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Thakro V, Malik N, Basu U, Srivastava R, Narnoliya L, Daware A, Varshney N, Mohanty JK, Bajaj D, Dwivedi V, Tripathi S, Jha UC, Dixit GP, Singh AK, Tyagi AK, Upadhyaya HD, Parida SK. A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea. PLANT PHYSIOLOGY 2023; 191:1884-1912. [PMID: 36477336 PMCID: PMC10022645 DOI: 10.1093/plphys/kiac550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/15/2022] [Indexed: 06/17/2023]
Abstract
Identifying potential molecular tags for drought tolerance is essential for achieving higher crop productivity under drought stress. We employed an integrated genomics-assisted breeding and functional genomics strategy involving association mapping, fine mapping, map-based cloning, molecular haplotyping and transcript profiling in the introgression lines (ILs)- and near isogenic lines (NILs)-based association panel and mapping population of chickpea (Cicer arietinum). This combinatorial approach delineated a bHLH (basic helix-loop-helix) transcription factor, CabHLH10 (Cicer arietinum bHLH10) underlying a major QTL, along with its derived natural alleles/haplotypes governing yield traits under drought stress in chickpea. CabHLH10 binds to a cis-regulatory G-box promoter element to modulate the expression of RD22 (responsive to desiccation 22), a drought/abscisic acid (ABA)-responsive gene (via a trans-expression QTL), and two strong yield-enhancement photosynthetic efficiency (PE) genes. This, in turn, upregulates other downstream drought-responsive and ABA signaling genes, as well as yield-enhancing PE genes, thus increasing plant adaptation to drought with reduced yield penalty. We showed that a superior allele of CabHLH10 introgressed into the NILs improved root and shoot biomass and PE, thereby enhancing yield and productivity during drought without compromising agronomic performance. Furthermore, overexpression of CabHLH10 in chickpea and Arabidopsis (Arabidopsis thaliana) conferred enhanced drought tolerance by improving root and shoot agro-morphological traits. These findings facilitate translational genomics for crop improvement and the development of genetically tailored, climate-resilient, high-yielding chickpea cultivars.
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Affiliation(s)
- Virevol Thakro
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Naveen Malik
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Rishi Srivastava
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Laxmi Narnoliya
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anurag Daware
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nidhi Varshney
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Mohanty
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vikas Dwivedi
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Uday Chand Jha
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - Girish Prasad Dixit
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - Ashok K Singh
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Akhilesh K Tyagi
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
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Transcriptome analysis identifies differentially expressed genes involved in lignin biosynthesis in barley. Int J Biol Macromol 2023; 236:123940. [PMID: 36894063 DOI: 10.1016/j.ijbiomac.2023.123940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/18/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Lignin is an essential metabolite for plant growth but negatively affects the quality of forage barley. Genetic modification of quality traits to improve the forage digestibility requires an understanding of the molecular mechanism of lignin biosynthesis. RNA-Seq was used to quantify transcripts differentially expressed among leaf, stem and spike tissues from two barley genotypes. A total of 13,172 differentially expressed genes (DEGs) were identified, of which much more up-regulated DEGs were detected from the contrasting groups of leaf vs spike (L-S) and stem vs spike (S-S), and down-regulated DEGs were dominant in the group of stem vs leaf (S-L). 47 DEGs were successfully annotated to the monolignol pathway and six of them were candidate genes regulating the lignin biosynthesis. The qRT-PCR assay verified the expression profiles of the six candidate genes. Among them, four genes might positively regulate the lignin biosynthesis during forage barley development in terms of the consistency of their expression levels and changes of lignin content among the tissues, while the other two genes may have the reverse effects. These findings provide target genes for further investigations on molecular regulatory mechanisms of lignin biosynthesis and genetic resources for improvement of forage quality in barley molecular breeding programme.
