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Bao Y, Zou Y, An X, Liao Y, Dai L, Liu L, Peng D, Huang X, Wang B. Overexpression of a Ramie ( Boehmaeria nivea L. Gaud) Group I WRKY Gene, BnWRKY49, Increases Drought Resistance in A rabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2024; 13:379. [PMID: 38337912 PMCID: PMC10857251 DOI: 10.3390/plants13030379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
Plants face multiple stresses in their natural habitats. WRKY transcription factors (TFs) play an important regulatory role in plant stress signaling, regulating the expression of multiple stress-related genes to improve plant stress resistance. In this study, we analyzed the expression profiles of 25 BnWRKY genes in three stages of ramie growth (the seedling stage, the rapid-growth stage, and the fiber maturity stage) and response to abiotic stress through qRT-PCR. The results indicated that 25 BnWRKY genes play a role in different growth stages of ramie and were induced by salt and drought stress in the root and leaf. We selected BnWRKY49 as a candidate gene for overexpression in Arabidopsis. BnWRKY49 was localized in the nucleus. Overexpression of BnWRKY49 affected root elongation under drought and salt stress at the Arabidopsis seedling stage and exhibited increased tolerance to drought stress. Further research found that BnWRKY49-overexpressing lines showed decreased stomatal size and increased cuticular wax deposition under drought compared with wild type (WT). Antioxidant enzyme activities of SOD, POD, and CAT were higher in the BnWRKY49-overexpressing lines than the WT. These findings suggested that the BnWRKY49 gene played an important role in drought stress tolerance in Arabidopsis and laid the foundation for further research on the functional analysis of the BnWRKYs in ramie.
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Affiliation(s)
- Yaning Bao
- Guizhou Key Laboratory for Tobacco Quality Research, College of Tobacco Science, Guizhou University, Guiyang 550025, China
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifei Zou
- Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
| | - Xia An
- Zhejiang Xiaoshan Institute of Cotton & Bast Fiber Crops, Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou 311251, China
| | - Yiwen Liao
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lunjin Dai
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Zeng Z, Zhu S, Wang Y, Bai X, Liu C, Chen J, Zhang T, Wei Y, Li F, Bao Z, Yan L, Wang H, Liu T. Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:323-334. [PMID: 34558775 PMCID: PMC8753365 DOI: 10.1111/pbi.13714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/13/2021] [Indexed: 05/27/2023]
Abstract
Ramie is an important fibre-producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fibre yield-related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fibre abundance, providing the first evidence for the role of pectin methylesterase in fibre growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focussed on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin-signalling-repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fibre yield traits in ramie. Moreover, the identification of fibre yield-related genetic loci and large-scale genomic variation represent valuable resources for genomics-assisted breeding of this crop.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Siyuan Zhu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Yanzhou Wang
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Xuehua Bai
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Chan Liu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Jianrong Chen
- College of Biological and Environmental EngineeringChangsha UniversityChangshaChina
| | - Ting Zhang
- Shanghai OE Biotech. Co., LtdShanghaiChina
| | - Yiping Wei
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Fu Li
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Zhigui Bao
- Shanghai OE Biotech. Co., LtdShanghaiChina
| | - Li Yan
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | | | - Touming Liu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
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Identification of proteins associated with bast fiber growth of ramie by differential proteomic analysis. BMC Genomics 2021; 22:865. [PMID: 34856929 PMCID: PMC8638140 DOI: 10.1186/s12864-021-08195-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Background Ramie is an important fiber-producing crop in China, and its fibers are widely used as textile materials. Fibers contain specialized secondary cellular walls that are mainly composed of cellulose, hemicelluloses, and lignin. Understanding the mechanism underlying the secondary wall biosynthesis of fibers will benefit the improvement of fiber yield and quality in ramie. Results Here, we performed a proteomic analysis of the bark from the top and middle parts of the stem, where fiber growth is at different stages. We identified 6971 non-redundant proteins from bast bark. Proteomic comparison revealed 983 proteins with differential expression between the two bark types. Of these 983 proteins, 46 were identified as the homolog of known secondary wall biosynthetic proteins of Arabidopsis, indicating that they were potentially associated with fiber growth. Then, we proposed a molecular model for the secondary wall biosynthesis of ramie fiber. Furthermore, interaction analysis of 46 candidate proteins revealed two interacting networks that consisted of eight cellulose biosynthetic enzymes and seven lignin biosynthetic proteins, respectively. Conclusion This study sheds light on the proteomic basis underlying bast fiber growth in ramie, and the identification of many candidates associated with fiber growth provides important basis for understanding the fiber growth in this crop. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08195-9.
