scholarly journals De NovoAssembly and Characterization ofOryza officinalisLeaf Transcriptome by Using RNA-Seq

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Ying Bao ◽  
Si Xu ◽  
Xiang Jing ◽  
Lu Meng ◽  
Zongyan Qin
Keyword(s):  
Wild Rice ◽  
De Novo ◽  
Sequence Similarity ◽  
Cultivated Rice ◽  
Protein Database ◽  
Next Generation Sequencing Technology ◽  
Functional Annotations ◽  
Wild Rice Species ◽  
Leaf Transcriptome ◽  
Clusters Of Orthologous Groups

Although endeavors have been made to identify useful wild rice genes that can be used to improve cultivated rice, the virtual reservoir of genetic variation hidden within the wild relatives of cultivated rice is largely untapped. Here, using next-generation sequencing technology, we investigated the leaf transcriptome of a wild riceO. officinaliswith CC genome. Approximately 23 million reads were produced in the species leaf transcriptome analysis andde novoassembly methods constructed 68,132 unigenes. Functional annotations for the unigenes were conducted using sequence similarity comparisons against the following databases: the nonredundant nucleotide database, the nonredundant protein database, the SWISS-PROT database, the Clusters of Orthologous Groups of proteins database, the Kyoto Encyclopedia of Genes and Genomes database, the Gene Ontology Consortium database, and the InterPro domains database. In addition, a total of 476 unigenes related to disease resistance were identified inO. officinalis, and these unigenes can serve as important genetic resources for cultivated rice breeding and quality improvement. The present study broadens our understanding of the genetic background of non-AA genomic wild rice species and it also provides a bridge to extend studies to otherOryzaspecies with CC genomes.

scholarly journals A Computational Strategy for Protein Function Assignment which Addresses the Multidomain Problem

2002 ◽  
Vol 3 (5) ◽  
pp. 423-440 ◽  
Author(s):  
A. J. Pérez ◽  
A. Rodríguez ◽  
O. Trelles ◽  
G. Thode
Keyword(s):  
Protein Function ◽  
Sequence Similarity ◽  
Protein Database ◽  
Specific Sequence ◽  
Functional Annotations ◽  
Cluster Set ◽  
Sequence Position ◽  
Computational Strategy ◽  
Function Assignment

A method for assigning functions to unknown sequences based on finding correlations between short signals and functional annotations in a protein database is presented. This approach is based on keyword (KW) and feature (FT) information stored in the SWISS-PROT database. The former refers to particular protein characteristics and the latter locates these characteristics at a specific sequence position. In this way, a certain keyword is only assigned to a sequence if sequence similarity is found in the position described by the FT field. Exhaustive tests performed over sequences with homologues (cluster set) and without homologues (singleton set) in the database show that assigning functions is much ’cleaner’ when information about domains (FT field) is used, than when only the keywords are used.

Whole grain morphology of Australian rice species

2009 ◽  
Vol 8 (1) ◽  
pp. 74-81 ◽  
Author(s):  
S. Kasem ◽  
D. L. E. Waters ◽  
N. Rice ◽  
F. M. Shapter ◽  
R. J. Henry
Keyword(s):  
Wild Rice ◽  
Grain Morphology ◽  
Whole Grain ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Wild Rice Species ◽  
Breeding Programmes ◽  
Standard Classification ◽  
Novel Alleles ◽  
Grain Colour

The grain morphology of 17 wild rice relatives were studied by light and scanning electron microscopy and compared to two cultivated rice varieties (Oryza sativa cv. Nipponbare and O. sativa cv. Teqing). Observations were made of the grain colour, size and shape. Grains from wild rice species exhibited a variety of colours that have potential aesthetic and nutritional value. The grains of these species exhibited a wide array of sizes and shapes, but still fell within the standard classification scale that rice breeders use for routine breeding evaluation. These results highlight the potential of these species as whole grain foods or as sources of novel alleles in conventional rice breeding programmes.

scholarly journals Enhancement of Rice Leaf Photosynthesis by Crossing between Cultivated Rice,Oryza sativaand Wild Rice Species,Oryza rufipogon

2004 ◽  
Vol 7 (3) ◽  
pp. 252-259 ◽  
Author(s):  
Chisato Masumoto ◽  
Takashige Ishii ◽  
Sono Kataoka ◽  
Tomoko Hatanaka ◽  
Naotsugu Uchida
Keyword(s):  
Wild Rice ◽  
Oryza Rufipogon ◽  
Leaf Photosynthesis ◽  
Cultivated Rice ◽  
Rice Leaf ◽  
Wild Rice Species

scholarly journals Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China

2016 ◽  
Author(s):  
Ying Wang ◽  
Kun Liu ◽  
De Bi ◽  
Biao Shou Zhou ◽  
Wen Jian Shao
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Sequence Similarity ◽  
Molecular Study ◽  
Sequence Information ◽  
Sequencing Data ◽  
Protein Database ◽  
Illumina Hiseq ◽  
Significant Similarity ◽  
Assembly Technology