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Zhang G, Huang S, Zhang C, Wu Y, Li D, Deng J, Shan S, Qi J. Comparative transcriptome sequencing analysis and functional identification of a NAM-2-like gene in jute (Corchorus capsularis L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:25-35. [PMID: 33561658 DOI: 10.1016/j.plaphy.2021.01.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Jute (Corchorus capsularis L.) is one of the most important sources of natural fibre. Drought is among the main factors affecting the production of jute. It is essential for drought tolerance improvement to discover the genes associated with jute development during drought stress. In this study, we analyzed the transcriptome of jute under drought stress and identified new genes involved in drought stress response. In total, 120,219 transcripts with an average length of 764 bp were obtained, these transcripts included 94,246 unigenes (average length, 622 bp). Differentially expressed genes (DEGs) were discovered in drought stress (1329), among which 903 genes showed up-regulated expression, while 426 genes showed down-regulated expression. GO enrichment analyses indicated most of the enriched biological pathways were biosynthesis pathways of organic ring compounds and cellular nitrogen compounds. KEGG enrichment analyses indicated 573 DEGs were involved in 157 metabolic pathways. RT-qPCR experiments indicated that the expression trends were consistent with the results of the high-throughput sequencing. Over-expression of no apical meristem (NAM) -2-like gene increased drought tolerance and knockdown plants were drought sensitive. It has expression peaks after 6 h of drought stress and regulate 3-ketoacyl-CoA synthase gene expression. Yeast-2-Hybrid assays validated the physical interaction between NAM-2-like protein and KCS. The results provide relatively comprehensive information regarding genes and metabolic pathways that lays the foundation for the breeding of drought-resistant varieties, and represent the first identification of NAM-2-like gene and provides new insight into the regulatory network of drought tolerance in Corchorus capsularis L.
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Affiliation(s)
- Gaoyang Zhang
- Shangrao Normal University, Shangrao, China; Chinese Academy of Agricultural Sciences Institute of Bast Fiber Crops, Changsha, China
| | - Siqi Huang
- Chinese Academy of Agricultural Sciences Institute of Bast Fiber Crops, Changsha, China
| | - Chao Zhang
- Shangrao Normal University, Shangrao, China
| | - Yingbao Wu
- Shangrao Normal University, Shangrao, China
| | - Defang Li
- Chinese Academy of Agricultural Sciences Institute of Bast Fiber Crops, Changsha, China.
| | | | | | - Jianmin Qi
- Fujian Agriculture and Forestry University, Fuzhou, China.
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Genome-wide identification of fasciclin-like arabinogalactan proteins in jute and their expression pattern during fiber formation. Mol Biol Rep 2020; 47:7815-7829. [PMID: 33011893 DOI: 10.1007/s11033-020-05858-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/23/2020] [Indexed: 10/23/2022]
Abstract
Fasciclin-like arabinogalactan proteins (FLAs), a class of arabinogalactan proteins (AGPs) are involved in plant growth and development via cell communication and adhesion. FLAs were also associated with fiber and wood formation in plants but no information is available about the roles of FLA proteins during fibre development of jute. Here, we performed molecular characterization, evolutionary relationship and expression profiling of FLAs proteins in jute (Corchorus olitorius). In total, nineteen CoFLA genes have been identified in jute genome, which were divided into four classes like FLAs of other species based on protein structure and similarity. All CoFLAs have N-terminal signal peptide and one or two FAS domain while two FLAs lack well defined AGP region and eight FLAs were devoid of C-terminal glycosylphosphatidylinositol (GPI) anchor. Expression analysis of different regions of jute stem suggested their involvement in different fiber development stages. Four genes CoFLA 11, 12, 20, and 23 were highly or predominately expressed in fiber containing bark tissues while the expression levels of six CoFLA genes 02, 03, 04, 06, 14 and 19 were comparatively higher in stick. Higher transcripts levels of CoFLA 12 and 20 in the middle bark tissues suggest their involvement in fiber elongation. In contrast, the CoFLA 11 and 23 were more expressed in bottom bark tissues suggesting their potential involvement in secondary cell wall synthesis. Our study can serve as solid foundation for further functional exploration of FLAs and in future breeding program of jute aiming fiber improvement.