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Zeng Z, Li F, Huang R, Wang Y, Liu T. Phosphoproteome analysis reveals an extensive phosphorylation of proteins associated with bast fiber growth in ramie. BMC PLANT BIOLOGY 2021; 21:473. [PMID: 34656094 PMCID: PMC8520194 DOI: 10.1186/s12870-021-03252-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Phosphorylation modification, one of the most common post-translational modifications of proteins, widely participates in the regulation of plant growth and development. Fibers extracted from the stem bark of ramie are important natural textile fibers; however, the role of phosphorylation modification in the growth of ramie fibers is largely unknown. RESULTS Here, we report a phosphoproteome analysis for the barks from the top and middle section of ramie stems, in which the fiber grows at different stages. A total of 10,320 phosphorylation sites from 9,170 unique phosphopeptides that were assigned to 3,506 proteins was identified, and 458 differentially phosphorylated sites from 323 proteins were detected in the fiber developmental barks. Twelve differentially phosphorylated proteins were the homologs of Arabidopsis fiber growth-related proteins. We further focused on the function of the differentially phosphorylated KNOX protein whole_GLEAN_10029667, and found that this protein dramatically repressed the fiber formation in Arabidopsis. Additionally, using a yeast two-hybridization assay, we identified a kinase and a phosphatase that interact with whole_GLEAN_10029667, indicating that they potentially target this KNOX protein to regulate its phosphorylation level. CONCLUSION The finding of this study provided insights into the involvement of phosphorylation modification in ramie fiber growth, and our functional characterization of whole_GLEAN_10029667 provide the first evidence to indicate the involvement of phosphorylation modification in the regulation of KNOX protein function in plants.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Renyan Huang
- Hunan Institute of Plant protection, Changsha, 410205, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Wang Y, Li F, He Q, Bao Z, Zeng Z, An D, Zhang T, Yan L, Wang H, Zhu S, Liu T. Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:787-800. [PMID: 33993558 DOI: 10.1111/tpj.15346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 05/27/2023]
Abstract
Ramie (Boehmeria nivea) is an economically important natural fiber-producing crop that has been cultivated for thousands of years in China; however, the evolution of this crop remains largely unknown. Here, we report a ramie domestication analysis based on genome assembly and resequencing of cultivated and wild accessions. Two chromosome-level genomes representing wild and cultivated ramie were assembled de novo. Numerous structural variations between two assemblies, together with the genetic variations from population resequencing, constituted a comprehensive genomic variation map for ramie. Domestication analysis identified 71 high-confidence selective sweeps comprising 320 predicted genes, and 29 genes from sweeps were associated with fiber growth in the expression. In addition, we identified seven genetic loci associated with the fiber yield trait in the segregated population derived from the crossing of two assembled accessions, and two of which showed an overlap with the selective sweeps. These findings indicated that bast fiber traits were focused on during the domestication history of ramie. This study sheds light on the domestication of ramie and provides a valuable resource for biological and breeding studies of this important crop.
