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Oryza coarctata

Manas R Prusty, Sung-Ryul Kim, Ricky Vinarao, Frederickson Entila, James Egdane, Maria G Q Diaz, Kshirod K Jena
Cultivated rice ( Oryza sativa L.) is very sensitive to salt stress. So far a few rice landraces have been identified as a source of salt tolerance and utilized in rice improvement. These tolerant lines primarily use Na+ exclusion mechanism in root which removes Na+ from the xylem stream by membrane Na+ and K+ transporters, and resulted in low Na+ accumulation in shoot. Identification of a new donor source conferring high salt tolerance is imperative. Wild relatives of rice having wide genetic diversity are regarded as a potential source for crop improvement...
2018: Frontiers in Plant Science
Tapan Kumar Mondal, Hukam Chand Rawal, Kishor Gaikwad, Tilak Raj Sharma, Nagendra Kumar Singh
Oryza coarctata plant, collected from Sundarban delta of West Bengal, India,  has been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time the draft genome with the coverage of 85.71 %  and  deposited the raw data in NCBI SRA, with BioProject ID PRJNA396417.
2017: F1000Research
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
Tapan Kumar Mondal, Showkat Ahmad Ganie, Ananda Bhusan Debnath
Oryza coarctata, a halophyte and wild relative of rice, is grown normally in saline water. MicroRNAs (miRNAs) are non-coding RNAs that play pivotal roles in every domain of life including stress response. There are very few reports on the discovery of salt-responsive miRNAs from halophytes. In this study, two small RNA libraries, one each from the control and salt-treated (450 mM NaCl for 24 h) leaves of O. coarctata were sequenced, which yielded 338 known and 95 novel miRNAs. Additionally, we used publicly available transcriptomics data of O...
2015: PloS One
N B Jelodar, N W Blackhall, T P Hartman, D S Brar, G Khush, M R Davey, E C Cocking, J B Power
Somatic hybrid plants were obtained following the electrofusion of rice (Oryza sativa L. cv 'Taipei 309', 2n = 2x = 24) cell suspension-derived protoplasts with non-dividing leaf protoplasts of Porteresia coarctata (2n = 4x = 48), a saline-tolerant wild species. Fusion-treated protoplasts were plated on the surface of cellulose nitrate filter membranes, overlaying Lolium multiflorum nurse cells. The nurse cells were embedded in KPR medium containing 0.5 mg l(-1) 2,4-dichlorophenoxyacetic acid and semi-solidified with SeaPlaque agarose...
August 1999: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Xu Zeng, Zhengrong Yuan, Xin Tong, Qiushi Li, Weiwei Gao, Minjian Qin, Zhihua Liu
Oryzoideae (Poaceae) plants have economic and ecological value. However, the phylogenetic position of some plants is not clear, such as Hygroryza aristata (Retz.) Nees. and Porteresia coarctata (Roxb.) Tateoka (syn. Oryza coarctata). Comprehensive molecular phylogenetic studies have been carried out on many genera in the Poaceae. The different DNA sequences, including nuclear and chloroplast sequences, had been extensively employed to determine relationships at both higher and lower taxonomic levels in the Poaceae...
May 2012: Molecular Biology Reports
Song Ge, Ang Li, Bao-Rong Lu, Shou-Zhou Zhang, De-Yuan Hong
Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for 26 species representing 11 genera of the tribe Oryzeae and three outgroup species. The sequenced fragments varied from 1522 base pairs (bp) to 1534 bp in length with 15.4% variable and 7.9% phylogenetically informative sites when the outgroups were excluded. The aligned sequences were analyzed by maximum parsimony and neighbor-joining methods. Analyses of the sequence data indicated that species of Oryzeae form a strongly supported monophyletic group, concordant with previous morphological and anatomical evidence...
December 2002: American Journal of Botany
N Rameshkumar, Cathrin Sproer, Elke Lang, Sudha Nair
The taxonomic status of a nitrogen-fixing bacterium, strain MSSRF38(T), isolated from the rhizosphere of mangrove-associated wild rice (Porteresia coarctata Tateoka), in Pichavaram, India, was studied using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel strain MSSRF38(T) was most closely related to Vibrio ruber DSM 16370(T) (98.3% gene sequence similarity), Vibrio rhizosphaerae DSM 18581(T) (98.2% sequence similarity) and <96% to the remaining Vibrio species...