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Zhang L, Wan X, Xu Y, Niyitanga S, Qi J, Zhang L. De novo assembly of transcriptome and genome-wide identification reveal GA 3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis). BMC PLANT BIOLOGY 2020; 20:403. [PMID: 32867682 PMCID: PMC7460746 DOI: 10.1186/s12870-020-02617-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 08/23/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis. RESULTS A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress. CONCLUSIONS A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.
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Affiliation(s)
- Lilan Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xuebei Wan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Yi Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.). BMC Genomics 2020; 21:406. [PMID: 32546133 PMCID: PMC7298812 DOI: 10.1186/s12864-020-06805-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenced by many factors. Therefore, to understand the molecular mechanisms of tissue development, it is necessary to study tissue-specific gene expression and regulation. We used weighted gene coexpression network analysis, to predict the functional roles of gene coexpression modules and individual genes, including those underlying the development of different tissue types. Although several transcriptome studies have been conducted on C. capsularis, there have not yet been any systematic and comprehensive transcriptome analyses for this species. RESULTS There was significant variation in gene expression between plant tissues. Comparative transcriptome analysis and weighted gene coexpression network analysis were performed for different C. capsularis tissues at different developmental stages. We identified numerous tissue-specific differentially expressed genes for each tissue, and 12 coexpression modules, comprising 126 to 4203 genes, associated with the development of various tissues. There was high consistency between the genes in modules related to tissues, and the candidate upregulated genes for each tissue. Further, a gene network including 21 genes directly regulated by transcription factor OMO55970.1 was discovered. Some of the genes, such as OMO55970.1, OMO51203.1, OMO50871.1, and OMO87663.1, directly involved in the development of stem bast tissue. CONCLUSION We identified genes that were differentially expressed between tissues of the same developmental stage. Some genes were consistently up- or downregulated, depending on the developmental stage of each tissue. Further, we identified numerous coexpression modules and genes associated with the development of various tissues. These findings elucidate the molecular mechanisms underlying the development of each tissue, and will promote multipurpose molecular breeding in jute and other fiber crops.
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Conover JL, Karimi N, Stenz N, Ané C, Grover CE, Skema C, Tate JA, Wolff K, Logan SA, Wendel JF, Baum DA. A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods? JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:12-31. [PMID: 30474311 DOI: 10.1111/jipb.12746] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.
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Affiliation(s)
- Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Nisa Karimi
- Department of Botany, University of Wisconsin Madison, WI, 53706, USA
| | - Noah Stenz
- Department of Botany, University of Wisconsin Madison, WI, 53706, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin Madison, WI, 53706, USA
- Department of Statistics, University of Wisconsin Madison, WI, 53706, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Cynthia Skema
- Morris Arboretum of the University of Pennsylvania, 100 E. Northwestern Avenue, Philadelphia, PA, 19118, USA
| | - Jennifer A Tate
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Kirsten Wolff
- School of Natural and Environmental Sciences, Newcastle University, NE1 7RU, UK
| | - Samuel A Logan
- School of Natural and Environmental Sciences, Newcastle University, NE1 7RU, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - David A Baum
- Department of Botany, University of Wisconsin Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, 330 N Orchard St, Madison, WI 53715, USA
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Yang YH, Li MJ, Yi YJ, Li RF, Dong C, Zhang ZY. The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit. PLANT CELL REPORTS 2018; 37:611-625. [PMID: 29344683 DOI: 10.1007/s00299-018-2255-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 12/27/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants.
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Affiliation(s)
- Yan Hui Yang
- College of Bioengineering, Henan University of Technology, Lianhua Street 100, Zhengzhou High-technology Zero, Zhengzhou, 450001, Henan, China.
| | - Ming Jie Li
- College of Crop Sciences, Fujian Agriculture and Forestry University, Jinshan Road, Cangshan District, Fuzhou, 350002, China
| | - Yan Jie Yi
- College of Bioengineering, Henan University of Technology, Lianhua Street 100, Zhengzhou High-technology Zero, Zhengzhou, 450001, Henan, China
| | - Rui Fang Li
- College of Bioengineering, Henan University of Technology, Lianhua Street 100, Zhengzhou High-technology Zero, Zhengzhou, 450001, Henan, China
| | - Cheng Dong
- College of Bioengineering, Henan University of Technology, Lianhua Street 100, Zhengzhou High-technology Zero, Zhengzhou, 450001, Henan, China
| | - Zhong Yi Zhang
- College of Crop Sciences, Fujian Agriculture and Forestry University, Jinshan Road, Cangshan District, Fuzhou, 350002, China.
