The Experts below are selected from a list of 3006 Experts worldwide ranked by ideXlab platform
Xiurong Zhang - One of the best experts on this subject based on the ideXlab platform.
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sinbase an integrated database to study genomics genetics and comparative genomics in Sesamum indicum
Plant and Cell Physiology, 2015Co-Authors: Linhai Wang, Xiurong ZhangAbstract:Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/.
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development of simple sequence repeat ssr markers of sesame Sesamum indicum from a genome survey
Molecules, 2014Co-Authors: Xin Wei, Linhai Wang, Yanxin Zhang, Xiaoling Wang, Xia Ding, Jing Zhang, Xiurong ZhangAbstract:Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.
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development and characterization of 59 polymorphic cdna ssr markers for the edible oil crop Sesamum indicum pedaliaceae
American Journal of Botany, 2012Co-Authors: Linhai Wang, Yanxin Zhang, Yuan Gao, Xiurong ZhangAbstract:UNLABELLED PREMISE OF THE STUDY Polymorphic simple sequence repeat markers from transcript sequences (cDNA-simple sequence repeat [SSR]) were developed for the edible oil crop Sesamum indicum to facilitate the genetic study of this species. • METHODS AND RESULTS We found 7702 SSR loci in the 60960 unigenes, and 1550 primer pairs were designed and synthesized. In total, 59 primer pairs showed polymorphism within 36 individuals; the number of alleles per locus ranged from two to four, and the expected and observed heterozygosity ranged from 0.05 to 0.74 and 0 to 0.30, respectively. • CONCLUSIONS These polymorphic markers will greatly facilitate studies of the genetic structure of S. indicum populations as well as the identification and conservation of the species.
Linhai Wang - One of the best experts on this subject based on the ideXlab platform.
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the emerging oilseed crop Sesamum indicum enters the omics era
Frontiers in Plant Science, 2017Co-Authors: Xin Wei, Linhai Wang, Yanxin Zhang, Komivi Dossa, Diaga Diouf, Mareme Niang, Daniel Fonceka, Marie A MmadiAbstract:Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and QTLs for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an “orphan crop” to a “genomic resource-rich crop”. With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the “Omics” area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop.
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sinbase an integrated database to study genomics genetics and comparative genomics in Sesamum indicum
Plant and Cell Physiology, 2015Co-Authors: Linhai Wang, Xiurong ZhangAbstract:Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/.
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development of simple sequence repeat ssr markers of sesame Sesamum indicum from a genome survey
Molecules, 2014Co-Authors: Xin Wei, Linhai Wang, Yanxin Zhang, Xiaoling Wang, Xia Ding, Jing Zhang, Xiurong ZhangAbstract:Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.
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development and characterization of 59 polymorphic cdna ssr markers for the edible oil crop Sesamum indicum pedaliaceae
American Journal of Botany, 2012Co-Authors: Linhai Wang, Yanxin Zhang, Yuan Gao, Xiurong ZhangAbstract:UNLABELLED PREMISE OF THE STUDY Polymorphic simple sequence repeat markers from transcript sequences (cDNA-simple sequence repeat [SSR]) were developed for the edible oil crop Sesamum indicum to facilitate the genetic study of this species. • METHODS AND RESULTS We found 7702 SSR loci in the 60960 unigenes, and 1550 primer pairs were designed and synthesized. In total, 59 primer pairs showed polymorphism within 36 individuals; the number of alleles per locus ranged from two to four, and the expected and observed heterozygosity ranged from 0.05 to 0.74 and 0 to 0.30, respectively. • CONCLUSIONS These polymorphic markers will greatly facilitate studies of the genetic structure of S. indicum populations as well as the identification and conservation of the species.
Toshio Furumoto - One of the best experts on this subject based on the ideXlab platform.
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Biosynthesis of anthraquinone derivatives in a Sesamum indicum hairy root culture.