June 2010: FEMS Microbiology Letters
Sudipta Ray, Barunava Patra, Aparajita Das-Chatterjee, Arnab Ganguli, Arun Lahiri Majumder
The gene coding for rice chloroplastic L-myo-inositol-1-phosphate synthase (MIPS; EC has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive approximately 60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome...
April 2010: Planta
Sonali Sengupta, Arun Lahiri Majumder
Porteresia coarctata (Syn = Oryza coarctata) is a tetraploid wild rice growing abundantly in the coastal region of India and some other Asian countries. The salt tolerance property of this mangrove associate has been dealt with by a number of workers earlier. The distinct morphology and leaf architecture enabling the plant to exclude salt is a characteristic feature of Porteresia in comparison with Oryza sp. A number of genes have been isolated and characterized from Porteresia that are related to the salt-tolerance property of the plant...
April 2010: Plant, Cell & Environment
N Rameshkumar, Elke Lang, Sudha Nair
A facultatively anaerobic, nitrogen-fixing bacterium, strain MSSRF40(T), was isolated from roots of mangrove-associated wild rice (Porteresia coarctata Tateoka). On the basis of 16S rRNA gene sequence similarities, strain MSSRF40(T) was shown to belong to the family Enterobacteriaceae, most closely related to Cronobacter muytjensii E603(T) (97.2 % sequence similarity), Enterobacter cloacae subsp. dissolvens LMG 2683(T) (97.1 %), E. radicincitans D5/23(T) (97.1 %) and E. ludwigii EN-119(T) (97.0 %). Sequence analysis of rpoB, gyrB and hsp60 genes showed that strain MSSRF40(T) had relatively low sequence similarity (<91, <84 and <90 %) to recognized species of different genera of the family Enterobacteriaceae and formed an independent phyletic lineage in all phylogenetic analyses using the 16S rRNA, rpoB, gyrB and hsp60 genes, clearly indicating that strain MSSRF40(T) could not be affiliated to any of the recognized genera within the family Enterobacteriaceae...
January 2010: International Journal of Systematic and Evolutionary Microbiology
Fei Lu, Jetty S S Ammiraju, Abhijit Sanyal, Shengli Zhang, Rentao Song, Jinfeng Chen, Guisheng Li, Yi Sui, Xiang Song, Zhukuan Cheng, Antonio Costa de Oliveira, Jeffrey L Bennetzen, Scott A Jackson, Rod A Wing, Mingsheng Chen
Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza, this comparative approach can be used to investigate gene function, genome evolution, domestication, polyploidy, and ecological adaptation. A large genomic region surrounding the MONOCULM1 (MOC1) locus was chosen for study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Sequencing and annotation of 18 bacterial artificial chromosome clones for these species revealed highly conserved gene colinearity and structure in the MOC1 region...
February 10, 2009: Proceedings of the National Academy of Sciences of the United States of America
Sonali Sengupta, Arun Lahiri Majumder
Salinity poses a serious threat to yield performance of cultivated rice in South Asian countries. To understand the mechanism of salt-tolerance of the wild halophytic rice, Porteresia coarctata in contrast to the salt-sensitive domesticated rice Oryza sativa, we have compared P. coarctata with the domesticated O. sativa rice varieties under salinity stress with respect to several physiological parameters and changes in leaf protein expression. P. coarctata showed a better growth performance and biomass under salinity stress...
March 2009: Planta
Sonali Sengupta, Barunava Patra, Sudipta Ray, Arun Lahiri Majumder
Methylated inositol D-pinitol (3-O-methyl-D-chiro-inositol) accumulates in a number of plants naturally or in response to stress. Here, we present evidence for accumulation and salt-enhanced synthesis of pinitol in Porteresia coarctata, a halophytic wild rice, in contrast to its absence in domesticated rice. A cDNA for Porteresia coarctata inositol methyl transferase 1 (PcIMT1), coding for the inositol methyl transferase implicated in the synthesis of pinitol has been cloned from P. coarctata, bacterially overexpressed and shown to be functional in vitro...