Background. Resurrection plants constitute a unique cadre within angiosperms. Boea clarkeana Hemsl. (Boea, Gesneriaceae) is a desiccation-tolerant dicotyledonous herb that is endemic to China. Although research on angiosperms with DT could be instructive for crops, genomic resources for B. clarkeana remain scarce. In addition, transcriptome sequencing could be an effective way to study desiccation-tolerant plants. Methods. In the present study, we used the platform Illumina HiSeqTM 2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information obtained, we developed EST-SSR markers by means of EST-SSR mining, primer design and polymorphism identification. Results. A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana in this study. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to GO classifications and COG, respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with higher polymorphism rates were concentrated on dinucleotides, pentanucleotides and hexanucleotides. Finally, 17 pairs with highly polymorphic and stable loci were selected for polymorphism screening. There were a total of 65 alleles, with 2–6 alleles at each locus. Mainly due to the unique biological characteristics of plants, the HE, HO and PIC per locus were very low, ranging from 0 to 0.196, 0.082 to 0.14 and 0 to 0.155, respectively. Discussion. A substantial fraction transcriptome sequences of B. clarkeana were generated in this study, which is the first molecular-level analysis of this plant. These sequences are valuable resources for gene annotation and discovery and molecular marker development. These sequences could also provide a valuable basis for the future molecular study of B. clarkeana.

scholarly journals Comparison between wild and related cultivated rice species reveals strong impacts of crop domestication on methane metabolism of the rhizomicrobiome

2020 ◽  
Author(s):  
Lei Tian ◽  
Jingjing Chang ◽  
Shaohua Shi ◽  
Li Ji ◽  
Jianfeng Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Metabolism ◽  
Methane Production ◽  
Wild Rice ◽  
Nucleotide Metabolism ◽  
Cultivated Rice ◽  
Wild Rice Species ◽  
Methane Metabolism ◽  
First Time ◽  
Rice Domestication

Abstract Background Rice root-inhabited microbial communities are seriously affected by domestication as evidenced by comparing the rhizomicrobiomes of wild and related cultivated rice species. While earlier studies focused on the structures of the rhizomicrobiomes, here, we compared the functioning of the microbial communities in the rhizosphere of wild versus that of related cultivated rice species, which were originated from Africa and Asia. Results The microbial functions involved in carbon metabolism and nucleotide metabolism were found to be enriched in wild rice species, whereas those involved in nitrogen metabolism, lipid metabolism, metabolism of cofactors and vitamins, and xenobiotic biodegradation were more enriched in cultivated rice species. Among the overall carbon metabolism, specifically, methane metabolism of the rhizomicrobiomes clearly differed between wild and cultivated rice. The key enzymes in methane production and utilization were overrepresented in wild rice species, suggesting that the rhizomicrobiome of wild rice maintained a better ecological balance for methane production and utilization than the related cultivated rice species. Conclusions For the first time, the impacts of rice domestication on the main metabolic pathways of the rhizomicrobiome were assessed, which revealed the strong impacts of rice domestication on methane metabolism that is one of the most critical functions of the microbial community of the rhizosphere of rice. The results provide important guidelines for future breeding and cultivation of rice in the framework of more sustainable rice production.

scholarly journals SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation

2020 ◽  
Author(s):  
Wei Li ◽  
Kui Li ◽  
Ying Huang ◽  
Cong Shi ◽  
Wu-Shu Hu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Wild Rice ◽  
De Novo ◽  
Rice Genome ◽  
Gene Families ◽  
Oryza Rufipogon ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Cultivated Rice ◽  
Reproductive Process

AbstractAsian cultivated rice is believed to have been domesticated from an immediate ancestral progenitor, Oryza rufipogon, which provides promising sources of novel alleles for world rice improvement. Here we first present a high-quality de novo assembly of the typical O. rufipogon genome through the integration of single-molecule sequencing (SMRT), 10× and Hi-C technologies. This chromosome-based reference genome allows a multi-species comparative analysis of the annual selfing O. sativa and its two wild progenitors, the annual selfing O. nivara and perennial outcrossing O. rufipogon, identifying massive numbers of dispensable genes that are functionally enriched in reproductive process. Comparative genomic analyses identified millions of genomic variants, of which large-effect mutations (e.g., SVs, CNV and PAVs) may affect the variation of agronomically significant traits. We demonstrate how lineage-specific expansion of rice gene families may have contributed to the formation of reproduction isolation (e.g., the recognition of pollen and male sterility), thus brightening the role in driving mating system evolution during the evolutionary process of recent speciation. We document thousands of positively selected genes that are mainly involved in flower development, ripening, pollination, reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as crucial forces to govern substantial genomic alterations among the three rice species that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats. This first chromosome-based wild rice genome in the genus Oryza will become powerful to accelerate the exploration of untapped genomic diversity from wild rice for the enhancement of elite rice cultivars.