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Affiliation(s)
- Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Zhigui Bao
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Dong An
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Ting Zhang
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Li Yan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Hengyun Wang
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
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He Q, Zeng Z, Li F, Huang R, Wang Y, Liu T. Ubiquitylome analysis reveals the involvement of ubiquitination in the bast fiber growth of ramie. PLANTA 2021; 254:1. [PMID: 34081200 DOI: 10.1007/s00425-021-03652-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
A total of 249 sites from 197 proteins showed a differential ubiquitination level in the fiber development of ramie barks. The function of two differentially ubiquitinated proteins for fiber growth was demonstrated. Ubiquitination is one of the most common post-translational modifications of proteins, and it plays essential roles in plant growth and development. However, the involvement of ubiquitination in the growth of plant fibers remains largely unknown. We compared the ubiquitylome of the top and middle stems of ramie bark, with different fiber growth stages. We identified 249 differentially ubiquitinated sites in 197 proteins in fiber-developing barks in the stems and found that seven were homologs of Arabidopsis proteins associated with fiber growth. Overexpression of the differentially ubiquitinated proteins, RWA3 homolog whole_GLEAN_10024150 and MYB protein whole_GLEAN_10015497, significantly promoted fiber growth in transgenic Arabidopsis, indicating their involvement in this process. We also found that the abundance of these proteins decreased when their ubiquitination levels increased and vice versa in the fiber-developing bark. These results indicated that the abundance of these two proteins was adjusted through ubiquitin-dependent degradation. Collectively, our findings provide important insights into the involvement of ubiquitination in the growth of ramie fibers.
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Affiliation(s)
- Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Renyan Huang
- Hunan Institute of Plant Protection, Changsha, 410125, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Bai S, Zhao Y, Zhou Y, Wang M, Li Y, Luo X, Li L. Identification and expression of main genes involved in non-target site resistance mechanisms to fenoxaprop-p-ethyl in Beckmannia syzigachne. PEST MANAGEMENT SCIENCE 2020; 76:2619-2626. [PMID: 32083373 DOI: 10.1002/ps.5800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/12/2020] [Accepted: 02/21/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Non-target-site resistance (NTSR) to herbicides is a serious threat to global agriculture. Although metabolic resistance is the dominant mechanism of NTSR, the molecular mechanisms are not yet well-characterized. This study aimed to uncover the likely metabolism-related genes in Beckmannia syzigachne (American sloughgrass) resistant to fenoxaprop-p-ethyl. RESULTS Ultra-performance liquid chromatography - tandem mass spectrometry experiments showed that the resistant American sloughgrass biotype (R, SD-04-SS) showed enhanced degradation of this herbicide compared to the susceptible biotype (S, SD-12). R and S biotype were harvested at 24 h after fenoxaprop-p-ethyl treatment to conduct RNA sequencing (RNA-Seq) analysis to investigate the likely fenoxaprop-p-ethyl metabolic genes. The RNA-Seq libraries yield 417 969 980 clean reads. The de novo assembly generated 115 112 unigenes, of which 57 906 unigenes were annotated. Finally, we identified 273 cytochrome P450s, 178 oxidases, 47 glutathione S-transferases (GSTs), 166 glucosyltransferases (GTs) and 180 ABC transporter genes to determine the likely fenoxaprop-p-ethyl metabolism-related genes in R biotype. Twelve overlapping up-regulated genes in the R biotype (fenoxaprop-p-ethyl-treated R/non-treated R, fenoxaprop-p-ethyl-treated R/fenoxaprop-p-ethyl-treated S) were identified by RNA-Seq and the results were validated using qRT-PCR. Ten were identified as fenoxaprop-p-ethyl metabolism-related genes, including three P450s (homologous to CYP71D7, CYP99A2 and CYP71D10), one GST (homologous to GSTF1), two GTs (homologous to UGT90A1 and UGT83A1) and four oxidase genes. CONCLUSION This work demonstrates that the NTSR mechanism by means of enhanced detoxification of fenoxaprop-p-ethyl in American sloughgrass is very likely driven by herbicide metabolism related genes. The RNA-Seq data presented here provide a valuable resource for understanding the molecular mechanism of NTSR in American sloughgrass. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Shuang Bai
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
| | - Yanfang Zhao
- College of Chemistry and Pharmacy, Qingdao Agricultural University, Qingdao, China
| | - Yuanming Zhou
- Central Laboratory of Qingdao Agricultural University, Qingdao, China
| | - Mingliang Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
| | - Yihui Li
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
| | - Xiaoyong Luo
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
| | - Lingxu Li
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao, China
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Xie J, Li J, Jie Y, Xie D, Yang D, Shi H, Zhong Y. Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. gaud (ramie). BMC Genomics 2020; 21:40. [PMID: 31931705 PMCID: PMC6958601 DOI: 10.1186/s12864-020-6457-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 01/07/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie. RESULTS In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed and de novo transcriptome was assembled. Unigenes and differentially expressed genes (DEGs) in these three samples were identified. The analysis of DEGs by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed clear differences in gene expression between ER and FER. Some unigenes involved in secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, the ethylene respond factors (ERFs) in the ethylene signaling pathway were up-regulated in FER, and ent-kaurenoic acid oxidase (KAO) and GA 20-oxidase (GA20ox) for gibberellins biosynthesis were up-regulated while GA 2-oxidase (GA2ox) for gibberellin inactivation was down-regulated in FER. CONCLUSIONS Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.