October 2008: Plant, Cell & Environment
N Rameshkumar, Youhei Fukui, Tomoo Sawabe, Sudha Nair
Two facultatively anaerobic, nitrogen-fixing bacteria (strains MSSRF30(T) and MSSRF31) were isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka). These strains were determined to be nitrogen-fixers using the acetylene reduction assay and by PCR detection of a nifH gene amplicon. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel strains were most closely related to Vibrio fluvialis LMG 7894(T) (96.8 % gene sequence similarity), Vibrio furnissii LMG 7910(T) (96...
July 2008: International Journal of Systematic and Evolutionary Microbiology
N Ramesh Kumar, Sudha Nair, Stefan Langer, Hans-Jürgen Busse, Peter Kämpfer
A Gram-negative, rod-shaped, non-spore-forming organism, strain MSSRF26T, was isolated from mangrove-associated wild rice in India. On the basis of 16S rRNA gene sequence similarities, strain MSSRF26T was shown to belong to the Alphaproteobacteria, most closely related to Altererythrobacter luteolus and Altererythrobacter epoxidivorans (96.1 and 95.9 % similarity to the respective type strains). Chemotaxonomic data [major ubiquinones Q-10 (91 %) and Q-9 (9 %); major polyamine spermidine, with putrescine, cadaverine and spermine detected only in trace amounts; major polar lipids phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid; major fatty acid C18 : 1 omega 7c and C(14 : 0) 2-OH as hydroxylated fatty acid] supported the affiliation of MSSRF26T to the genus Altererythrobacter...
April 2008: International Journal of Systematic and Evolutionary Microbiology
Srinivasan Bharathkumar, Diby Paul, Sudha Nair
A study was conducted to understand the complexity of bacterial diversity of rhizosphere of Porteresia coarctata based on culture dependent method. A large number of bacteria were isolated on nutrient agar medium supplemented with 1% NaCl and the dominant ones were further analyzed with PCR-RFLP method. The sequence analyses of the dominant strains revealed that most of the sequences belonged to members of gamma proteobacteria, firmicutes, bacteroidetes and uncultured bacteria. The phylogenetic analysis of 16S rRNA gene sequences revealed close relationships to a wide range of clones or bacterial species of various divisions...
February 2008: Journal of Basic Microbiology
N Ramesh Kumar, Sudha Nair
Two novel red-pigmented Vibrio strains, MSSRF3(T) and MSSRF10, with antibacterial activity against phytopathogens were isolated from the rhizosphere region of mangrove-associated wild rice (Porteresia coarctata Tateoka), in Pichavaram, India. The cells were Gram-negative, facultatively anaerobic and rod-shaped and were motile by means of single polar flagella. The two strains were catalase-positive and oxidase-negative, and were able to grow in 0.1-10 % NaCl (with optimum growth in 2 % NaCl) and at temperatures of 20-42 degrees C (optimum growth at 25-30 degrees C)...
October 2007: International Journal of Systematic and Evolutionary Microbiology
Andrea Zuccolo, Aswathy Sebastian, Jayson Talag, Yeisoo Yu, HyeRan Kim, Kristi Collura, Dave Kudrna, Rod A Wing
BACKGROUND: The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus...
2007: BMC Evolutionary Biology
Chandan Sahi, Amanjot Singh, Krishan Kumar, Eduardo Blumwald, Anil Grover
Significant progress has been made in unraveling the molecular biology of rice in the past two decades. Today, rice stands as a forerunner amongst the cereals in terms of details known on its genetics. Evidence show that salt tolerance in plants is a quantitative trait. Several traditional cultivars, landraces, and wild types of rice like Pokkali, CSR types, and Porteresia coarctata appear as promising materials for donation of requisite salt tolerance genes. A large number of quantitative trait loci (QTL) have been identified for salt tolerance in rice through generation of recombinant inbred lines and are being mapped using different types of DNA markers...
October 2006: Functional & Integrative Genomics
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