scholarly journals Spesies Padi Liar (Oryza sp.) sebagai Sumber Gen Ketahanan Cekaman Abiotik dan Biotik pada Padi Budidaya

2017 ◽  
Vol 35 (4) ◽  
pp. 197
Author(s):  
Tintin Suhartini
Keyword(s):  
Resistance Gene ◽  
Resistance Genes ◽  
Abiotic Stresses ◽  
Wild Rice ◽  
Brown Planthopper ◽  
Cultivated Rice ◽  
Biotic And Abiotic Stresses ◽  
Rice Varieties ◽  
Wild Rice Species ◽  
Oryza Meyeriana

<p>ABSTRACT<br />Wild rice species could be used  for improvement of rice varieties because they have a good character for resistance to biotic and abiotic stresses. Some of Indonesian wild rice species are Oryza meyeriana, O. granulata, O. longiglumis, O. officinalis, O. ridleyi, O. rufipogon and O. schlechteri. IRRI has a collection of 2,500 accesions of wild rice and 18 species were collected in ICABIOGRAD, Bogor. Some species of wild rice are known to have resistance genes to biotic and abiotic stresses. A number of<br />accessions of O.  officinalis contained resistance gene to brown planthopper, blast disease, bacterial leaf blight (BLB) and sheath rot. One of the species that has resistance to pests and diseases is O. minuta. The resistance to tungro virus occurs in O. punctata. Tolerance to drought, Al and Fe toxicities occurs in wild rice species of O. sativa genome AA group. Resistance genes from wild rice species can be inserted into cultivated rice through conventional techniques in combination with biotechnology, while gene transfer and gene detection from wild rice to cultivated rice can be done through cross breeding, molecular markers, backcrossing and embryo rescue. The success of introgression of resistance genes from wild rice species to cultivated rice will increase genetic diversity of rice. As an example O. minuta has been implemented in introgression of BLB resistance gene on IR64. Introgression of O. nivara gene in IRRI had improved some superior rice varieties in Indonesia, namely IR30, IR32, IR34, IR36 and IR38, which were tolerant to brown planthopper, dwarf virus and bacterial leaf blight. Oryza rufipogon wich has BLB and blast resistance gene has been used for improvement of new varieties Inpari Blas and Inpari HDB which were released in 2013.<br />Keywords: Oryza spp., varietal improvement, resistance genes, biotic stresses, abiotic stresses</p><p>Abstrak</p><p>Spesies padi liar dapat dimanfaatkan dalam perakitan varietas unggul karena memiliki gen ketahanan terhadap cekaman biotik dan abiotik. Spesies padi liar yang ada di Indonesia adalah Oryza meyeriana, O. granulata, O. longiglumis, O. officinalis, O. ridleyi, O. rufipogon, dan O. schlechteri. IRRI memiliki koleksi 2.500 aksesi padi liar dan 18 spesies dikoleksi di BB Biogen. Sejumlah aksesi O. officinalis memiliki gen ketahanan terhadap wereng coklat, penyakit blas, hawar daun bakteri (HDB), dan busuk pelepah. Salah satu spesies yang memiliki ketahanan terhadap hama-penyakit tersebut adalah O. minuta. Ketahanan terhadap virus tungro terdapat pada O. punctata. Toleransi terhadap kekeringan, keracunan Al, dan Fe terdapat pada spesies padi liar kelompok O. sativa genom AA. Gen ketahanan dari spesies padi liar dapat dimasukkan (introgresi) ke dalam padi budi daya melalui teknik konvensional yang dikombinasikan dengan bioteknologi, sementara transfer gen dapat melalui persilangan, marka molekuler, silang balik, dan penyelamatan embrio. Keberhasilan introgresi gen ketahanan dari spesies padi liar ke padi budi daya akan meningkatkan keragaman genetik tanaman. Spesies padi liar O. minuta telah dimanfaatkan dalam introgresi gen ketahanan HDB pada varietas IR64. Introgresi gen asal O. nivara di IRRI menambah varietas unggul di Indonesia, yaitu IR30, IR32, IR34, IR36, dan IR38, yang toleran terhadap wereng coklat, virus kerdil rumput, dan HDB. Spesies padi liar O. rufipogon yang memiliki gen ketahanan HDB dan blas telah digunakan dalam pembentukan varietas unggul baru Inpari HDB dan Inpari Blas yang dilepas pada 2013.<br /><br /></p>

scholarly journals Endophytic Colonization and In Planta Nitrogen Fixation by a Herbaspirillum sp. Isolated from Wild Rice Species