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Affiliation(s)
- Jiyong Xie
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jiaqi Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Yucheng Jie
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Deyu Xie
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Di Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Yingli Zhong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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Zeng Z, Wang Y, Liu C, Yang X, Wang H, Li F, Liu T. Linkage mapping of quantitative trait loci for fiber yield and its related traits in the population derived from cultivated ramie and wild B. nivea var. tenacissima. Sci Rep 2019; 9:16855. [PMID: 31728008 PMCID: PMC6856109 DOI: 10.1038/s41598-019-53399-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/29/2019] [Indexed: 12/02/2022] Open
Abstract
Ramie is an important natural fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood, which has dramatically hindered the breeding of high yield in this fiber crop. Herein, a high-density genetic map with 6,433 markers spanning 2476.5 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in a total of 47 QTLs identified. Forty QTLs were mapped into 12 genomic regions, thus forming 12 QTL clusters. Among 47 QTLs, there were 14 QTLs whose wild allele from BNT was beneficial. Interestingly, all QTLs in Cluster 10 displayed overdominance, indicating that the region of this cluster was likely heterotic loci. In addition, four fiber yield-related genes underwent positive selection were found either to fall into the FY-related QTL regions or to be near to the identified QTLs. The dissection of FY and FY-related traits not only improved our understanding to the genetic basis of these traits, but also provided new insights into the domestication of FY in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Chan Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | | | | | - Fu Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
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Chen J, Rao J, Wang Y, Zeng Z, Liu F, Tang Y, Chen X, Liu C, Liu T. Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis. Genes (Basel) 2019; 10:genes10110842. [PMID: 31653111 PMCID: PMC6896145 DOI: 10.3390/genes10110842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022] Open
Abstract
Ramie fibers, one of the most important natural fibers in China, are mainly composed of lignin, cellulose, and hemicellulose. As the high lignin content in the fibers results in a prickly texture, the lignin content is deemed to be an important trait of the fiber quality. In this study, the genetic basis of the fiber lignin content was evaluated, resulting in the identification of five quantitative trait loci (QTLs). Three genes, whole_GLEAN_10021050, whole_GLEAN_10026962, and whole_GLEAN_10009464 that were identified on the QTL regions of qLC7, qLC10, and qLC13, respectively, were found to be homologs of the Arabidopsis lignin biosynthetic genes. Moreover, all three genes displayed differential expression in the barks located in the top and middle parts of the stem, where lignin was not being synthesized and where it was being biosynthesized, respectively. Sequence comparison found that these three genes had wide variations in their coding sequences (CDSs) and putative promoter regions between the two parents, especially the MYB gene whole_GLEAN_10021050, whose protein had insertions/deletions of five amino acids and substitutions of two amino acids in the conserved domain. This evidence indicates that these three genes are potentially involved in lignin biosynthesis in ramie fibers. The QTLs identified from this study provide a basis for the improvement of lignin content and fiber quality in ramie breeding. The characterization of the three candidate genes here will be helpful for the future clarification of their functions in ramie.
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Affiliation(s)
- Jianrong Chen
- College of Biological and Environmental Engineering, Changsha University, Changsha 410003, China.
| | - Jing Rao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Fang Liu
- College of Biological and Environmental Engineering, Changsha University, Changsha 410003, China.
| | - Yinghong Tang
- College of biological and environmental sciences, Hunan University of Arts and Science, Changde 410128, China.
| | - Xiaorong Chen
- Laboratory of ramie, Yichun Institute of Agricultural Sciences, Yichun 336000, China.
