The Experts below are selected from a list of 17421 Experts worldwide ranked by ideXlab platform
Yan Wang - One of the best experts on this subject based on the ideXlab platform.
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de novo taproot transcriptome sequencing and analysis of major genes involved in sucrose metabolism in radish raphanus sativus l
Frontiers in Plant Science, 2016Co-Authors: Rugang Yu, Ronghua Wang, Liang Xu, Yan Wang, Wei Zhang, Benard KaranjaAbstract:Radish (Raphanus sativus L.) is an important annual or biennial root vegetable crop. The fleshy taproot comprises the main edible portion of the plant with high nutrition and medical value. Molecular biology study of radish begun rather later, and lacks sufficient transcriptomic and genomic data in pubic databases for understanding of the molecular mechanism during the radish taproot formation. To develop a comprehensive overview of the ‘NAU-YH’ root transcriptome, a cDNA library, prepared from three equally mixed RNA of taproots at different developmental stages including pre-cortex splitting stage, cortex splitting stage and expanding stages was sequenced using high-throughput Illumina RNA sequencing. From approximately 51 million clean reads, a total of 70,168 unigene with a total length of 50.28 Mb, an average length of 717 bp and a N50 of 994 bp were obtained. In total, 63,991 (about 91.20% of the assembled Unigenes) Unigenes were successfully annotated in five public databases including NR, GO, COG, KEGG and Nt. GO term analysis revealed that the majority of these Unigenes were predominately involved in basic physiological and metabolic processes, catalytic, binding and cellular process.In addition, a total of 103 Unigenes encoding eight enzymes in the sucrose metabolism related pathways were also identified by KEGG pathways analysis. Sucrose synthase (29 Unigenes), invertase (17 Unigenes), sucrose-phosphate synthase (16 Unigenes), fructokinase (16 Unigenes) and hexokinase (11 Unigenes) ranked top five enzymes in these eight key enzymes. From which, two genes (RsSuSy1, RsSPS1) were validated by T-A cloning and sequenced in radish, while six Unigenes were validated by RT-qPCR analysis. These results would be served as an important public reference platform to identify the related key genes during taproot thickening and facilitate the revealing of molecular mechanisms underlying taproot thickening in radish.
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de novo transcriptome sequencing of radish raphanus sativus l and analysis of major genes involved in glucosinolate metabolism
BMC Genomics, 2013Co-Authors: Rugang Yu, Liang Xu, Yan Wang, Lulu Zhai, Yiqin GongAbstract:Radish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish. In this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 Unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled Unigenes) Unigenes exhibit similarity (e –value ≤ 1.0e-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling. The ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during taproot formation in radish.
Rugang Yu - One of the best experts on this subject based on the ideXlab platform.
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de novo taproot transcriptome sequencing and analysis of major genes involved in sucrose metabolism in radish raphanus sativus l
Frontiers in Plant Science, 2016Co-Authors: Rugang Yu, Ronghua Wang, Liang Xu, Yan Wang, Wei Zhang, Benard KaranjaAbstract:Radish (Raphanus sativus L.) is an important annual or biennial root vegetable crop. The fleshy taproot comprises the main edible portion of the plant with high nutrition and medical value. Molecular biology study of radish begun rather later, and lacks sufficient transcriptomic and genomic data in pubic databases for understanding of the molecular mechanism during the radish taproot formation. To develop a comprehensive overview of the ‘NAU-YH’ root transcriptome, a cDNA library, prepared from three equally mixed RNA of taproots at different developmental stages including pre-cortex splitting stage, cortex splitting stage and expanding stages was sequenced using high-throughput Illumina RNA sequencing. From approximately 51 million clean reads, a total of 70,168 unigene with a total length of 50.28 Mb, an average length of 717 bp and a N50 of 994 bp were obtained. In total, 63,991 (about 91.20% of the assembled Unigenes) Unigenes were successfully annotated in five public databases including NR, GO, COG, KEGG and Nt. GO term analysis revealed that the majority of these Unigenes were predominately involved in basic physiological and metabolic processes, catalytic, binding and cellular process.In addition, a total of 103 Unigenes encoding eight enzymes in the sucrose metabolism related pathways were also identified by KEGG pathways analysis. Sucrose synthase (29 Unigenes), invertase (17 Unigenes), sucrose-phosphate synthase (16 Unigenes), fructokinase (16 Unigenes) and hexokinase (11 Unigenes) ranked top five enzymes in these eight key enzymes. From which, two genes (RsSuSy1, RsSPS1) were validated by T-A cloning and sequenced in radish, while six Unigenes were validated by RT-qPCR analysis. These results would be served as an important public reference platform to identify the related key genes during taproot thickening and facilitate the revealing of molecular mechanisms underlying taproot thickening in radish.