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De Novo Sequencing and Assembly Analysis of Transcriptome in Pinus bungeana Zucc. ex Endl. FORESTS 2018. [DOI: 10.3390/f9030156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Yang H, Cai Y, Zhuo Z, Yang W, Yang C, Zhang J, Yang Y, Wang B, Guan F. Transcriptome analysis in different developmental stages of Batocera horsfieldi (Coleoptera: Cerambycidae) and comparison of candidate olfactory genes. PLoS One 2018; 13:e0192730. [PMID: 29474419 PMCID: PMC5825065 DOI: 10.1371/journal.pone.0192730] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/29/2018] [Indexed: 11/29/2022] Open
Abstract
The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber industry. Moreover olfactory proteins are crucial components to function in related processes, but the B. horsfieldi genome is not readily available for olfactory proteins analysis. In the present study, developmental transcriptomes of larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing to establish a genetic background that may help understand olfactory genes. Approximately 199 million clean reads were obtained and assembled into 171,664 transcripts, which were classified into 23,380, 26,511, 22,393, 30,270, and 87, 732 unigenes for larvae, pupae, females, males, and combined datasets, respectively. The unigenes were annotated against NCBI’s non-redundant nucleotide and protein sequences, Swiss-Prot, Gene Ontology (GO), Pfam, Clusters of Eukaryotic Orthologous Groups (KOG), and KEGG Orthology (KO) databases. A total of 43,197 unigenes were annotated into 55 sub-categories under the three main GO categories; 25,237 unigenes were classified into 26 functional KOG categories, and 25,814 unigenes were classified into five functional KEGG Pathway categories. RSEM software identified 2,983, 3,097, 870, 2,437, 5,161, and 2,882 genes that were differentially expressed between larvae and males, larvae and pupae, larvae and females, males and females, males and pupae, and females and pupae, respectively. Among them, genes encoding seven candidate odorant binding proteins (OBPs) and three chemosensory proteins (CSPs) were identified. RT-PCR and RT-qPCR analyses showed that BhorOBP3, BhorCSP2, and BhorOBPC1/C3/C4 were highly expressed in the antenna of males, indicating these genes may may play key roles in foraging and host-orientation in B. horsfieldi. Our results provide valuable molecular information about the olfactory system in B. horsfieldi and will help guide future functional studies on olfactory genes.
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Affiliation(s)
- Hua Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Cai
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhihang Zhuo
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wei Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail:
| | - Chunping Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jin Zhang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yang Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Baoxin Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, Sichuan, China
| | - Fengrong Guan
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, China
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11
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Yang Z, Dai Z, Xie D, Chen J, Tang Q, Cheng C, Xu Y, Wang T, Su J. Development of an InDel polymorphism database for jute via comparative transcriptome analysis. Genome 2018; 61:323-327. [PMID: 29420906 DOI: 10.1139/gen-2017-0191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31. Further, we found 94 InDel types, varying from 1 to 159 bp; the most common were single-nucleotide (23 028), binucleotide (9824), and trinucleotide (9182). In total, 49 563 InDels in 18 445 transcripts were discovered in the comparison between TC and YG, followed by 48 934 InDels in 18 408 transcripts between NY and YG, and 3570 InDels in 2701 unigenes between NY and TC. Additionally, there were 1273 InDel sites in 1129 unigenes with polymorphisms between any two of the three accessions. Twenty-nine (58%) primer pairs represented polymorphisms when compared to the jute accessions, and PIC varied from 0.340 to 0.680, with an average of 0.491.
