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14. De Novo assembly of expressed transcripts and global transcriptomic analysis from seedlings of the paper mulberry (Broussonetia kazinoki x Broussonetia papyifera).

Author

Peng Xianjun, Teng Linhong, Wang Xiaoman, Wang Yucheng, and Shen Shihua

Subjects
Medicine, Science
Abstract

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry.

Published
2014
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20. A Chromosome-Scale Genome Assembly of Paper Mulberry (Broussonetia papyrifera) Provides New Insights into Its Forage and Papermaking Usage

Author

Peng, Xianjun, primary, Liu, Hui, additional, Chen, Peilin, additional, Tang, Feng, additional, Hu, Yanmin, additional, Wang, Fenfen, additional, Pi, Zhi, additional, Zhao, Meiling, additional, Chen, Naizhi, additional, Chen, Hui, additional, Zhang, Xiaokang, additional, Yan, Xueqing, additional, Liu, Min, additional, Fu, Xiaojun, additional, Zhao, Guofeng, additional, Yao, Pu, additional, Wang, Lili, additional, Dai, He, additional, Li, Xuming, additional, Xiong, Wei, additional, Xu, Wencai, additional, Zheng, Hongkun, additional, Yu, Haiyan, additional, and Shen, Shihua, additional

Published
2019
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21. Improved drought and salt tolerance of Arabidopsis thaliana by transgenic expression of a novel DREB gene from Leymus chinensis

Author

Byung-Hyun Lee, Iftekhar Alam, Liu Gongshe, Fan Weihong, Su Man, Cheng Li-qin, Shen Shihua, Ma Xingyong, Qi Dongmei, and Peng Xianjun

Subjects
Transcriptional Activation, DNA, Complementary, Arabidopsis, Plant Science, Poaceae, Gene product, Rapid amplification of cDNA ends, Gene Expression Regulation, Plant, Stress, Physiological, Onions, Arabidopsis thaliana, Transgenes, Cloning, Molecular, Transcription factor, Plant Proteins, Genetics, Regulation of gene expression, Reporter gene, biology, Abiotic stress, food and beverages, Salt-Tolerant Plants, General Medicine, Plants, Genetically Modified, biology.organism_classification, Droughts, Cold Temperature, RNA, Plant, Agronomy and Crop Science, Abscisic Acid, Signal Transduction, Transcription Factors
Abstract

Dehydration-responsive element-binding (DREB) proteins are important transcription factors in plant stress responses and signal transduction. Based on high-throughput sequencing results, a new cDNA sequence encoding an LcDREB3a transcription factor from the drought-resistant forage grass, Leymus chinensis, was isolated by RACE PCR. Sequence similarity analysis indicates that the gene product is active in the ABA-responsive pathway, and real-time PCR-based expression analysis shows the transcript accumulates in response to a variety of stress treatments. These results indicate that LcDREB3a is involved in both ABA-dependent and -independent signal transduction in the stress-responsive process of L. chinensis. The identity of the gene product as a DREB transcription factor is supported by observations of its nuclear localization when transiently expressed as a GFP fusion in onion epidermal cells. Furthermore, LcDREB3a is able to activate reporter gene expression, and the protein is shown to specifically bind to the conserved DRE element in a yeast one-hybrid assay. The transgenic expression of LcDREB3a in Arabidopsis causes no growth retardation and induces the increased expression of stress tolerance genes compared to control, resulting in improved drought and salt stress tolerance. Thus, LcDREB3a, encoding a stress-inducible DREB transcription factor, could enhance the abiotic stress tolerance of plants.

Published
2011

26. De Novo assembly of expressed transcripts and global transcriptomic analysis from seedlings of the paper mulberry (Broussonetia kazinoki x Broussonetia papyifera)

Author

Wang Yucheng, Wang Xiaoman, Shen Shihua, Peng Xianjun, and Teng Linhong

Subjects
Sequence assembly, Gene Expression, Plant Science, Plant Genetics, Plant Roots, Trees, Transcriptome, Gene Expression Regulation, Plant, Molecular Cell Biology, Plant Genomics, Genetics, Plant Growth and Development, Multidisciplinary, biology, Plant Stems, Genomics, Plants, Functional Genomics, Organ Specificity, Multigene Family, Medicine, Transcriptome Analysis, Metabolic Networks and Pathways, Research Article, Biotechnology, Science, Genes, Plant, KEGG, Secondary metabolism, Gene, Gene Expression Profiling, Organisms, Biology and Life Sciences, Computational Biology, Molecular Sequence Annotation, Cell Biology, Broussonetia, biology.organism_classification, Genome Analysis, Gene expression profiling, Plant Leaves, Metabolic pathway, Seedlings, Plant Biotechnology, Morus, Gene Function, Genome Expression Analysis, Developmental Biology
Abstract

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry.