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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Wang Y, Zeng Z, Li F, Yang X, Gao X, Ma Y, Rao J, Wang H, Liu T. A genomic resource derived from the integration of genome sequences, expressed transcripts and genetic markers in ramie. BMC Genomics 2019; 20:476. [PMID: 31185891 PMCID: PMC6558782 DOI: 10.1186/s12864-019-5878-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022] Open
Abstract
Background The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber crop. Results We obtained a high-quality transcriptome consisting of 30,591 non-redundant transcripts using single-molecule long-read sequencing and proposed it as a universal ramie transcriptome. Additionally, 55,882 single nucleotide polymorphisms (SNPs) were identified and a high-density genetic map was developed. Based on this genetic map, 181.7 Mb ramie genome sequences were assembled into 14 chromosomes. For the convenient use of these resources, 29,286 (~ 95.7%) of the transcripts and all 55,882 SNPs, along with 1827 previously reported sequence repeat markers (SSRs), were mapped into the ramie genome, and 22,343 (~ 73.0%) transcripts, 50,154 (~ 89.7%) SNPs, and 1466 (~ 80.3%) SSRs were assigned to a specific location in the corresponding chromosome. Conclusion This is the first study to characterize the ramie transcriptome by long-read sequencing, and the substantial number of transcripts of significant length obtained will accelerate our understanding of ramie growth and development. This integration of genome sequences, expressed transcripts, and genetic markers will provide an extremely useful resource for genetic, molecular, and breeding studies of ramie. Electronic supplementary material The online version of this article (10.1186/s12864-019-5878-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanzhou Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Fu Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | | | - Xinyue Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Yonghong Ma
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jing Rao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | | | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
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12
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Huang K, Zhu A, Chen X, Shi Y, Tang Q, Wang X, Sun Z, Luan M, Chen J. Comparative transcriptomics reveals the selection patterns of domesticated ramie. Ecol Evol 2019; 9:7057-7068. [PMID: 31380033 PMCID: PMC6662332 DOI: 10.1002/ece3.5271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 04/08/2019] [Accepted: 04/29/2019] [Indexed: 11/20/2022] Open
Abstract
Although domestication has dramatically altered the phenotype, physiology, and life history of ramie (Boehmeria nivea) plants, few studies have investigated the effects of domestication on the structure and expression pattern of genes in this fiber crop. To investigate the selective pattern and genetic relationships among a cultivated variety of ramie (BNZ: B. nivea, ZZ1) and four wild species, BNT (B. nivea var. tenacissima), BNN (B. nivea var. nipononivea), BNW (B. nivea var. nivea), and BAN (B. nivea var. viridula), in the section Tilocnide, we performed an RNA sequencing analysis of these ramie species. The de novo assembly of the "all-ramie" transcriptome yielded 119,114 unigenes with an average length of 633 bp, and a total of 7,084 orthologous gene pairs were identified. The phylogenetic tree showed that the cultivar BNZ clustered with BAN in one group, BNW was closely related to BNT, and BNN formed a separate group. Introgression analysis indicated that gene flow occurred from BNZ to BNN and BAN, and between BAN and BNN. Among these orthologs, 2,425 and 269 genes underwent significant purifying and positive selection, respectively. For these positively selected genes, oxidation-reduction process (GO:0055114) and stress response pathways (GO:0006950) were enriched, indicating that modulation of the cellular redox status was important during both ramie fiber evolution and improvement. Two genes related to the suppression of flowering and one gene annotated as a flowering-promoting factor were subjected to positive selection, probably caused by human manipulation. Additionally, five genes were homologs of those involved in abiotic stress tolerance and disease resistance, with higher expression levels in the cultivar BNZ than in the wild species. Collectively, the results of this study indicated that domestication has resulted in the upregulation of many genes involved in the abiotic and biotic stress responses, fiber yield, and plant growth of ramie.