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Affiliation(s)
- Zemao Yang
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Zhigang Dai
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Dongwei Xie
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Jiquan Chen
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Qing Tang
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Chaohua Cheng
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Ying Xu
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Tingzhang Wang
- b Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jianguang Su
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
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12
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Transcriptome Analysis of Two Species of Jute in Response to Polyethylene Glycol (PEG)- induced Drought Stress. Sci Rep 2017; 7:16565. [PMID: 29185475 PMCID: PMC5707433 DOI: 10.1038/s41598-017-16812-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/16/2017] [Indexed: 11/08/2022] Open
Abstract
Drought stress results in significant crop yield losses. Comparative transcriptome analysis between tolerant and sensitive species can provide insights into drought tolerance mechanisms in jute. We present a comprehensive study on drought tolerance in two jute species-a drought tolerant species (Corchorus olitorius L., GF) and a drought sensitive species (Corchorus capsularis L., YY). In total, 45,831 non-redundant unigenes with average sequence length of 1421 bp were identified. Higher numbers of differentially expressed genes (DEGs) were discovered in YY (794) than in GF (39), implying that YY was relatively more vulnerable or hyper-responsive to drought stress at the molecular level; the two main pathways, phenylpropanoid biosynthesis and peroxisome pathway, significantly involved in scavenging of reactive oxygen species (ROS) and 14 unigenes in the two pathways presented a significant differential expression in response to increase of superoxide. Our classification analysis showed that 1769 transcription factors can be grouped into 81 families and 948 protein kinases (PKs) into 122 families. In YY, we identified 34 TF DEGs from and 23 PK DEGs, including 19 receptor-like kinases (RLKs). Most of these RLKs were downregulated during drought stress, implying their role as negative regulators of the drought tolerance mechanism in jute.
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Saha D, Rana RS, Chakraborty S, Datta S, Kumar AA, Chakraborty AK, Karmakar PG. Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.02.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Yang Z, Lu R, Dai Z, Yan A, Tang Q, Cheng C, Xu Y, Yang W, Su J. Salt-Stress Response Mechanisms Using de Novo Transcriptome Sequencing of Salt-Tolerant and Sensitive Corchorus spp. Genotypes. Genes (Basel) 2017; 8:genes8090226. [PMID: 28927022 PMCID: PMC5615359 DOI: 10.3390/genes8090226] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 01/07/2023] Open
Abstract
High salinity is a major environmental stressor for crops. To understand the regulatory mechanisms underlying salt tolerance, we conducted a comparative transcriptome analysis between salt-tolerant and salt-sensitive jute (Corchorus spp.) genotypes in leaf and root tissues under salt stress and control conditions. In total, 68,961 unigenes were identified. Additionally, 11,100 unigenes (including 385 transcription factors (TFs)) exhibited significant differential expression in salt-tolerant or salt-sensitive genotypes. Numerous common and unique differentially expressed unigenes (DEGs) between the two genotypes were discovered. Fewer DEGs were observed in salt-tolerant jute genotypes whether in root or leaf tissues. These DEGs were involved in various pathways, such as ABA signaling, amino acid metabolism, etc. Among the enriched pathways, plant hormone signal transduction (ko04075) and cysteine/methionine metabolism (ko00270) were the most notable. Eight common DEGs across both tissues and genotypes with similar expression profiles were part of the PYL-ABA-PP2C (pyrabactin resistant-like/regulatory components of ABA receptors-abscisic acid-protein phosphatase 2C). The methionine metabolism pathway was only enriched in salt-tolerant jute root tissue. Twenty-three DEGs were involved in methionine metabolism. Overall, numerous common and unique salt-stress response DEGs and pathways between salt-tolerant and salt-sensitive jute have been discovered, which will provide valuable information regarding salt-stress response mechanisms and help improve salt-resistance molecular breeding in jute.
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Affiliation(s)
- Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410125, China.
| | - Ruike Lu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410125, China.
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410125, China.
| | - An Yan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore.
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410125, China.
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410125, China.
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410125, China.
| | - Wenting Yang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410125, China.