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de novo transcriptome sequencing of radish raphanus sativus l and analysis of major genes involved in glucosinolate metabolism
BMC Genomics, 2013Co-Authors: Rugang Yu, Liang Xu, Yan Wang, Lulu Zhai, Yiqin GongAbstract:Radish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish. In this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 Unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled Unigenes) Unigenes exhibit similarity (e –value ≤ 1.0e-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling. The ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during taproot formation in radish.
Zhifen Pan - One of the best experts on this subject based on the ideXlab platform.
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RESEARCH ARTICLE RNA-Seq Based Identification of Candidate Parasitism Genes of Cereal Cyst Nematode (Heterodera avenae) during Incompatible Infection to Aegilops variabilis
2016Co-Authors: Minghui Zheng, Hai Long, Guangbing Deng, Yun Zhao, Haili Zhang, Feng Liu, Zhifen PanAbstract:One of the reasons for the progressive yield decline observed in cereals production is the rapid build-up of populations of the cereal cyst nematode (CCN, Heterodera avenae). These nematodes secrete so-call effectors into their host plant to suppress the plant defense responses, alter plant signaling pathways and then induce the formation of syncytium after infection. However, little is known about its molecular mechanism and parasitism during incompatible infection. To gain insight into its repertoire of parasitism genes, we investi-gated the transcriptome of the early parasitic second-stage (30 hours, 3 days and 9 days post infection) juveniles of the CCN as well as the CCN infected tissue of the host Aegilops variabilis by Illumina sequencing. Among all assembled Unigenes, 681 putative genes of parasitic nematode were found, in which 56 putative effectors were identified, including novel pioneer genes and genes corresponding to previously reported effectors. All the 681 CCN Unigenes were mapped to 229 GO terms and 200 KEGG pathways, including growth, development and several stimulus-related signaling pathways. Sixteen clusters were involved in the CCN unigene expression atlas at the early stages during infection process
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rna seq based identification of candidate parasitism genes of cereal cyst nematode heterodera avenae during incompatible infection to aegilops variabilis
PLOS ONE, 2015Co-Authors: Minghui Zheng, Hai Long, Guangbing Deng, Yun Zhao, Haili Zhang, Feng Liu, Zhifen PanAbstract:One of the reasons for the progressive yield decline observed in cereals production is the rapid build-up of populations of the cereal cyst nematode (CCN, Heterodera avenae). These nematodes secrete so-call effectors into their host plant to suppress the plant defense responses, alter plant signaling pathways and then induce the formation of syncytium after infection. However, little is known about its molecular mechanism and parasitism during incompatible infection. To gain insight into its repertoire of parasitism genes, we investigated the transcriptome of the early parasitic second-stage (30 hours, 3 days and 9 days post infection) juveniles of the CCN as well as the CCN infected tissue of the host Aegilops variabilis by Illumina sequencing. Among all assembled Unigenes, 681 putative genes of parasitic nematode were found, in which 56 putative effectors were identified, including novel pioneer genes and genes corresponding to previously reported effectors. All the 681 CCN Unigenes were mapped to 229 GO terms and 200 KEGG pathways, including growth, development and several stimulus-related signaling pathways. Sixteen clusters were involved in the CCN unigene expression atlas at the early stages during infection process, and three of which were significantly gene-enriched. Besides, the protein-protein interaction network analysis revealed 35 node Unigenes which may play an important role in the plant-CCN interaction. Moreover, in a comparison of differentially expressed genes between the pre-parasitic juveniles and the early parasitic juveniles, we found that hydrolase activity was up-regulated in pre J2s whereas binding activity was upregulated in infective J2s. RT-qPCR analysis on some selected genes showed detectable expression, indicating possible secretion of the proteins and putative role in infection. This study provided better insights into the incompatible interaction between H. avenae and the host plant Ae. varabilis. Moreover, RNAi targets with potential lethality were screened out and primarily validated, which provide candidates for engineering-based control of cereal cyst nematode in crops breeding.
Melvin G. Mcinnis - One of the best experts on this subject based on the ideXlab platform.