Bioscience biotechnology and biochemistry, 2017Co-Authors: Toshio Furumoto, Ryuta SatoAbstract:In order to investigate the intermediacy of 2-(4-methylpent-3-en-1-yl)anthraquinone (MPAQ), a possible intermediate for the biosynthesis of anthraquinone derivatives in sesame (Sesamum indicum), 2H-labeled MPAQ was administered to a hairy root culture of S. indicum. Efficient conversion of fed MPAQ to 2-[(Z)-4-methylpenta-1,3-dien-1-yl]anthraquinone ((Z)-MPDEAQ) was observed. Furthermore, administration experiment with 2H-labeled 2-geranyl-1,4-naphthohydroquinone, another possible intermediate, showed that it was converted to MPAQ and (Z)-MPDEAQ. The results clearly demonstrated that these substrates are the actual precursors for the production of (Z)-MPDEAQ. In contrast, neither MPAQ nor 2-geranyl-1,4-naphthohydroquinone was converted to anthrasesamone B and 2,3-epoxyanthrasesamone B, other anthraquinone derivatives in the hairy roots, suggesting that these substrates may not be the common precursors in the biosynthesis of anthraquinone derivatives.
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Biosynthetic origin of 2-geranyl-1,4-naphthoquinone and its related anthraquinone in a Sesamum indicum hairy root culture
Phytochemistry, 2011Co-Authors: Toshio Furumoto, Arata HoshikumaAbstract:Abstract In order to clarify the biosynthetic origin of 2-geranyl-1,4-naphthoquinone and its biogenetically related anthraquinone, which are possible intermediates of anthrasesamones, [1– 13 C]glucose was administered to a hairy root culture of Sesamum indicum . The labeling patterns of these quinone derivatives indicated that the naphthoquinone ring and geranyl side-chain of geranylnaphthoquinone were respectively biosynthesized through the shikimate and methylerythritol phosphate pathways, and that these quinone derivatives have the same biosynthetic origin.
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2 geranyl 1 4 naphthoquinone a possible intermediate of anthraquinones in a Sesamum indicum hairy root culture
Bioscience Biotechnology and Biochemistry, 2007Co-Authors: Toshio Furumoto, Tomoko Ohara, Tetsuya Kubo, Yasuhiro Kawanami, Hiroshi FukuiAbstract:2-Geranyl-1,4-naphthoquinone was isolated from the hairy root culture of Sesamum indicum. The structure was determined to be 2-[(E)-3,7-dimethylocta-2,6-dienyl]-1,4-naphthoquinone on the basis of spectroscopic evidence and chemical synthesis. The production of anthrasesamones A, B and C by the hairy root culture was also confirmed for the first time.
Arata Hoshikuma - One of the best experts on this subject based on the ideXlab platform.
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Biosynthetic origin of 2-geranyl-1,4-naphthoquinone and its related anthraquinone in a Sesamum indicum hairy root culture
Phytochemistry, 2011Co-Authors: Toshio Furumoto, Arata HoshikumaAbstract:Abstract In order to clarify the biosynthetic origin of 2-geranyl-1,4-naphthoquinone and its biogenetically related anthraquinone, which are possible intermediates of anthrasesamones, [1– 13 C]glucose was administered to a hairy root culture of Sesamum indicum . The labeling patterns of these quinone derivatives indicated that the naphthoquinone ring and geranyl side-chain of geranylnaphthoquinone were respectively biosynthesized through the shikimate and methylerythritol phosphate pathways, and that these quinone derivatives have the same biosynthetic origin.
Marie A Mmadi - One of the best experts on this subject based on the ideXlab platform.
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the emerging oilseed crop Sesamum indicum enters the omics era
Frontiers in Plant Science, 2017Co-Authors: Xin Wei, Linhai Wang, Yanxin Zhang, Komivi Dossa, Diaga Diouf, Mareme Niang, Daniel Fonceka, Marie A MmadiAbstract:Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and QTLs for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an “orphan crop” to a “genomic resource-rich crop”. With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the “Omics” area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop.