2001 ◽  
Vol 67 (11) ◽  
pp. 5285-5293 ◽  
Author(s):  
Adel Elbeltagy ◽  
Kiyo Nishioka ◽  
Tadashi Sato ◽  
Hisa Suzuki ◽  
Bin Ye ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Wild Rice ◽  
Fluorescent Protein ◽  
In Planta ◽  
Cultivated Rice ◽  
Phenotypic Properties ◽  
Rice Varieties ◽  
Bacterial Populations ◽  
Rdna Sequences ◽  
Wild Rice Species

ABSTRACT Nitrogen-fixing bacteria were isolated from the stems of wild and cultivated rice on a modified Rennie medium. Based on 16S ribosomal DNA (rDNA) sequences, the diazotrophic isolates were phylogenetically close to four genera: Herbaspirillum,Ideonella, Enterobacter, andAzospirillum. Phenotypic properties and signature sequences of 16S rDNA indicated that three isolates (B65, B501, and B512) belong to the Herbaspirillum genus. To examine whether Herbaspirillum sp. strain B501 isolated from wild rice, Oryza officinalis, endophytically colonizes rice plants, the gfp gene encoding green fluorescent protein (GFP) was introduced into the bacteria. Observations by fluorescence stereomicroscopy showed that the GFP-tagged bacteria colonized shoots and seeds of aseptically grown seedlings of the original wild rice after inoculation of the seeds. Conversely, for cultivated rice Oryza sativa, no GFP fluorescence was observed for shoots and only weak signals were observed for seeds. Observations by fluorescence and electron microscopy revealed that Herbaspirillum sp. strain B501 colonized mainly intercellular spaces in the leaves of wild rice. Colony counts of surface-sterilized rice seedlings inoculated with the GFP-tagged bacteria indicated significantly more bacterial populations inside the original wild rice than in cultivated rice varieties. Moreover, after bacterial inoculation, in planta nitrogen fixation in young seedlings of wild rice, O. officinalis, was detected by the acetylene reduction and 15N2gas incorporation assays. Therefore, we conclude thatHerbaspirillum sp. strain B501 is a diazotrophic endophyte compatible with wild rice, particularly O. officinalis.

scholarly journals Rubisco activity, electron transport rate, and leaf features drive high photosynthesis rate in the selected wild rice

2019 ◽  
Author(s):  
Jyotirmaya Mathan ◽  
Anuradha Singh ◽  
Vikram Jathar ◽  
Aashish Ranjan
Keyword(s):  
Electron Transport ◽  
Wild Rice ◽  
Electron Transport Rate ◽  
Transport Rate ◽  
Leaf Photosynthesis ◽  
Cultivated Rice ◽  
Rubisco Activity ◽  
Rice Varieties ◽  
Mesophyll Cells ◽  
Wild Rice Species

AbstractThe importance of increasing photosynthetic efficiency for sustainable crop yield increases to feed the growing world population is well recognized. The natural genetic variation for leaf photosynthesis in crop plants is largely unexploited for increasing genetic yield potential. The genus Oryza, including cultivated rice and wild relatives, offers tremendous genetic variability to explore photosynthetic differences, and underlying biochemical, photochemical, and developmental basis. We quantified leaf photosynthesis and related physiological parameters for six cultivated and three wild rice genotypes, and identified photosynthetically efficient wild rice species. Fitting A/Ci curves followed by experimental validation showed that the leaf photosynthesis in cultivated rice varieties, IR64 and Nipponbare, was limited due to Rubisco activity and electron transport rate, compared to photosynthetically efficient wild rice species, Oryza australiensis and Oryza latifolia. The selected wild rice species with high leaf photosynthesis per unit area had striking anatomical features, such as larger mesophyll cells with more chloroplasts, larger and closer veins, and fewer mesophyll cells between two consecutive veins. Our results show the existence of desirable variations in Rubisco activity, electron transport rate, and mesophyll and vein features in the rice system itself that could possibly be targeted for increasing the photosynthetic efficiency of cultivated rice varieties.HighlightDistinct leaf biochemical, photochemical, and developmental features contribute to efficient photosynthesis in the selected wild rice that could potentially be exploited for increasing rice leaf photosynthesis.

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