Published
2013

27. Integrating genome-wide association and transcriptome analysis to provide molecular insights into heterophylly and eco-adaptability in woody plants

Author

Hu, Yanmin, Tang, Feng, Zhang, Dan, Shen, Shihua, and Peng, Xianjun

Abstract

Heterophylly is regard as an important adaptive mechanism in response to different environments within plants. However, the genetic mechanisms responsible for heterophylly in woody plants are still poorly understood. Herein, the divergence of heterophyllous leaves was investigated at morphogenesis and using microdissection and physiological indexes in paper mulberry, and the genetic basis of heterophylly was further revealed combined with genome-wide association study (GWAS), transcriptome analysis and weighted gene coexpression network analysis (WGCNA). Our results revealed that the flavonoid content and antioxidant activity increased gradually from the entire leaf to the palmatisect leaf, while the hormone content and net photosynthetic rate decreased. Through GWAS and transcriptome analysis, a total of 98 candidate genes and 2338 differentially expressed genes associated with heterophylly were identified. Importantly, we uncovered critical variations in the candidate genes Bp07g0981(WOX) and Bp07g0920(HHO), along with significant differences in haplotypes and expression levels among heterophyllous leaves. Our results also suggested that the genes involved in hormone signaling pathways, antioxidant activity, and flavonoid metabolism might be closely related to the heterophylly of paper mulberry, which could account for the physiological data. Indeed, CR-woxmutant lines showed significant changes in leaf phenotypes, and differential expression profile analysis also highlighted the expression of genes related to phytohormones and transcription factors. Together, the genetic variations and candidate genes detected in this study provide novel insights into the genetic mechanism of heterophylly, and would improve the understanding of eco-adaptability in heterophyllous woody plants.

Published
2023
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35. Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe

Author

Chen, Shuangyan, primary, Huang, Xin, additional, Yan, Xueqing, additional, Liang, Ye, additional, Wang, Yuezhu, additional, Li, Xiaofeng, additional, Peng, Xianjun, additional, Ma, Xingyong, additional, Zhang, Lexin, additional, Cai, Yueyue, additional, Ma, Tian, additional, Cheng, Liqin, additional, Qi, Dongmei, additional, Zheng, Huajun, additional, Yang, Xiaohan, additional, Li, Xiaoxia, additional, and Liu, Gongshe, additional

Published
2013
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37. Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe.

Author

Chen, Shuangyan, Huang, Xin, Yan, Xueqing, Liang, Ye, Wang, Yuezhu, Li, Xiaofeng, Peng, Xianjun, Ma, Xingyong, Zhang, Lexin, Cai, Yueyue, Ma, Tian, Cheng, Liqin, Qi, Dongmei, Zheng, Huajun, Yang, Xiaohan, Li, Xiaoxia, and Liu, Gongshe

Subjects
BASIN wildrye, GRASSES, AMINO acid sequence, PHYLOGENY, PLANT species, PLANT biotechnology, PLANT genetics
Abstract

Background: Sheepgrass [Leymus chinensis (Trin.) Tzvel.] is an important perennial forage grass across the Eurasian Steppe and is known for its adaptability to various environmental conditions. However, insufficient data resources in public databases for sheepgrass limited our understanding of the mechanism of environmental adaptations, gene discovery and molecular marker development. Results: The transcriptome of sheepgrass was sequenced using Roche 454 pyrosequencing technology. We assembled 952,328 high-quality reads into 87,214 unigenes, including 32,416 contigs and 54,798 singletons. There were 15,450 contigs over 500 bp in length. BLAST searches of our database against Swiss-Prot and NCBI non-redundant protein sequences (nr) databases resulted in the annotation of 54,584 (62.6%) of the unigenes. Gene Ontology (GO) analysis assigned 89,129 GO term annotations for 17,463 unigenes. We identified 11,675 core Poaceae-specific and 12,811 putative sheepgrass-specific unigenes by BLAST searches against all plant genome and transcriptome databases. A total of 2,979 specific freezing-responsive unigenes were found from this RNAseq dataset. We identified 3,818 EST-SSRs in 3,597 unigenes, and some SSRs contained unigenes that were also candidates for freezing-response genes. Characterizations of nucleotide repeats and dominant motifs of SSRs in sheepgrass were also performed. Similarity and phylogenetic analysis indicated that sheepgrass is closely related to barley and wheat. Conclusions: This research has greatly enriched sheepgrass transcriptome resources. The identified stress-related genes will help us to decipher the genetic basis of the environmental and ecological adaptations of this species and will be used to improve wheat and barley crops through hybridization or genetic transformation. The EST-SSRs reported here will be a valuable resource for future gene-phenotype studies and for the molecular breeding of sheepgrass and other Poaceae species. [ABSTRACT FROM AUTHOR]

Published
2013
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