Jie Wang, Tingting Jiang, Silin Zhong, Chunming Xu, Bao Liu
Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed "transcriptome shock". Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp...
February 2016: Journal of Integrative Plant Biology
K Vaidyanath, K K Raju, G M Reddy
Using the two-dimensional paper-chromatographic technique, free-aminoacid analysis was made on nine diploids and five allotetraploid species of Oryza, to study the biochemical and physiological bases of species relationships. The relationship between different species was inferred on the basis of similarity or differences in polygon patterns of aminoacids, drawn using Ellison's paired affinity values. Among the diploid species, O. sativa, O. perennis subsp. balunga, O. glaberrima and O. breviligulata showed similar polygon patterns, suggesting close relationships...
January 1974: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Yi Sui, Bo Li, Jinfeng Shi, Mingsheng Chen
BACKGROUND: Polyploid species contribute to Oryza diversity. However, the mechanisms underlying gene and genome evolution in Oryza polyploids remain largely unknown. The allotetraploid Oryza minuta, which is estimated to have formed less than one million years ago, along with its putative diploid progenitors (O. punctata and O. officinalis), are quite suitable for the study of polyploid genome evolution using a comparative genomics approach. RESULTS: Here, we performed a comparative study of a large genomic region surrounding the Shattering4 locus in O...
2014: BMC Genomics
Namiki Mitani-Ueno, Hisao Ogai, Naoki Yamaji, Jian Feng Ma
Cultivated rice (Oryza sativa) accumulates high concentration of silicon (Si), which is required for its high and sustainable production. High Si accumulation in cultivated rice is achieved by a high expression of both influx (Lsi1) and efflux (Lsi2) Si transporters in roots. Herein, we physiologically investigated Si uptake, isolated and functionally characterized Si transporters in six wild rice species with different genome types. Si uptake by the roots was lower in Oryza rufipogon, Oryza barthii (AA genome), Oryza australiensis (EE genome) and Oryza punctata (BB genome), but similar in Oryza glumaepatula and Oryza meridionalis (AA genome) compared with the cultivated rice (cv...
July 2014: Physiologia Plantarum
R Velusamy, B Thayumanavan, S Sadasivam
Rice plant volatiles extracted as steam distillates significantly affected the behavior of the rice leaffolder,Cnaphalocrocis medinalis (Guenée). Leaffolder moths laid significantly fewer eggs on TN1 rice plants treated with extracts of resistant wild species of rice,Oryza officinalis andOryza punctata, than on TN1 plants treated with extracts of resistant cultivated rices. Extracts ofO. officinalis andO. punctata adversely affected egg hatchability.O. officinalis andO. punctata extracts were more toxic to first-instar larvae than extracts of other resistant varieties...
July 1990: Journal of Chemical Ecology
A Kanno, A Hirai
Chloroplast DNAs (ctDNAs) were prepared from the mature green leaves of three species in the genus Oryza, namely, O. punctata (genome type BB), O. offici-nalis (CC), and O. australiensis (EE). After digestion with restriction enzymes, ctDNAs were cloned into a lambda phage vector and overlapping clone banks of the entire chloroplast genome from each of the three Oryza species were obtained. BamHI and PstI restriction maps of the ctDNAs were constructed, and the structures of the ctDNAs from O. sativa and the other three Oryza species were compared...
April 1992: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Z Y Wang, G Second, S D Tanksley
Ninety-three accessions representing 21 species from the genus Oryza were examined for restriction fragment length polymorphism. The majority (78%) of the accessions, for which five individuals were tested, were found to be monomorphic. Most of the polymorphic accessions segregated for only one or two probes and appeared to be mixed pure lines. For most of the Oryza species tested, the majority of the genetic variation (83%) was found between accessions from different species with only 17% between accessions within species...
March 1992: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Ting Zhu, Ping-Zhen Xu, Jiang-Peng Liu, Sheng Peng, Xin-Chun Mo, Li-Zhi Gao
Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding when and how they diversified have long been an issue of extensive interest but remain a mystery. Here, a data set comprising >60 kb of 53 singleton fragments and 16 intergenic regions is used to perform phylogenomic analyses of all eight AA- genome species plus four diploid Oryza species with BB-, CC-, EE- and GG- genomes...
January 2014: Molecular Phylogenetics and Evolution
Chengjun Zhang, Jun Wang, Nicholas C Marowsky, Manyuan Long, Rod A Wing, Chuanzhu Fan
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...
2013: Genome Biology and Evolution
Shao-An Fang, Tien-Inn Eu, Mei-Chu Chung
Wild species of rice with many valuable agronomic traits are an important genetic resource for improving cultivated rice by wide hybridization. Genome- or chromosome-specific markers are useful for monitoring genome introgression and for identifying genome components. From 47 random amplified polymorphic DNAs (RAPDs) of nine Oryza species, three bands (Ogla225, Opun225, and Opun246) were found to be genome specific with distinct sizes. Their specificities were further characterized by Southern hybridization, sequence analysis, and fluorescent in situ hybridization (FISH)...
September 2011: Plant Science: An International Journal of Experimental Plant Biology
Zhixi Tian, Yanjun Yu, Feng Lin, Yeisoo Yu, Phillip J Sanmiguel, Rod A Wing, Susan R McCouch, Jianxin Ma, Scott A Jackson
BACKGROUND: Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented. RESULTS: We previously identified a hotspot for genic rearrangement and transposon accumulation in the Orp region of Asian rice (Oryza sativa, AA) by comparison with its orthologous region in sorghum...
2011: BMC Genomics
Ryo Ishikawa, Takayuki Ohnishi, Yuki Kinoshita, Mitsugu Eiguchi, Nori Kurata, Tetsu Kinoshita
In angiosperms, interspecific crosses often display hybrid incompatibilities that are manifested as under-proliferation or over-proliferation of endosperm. Recent analyses using crosses between Arabidopsis thaliana and its related species with different ploidy levels have shown that interspecific hybridization causes delayed developmental transition and increased mitotic activity in the endosperm. In this study, we investigated endosperm development in interspecific crosses between diploid Oryza species. In a cross between female O...
March 2011: Plant Journal: for Cell and Molecular Biology
Abhijit Sanyal, Jetty S S Ammiraju, Fei Lu, Yeisoo Yu, Teri Rambo, Jennifer Currie, Kristi Kollura, Hye-Ran Kim, Jinfeng Chen, Jianxin Ma, Phillip San Miguel, Chen Mingsheng, Rod A Wing, Scott A Jackson
Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice...
November 2010: Molecular Biology and Evolution
Baosheng Wang, Zhuoya Ding, Wei Liu, Jin Pan, Changbao Li, Song Ge, Daming Zhang
BACKGROUND: Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process. RESULTS: Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes...
2009: BMC Evolutionary Biology
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