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Trapping and sequence analysis of 1138 putative exons from human chromosome 18
Molecular Psychiatry, 2003Co-Authors: N. Wang, Francis J Mcmahon, Dean F Mackinnon, James B. Potash, Pamela Sklar, Christopher A Ross, Stylianos E Antonarakis, J Raymond Depaulo, Melvin G. McinnisAbstract:In a search for novel genes on chromosome 18 (HC18), on which several regions have been linked to bipolar disorder, we applied exon trapping to HC18-specific cosmids. Among the 1138 exons trapped, 1052 of them have been mapped to HC18, and the remaining 86 have not been localized. No exons were localized to genomic regions other than HC18. BLAST database search revealed that 190 exons were identical to 98 Unigenes on HC18; 98 identical to additional 82 clusters of ESTs not present in the HC18 Unigene set; 39 homologous to genes from human and other species ( e
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trapping and sequence analysis of 1138 putative exons from human chromosome 18
Molecular Psychiatry, 2003Co-Authors: N. Wang, Raymond J. Depaulo, Francis J Mcmahon, Dean F Mackinnon, James B. Potash, Pamela Sklar, Christopher A Ross, Stylianos E Antonarakis, Melvin G. McinnisAbstract:In a search for novel genes on chromosome 18 (HC18), on which several regions have been linked to bipolar disorder, we applied exon trapping to HC18-specific cosmids. Among the 1138 exons trapped, 1052 of them have been mapped to HC18, and the remaining 86 have not been localized. No exons were localized to genomic regions other than HC18. BLAST database search revealed that 190 exons were identical to 98 Unigenes on HC18; 98 identical to additional 82 clusters of ESTs not present in the HC18 Unigene set; 39 homologous to genes from human and other species (e<10(-3)); and the remaining 811 exons had no significant homology to transcripts in public databases. The mapped exons were compared to the 867 annotated genes on HC18 in the Celera databases; 216 exons were identical to 104 Celera 'genes' and the remaining 836 exons were not found in the Celera databases. On average, there were two exons for a matched transcript (known genes and ESTs). Therefore, the 850 novel exons may represent hundreds of novel genes on chromosome 18.
Prakash C Sharma - One of the best experts on this subject based on the ideXlab platform.
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expressed sequence tag based identification and expression analysis of some cold inducible elements in seabuckthorn hippophae rhamnoides l
Plant Physiology and Biochemistry, 2012Co-Authors: Rajesh Ghangal, Saurabh Raghuvanshi, Prakash C SharmaAbstract:A cDNA library was constructed from the mature leaves of seabuckthorn (Hippophae rhamnoides). Expressed Sequence Tags (ESTs) were generated by single pass sequencing of 4500 cDNA clones. We submitted 3412 ESTs to dbEST of NCBI. Clustering of these ESTs yielded 1665 Unigenes comprising of 345 contigs and 1320 singletons. Out of 1665 Unigenes, 1278 Unigenes were annotated by similarity search while the remaining 387 unannotated Unigenes were considered as organism specific. Gene Ontology (GO) analysis of the unigene dataset showed 691 Unigenes related to biological processes, 727 to molecular functions and 588 to cellular component category. On the basis of similarity search and GO annotation, 43 Unigenes were found responsive to biotic and abiotic stresses. To validate this observation, 13 genes that are known to be associated with cold stress tolerance from previous studies in Arabidopsis and 3 novel transcripts were examined by Real time RT-PCR to understand the change in expression pattern under cold/freeze stress. In silico study of occurrence of microsatellites in these ESTs revealed the presence of 62 Simple Sequence Repeats (SSRs), some of which are being explored to assess genetic diversity among seabuckthorn collections. This is the first report of generation of transcriptome data providing information about genes involved in managing plant abiotic stress in seabuckthorn, a plant known for its enormous medicinal and ecological value.
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mining functional microsatellites in legume Unigenes
Bioinformation, 2011Co-Authors: Manish Roorkiwal, Prakash C SharmaAbstract:Highly polymorphic and transferable microsatellites (SSRs) are important for comparative genomics, genome analysis and phylogenetic studies. Development of novel species-specific microsatellite markers remains a costly and labor-intensive project. Therefore, interest has been shifted from genomic to genic markers owing to their high inter-species transferability as they are developed from conserved coding regions of the genome. This study concentrates on comparative analysis of genic microsatellites in nine important legume (Arachis hypogaea, Cajanus cajan, Cicer arietinum, Glycine max, Lotus japonicus, Medicago truncatula, Phaseolus vulgaris, Pisum sativum and Vigna unguiculata) and two model plant species (Oryza sativa and Arabidopsis thaliana). Screening of a total of 228090 putative unique sequences spanning 219610522 bp using a microsatellite search tool, MISA, identified 12.18% of the Unigenes containing 36248 microsatellite motifs excluding mononucleotide repeats. Frequency of legume unigene-derived SSRs was one SSR in every 6.0 kb of analyzed sequences. The trinucleotide repeats were predominant in all the Unigenes with the exception of C. cajan, which showed prevalence of dinucleotide repeats over trinucleotide repeats. Dinucleotide repeats along with trinucleotides counted for more than 90% of the total microsatellites. Among dinucleotide and trinucleotide repeats, AG and AAG motifs, respectively, were the most frequent. Microsatellite positive chickpea Unigenes were assigned Gene Ontology (GO) terms to identify the possible role of Unigenes in various molecular and biological functions. These unigene based microsatellite markers will prove valuable for recording allelic variance across germplasm collections, gene tagging and searching for putative candidate genes.
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ugmicrosatdb database for mining microsatellites from Unigenes
Nucleic Acids Research, 2007Co-Authors: Veenu Aishwarya, Prakash C SharmaAbstract:Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web-based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type (simple perfect, compound perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar), and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target Unigenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite. UgMicroSatdb is available at http://ipu.ac.in/usbt/UgMicroSatdb.htm.