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15
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Identification of critical genes associated with lignin biosynthesis in radish (Raphanus sativus L.) by de novo transcriptome sequencing. Mol Genet Genomics 2017; 292:1151-1163. [PMID: 28667404 DOI: 10.1007/s00438-017-1338-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 06/19/2017] [Indexed: 01/23/2023]
Abstract
Radish is an important root vegetable crop with high nutritional, economic, and medicinal value. Lignin is an important secondary metabolite possessing a great effect on plant growth and product quality. To date, lignin biosynthesis-related genes have been identified in some important plant species. However, little information on characterization of critical genes involved in plant lignin biosynthesis is available in radish. In this study, a total of 71,148 transcripts sequences were obtained from radish root, of which 66 assembled unigenes and ten candidate genes were identified to be involved in lignin monolignol biosynthesis. Full-length cDNA sequences of seven randomly selected genes were isolated and sequenced from radish root, and the assembled unigenes covered more than 80% of their corresponding cDNA sequences. Moreover, the lignin content gradually accumulated in leaf during the developmental stages, and it increased from pre-cortex to cortex splitting stage, followed by a decrease at thickening stage and then increased at mature stage in root. RT-qPCR analysis revealed that all these genes except RsF5H exhibited relatively low expression level in root at thickening stage. The expression profiles of Rs4CL5, RsCCoAOMT1, and RsCOMT genes were consistent with the changes of root lignin content, implying that these candidate genes may play important roles in lignin formation in radish root. These findings would provide valuable information for identification of lignin biosynthesis-related genes and facilitate dissection of molecular mechanism underlying lignin biosynthesis in radish and other root vegetable crops.
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The developmental transcriptome of the bamboo snout beetle Cyrtotrachelus buqueti and insights into candidate pheromone-binding proteins. PLoS One 2017; 12:e0179807. [PMID: 28662071 PMCID: PMC5491049 DOI: 10.1371/journal.pone.0179807] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/05/2017] [Indexed: 11/25/2022] Open
Abstract
Cyrtotrachelus buqueti is an extremely harmful bamboo borer, and the larvae of this pest attack clumping bamboo shoots. Pheromone-binding proteins (PBPs) play an important role in identifying insect sex pheromones, but the C. buqueti genome is not readily available for PBP analysis. Developmental transcriptomes of eggs, larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing (RNA-Seq) in the present study to establish a sequence background of C. buqueti to help understand PBPs. Approximately 164.8 million clean reads were obtained and annotated into 108,854 transcripts. These were assembled into 24,338, 21,597, 24,798, 21,886, 24,642, and 83,115 unigenes for eggs, larvae, pupae, females, males, and the combined datasets, respectively. Unigenes were annotated against NCBI non-redundant protein sequences, NCBI non-redundant nucleotide sequences, Gene Ontology (GO), Protein family, Clusters of Orthologous Groups of Proteins/ Clusters of Eukaryotic Orthologous Groups (KOG), Swiss-Prot, and KEGG Orthology databases. A total of 17,213 unigenes were annotated into 55 sub-categories belonging to three main GO categories; 10,672 unigenes were classified into 26 functional categories by KOG classification, and 8,063 unigenes were classified into five functional KEGG categories. RSEM software for RNA sequencing showed that 4,816, 3,176, 3,661, 2,898, 4,316, 8,019, 7,273, 5,922, 5,844, and 4,570 genes were differentially expressed between larvae and males, larvae and eggs, larvae and pupae, larvae and females, males and females, males and eggs, males and pupae, females and eggs, females and pupae, and eggs and pupae, respectively. Of these, three were confirmed to be significantly differentially expressed between larvae, females, and males. Furthermore, PBP Cbuq7577_g1 was highly expressed in the antenna of males. A comprehensive sequence resource of a desirable quality was constructed from developmental transcriptomes of C. buqueti eggs, larvae, pupae, and adults. This work enriches the genomic data of C. buqueti, and facilitates our understanding of its metamorphosis, development, and response to environmental change. The identified candidate PBP Cbuq7577_g1 might play a crucial role in identifying sex pheromones, and could be used as a targeted gene to control C. buqueti numbers by disrupting sex pheromone communication.
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