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Affiliation(s)
- Kun‐Yong Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Ai‐Guo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | | | - Ya‐Liang Shi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Xiao‐Fei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Zhi‐Min Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Ming‐Bao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Jian‐Hua Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
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13
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Huang X, Wang B, Xi J, Zhang Y, He C, Zheng J, Gao J, Chen H, Zhang S, Wu W, Liang Y, Yi K. Transcriptome Comparison Reveals Distinct Selection Patterns in Domesticated and Wild Agave Species, the Important CAM Plants. Int J Genomics 2018; 2018:5716518. [PMID: 30596084 PMCID: PMC6282153 DOI: 10.1155/2018/5716518] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 08/21/2018] [Accepted: 09/24/2018] [Indexed: 01/19/2023] Open
Abstract
Agave species are an important family of crassulacean acid metabolism (CAM) plants with remarkable tolerance to heat and drought stresses (Agave deserti) in arid regions and multiple agricultural applications, such as spirit (Agave tequilana) and fiber (Agave sisalana) production. The agave genomes are commonly too large to sequence, which has significantly restricted our understanding to the molecular basis of stress tolerance and economic traits in agaves. In this study, we collected three transcriptome databases for comparison to reveal the phylogenic relationships and evolution patterns of the three agave species. The results indicated the close but distinctly domesticated relations between A. tequilana and A. sisalana. Natural abiotic and biotic selections are very important factors that have contributed to distinct economic traits in agave domestication together with artificial selection. Besides, a series of candidate unigenes regulating fructan, fiber, and stress response-related traits were identified in A. tequilana, A. sisalana, and A. deserti, respectively. This study represents the first transcriptome comparison within domesticated and wild agaves, which would serve as a guidance for further studies on agave evolution, environmental adaptation, and improvement of economically important traits.
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Affiliation(s)
- Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | | | - Chunping He
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jinlong Zheng
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jianming Gao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Helong Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Shiqing Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Weihuai Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yanqiong Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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14
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Liu C, Zeng L, Zhu S, Wu L, Wang Y, Tang S, Wang H, Zheng X, Zhao J, Chen X, Dai Q, Liu T. Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud). DNA Res 2018; 25:173-181. [PMID: 29149285 PMCID: PMC5909428 DOI: 10.1093/dnares/dsx047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/01/2017] [Indexed: 12/26/2022] Open
Abstract
Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58.2-Mb genome sequence and 4,304 molecular markers. A genomic comparison identified 1,075 unique gene families in ramie, containing 4,082 genes. Among these unique genes, five were cellulose synthase genes that were specifically expressed in stem bark, and 3 encoded a WAT1-related protein, suggesting that they are probably related to high bast fiber yield. An evolutionary analysis detected 106 positively selected genes, 22 of which were related to nitrogen metabolism, indicating that they are probably responsible for the crude protein content and vegetative growth of domesticated varieties. This study is the first to characterize the genome and develop a high-density genetic map of ramie and provides a basis for the genetic and molecular study of this crop.
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Affiliation(s)
- Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Liangbin Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Lingqing Wu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Hongwu Wang
- Xianning Agriculture Academy of sciences, Hubei, China
| | - Xia Zheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing, China
| | - Xiaorong Chen
- Yichun Institute of Agricultural Sciences, Jiangxi, China
| | - Qiuzhong Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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15
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Guo P, Zheng Y, Peng D, Liu L, Dai L, Chen C, Wang B. Identification and expression characterization of the Phloem Protein 2 (PP2) genes in ramie (Boehmeria nivea L. Gaudich). Sci Rep 2018; 8:10734. [PMID: 30013165 PMCID: PMC6048116 DOI: 10.1038/s41598-018-28953-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 06/28/2018] [Indexed: 11/20/2022] Open
Abstract
Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in sieve elements and companion cells, which play important roles in the maintenance of morphology, photoassimilate transportation and wound protection in higher plants, but to date, no PP2 (BnPP2) genes had been identified in ramie. Here, a total of 15 full-length BnPP2 genes were identified. These BnPP2 genes exhibited different responses to abiotic stresses. Interestingly, the BnPP2 genes are more sensitive to insect pests than to other stresses. A study of the BnPP2-15 promoter revealed that pBnPP2-15 could drive specific GUS expression in the petiole, root and stamen and could also be induced by mechanical wounding and aphid infection in transgenic Arabidopsis lines. The subcellular localization of six BnPP2 proteins showed that GFP-BnPP2-1, GFP-BnPP2-6, GFP-BnPP2-7, GFP-BnPP2-9, GFP-BnPP2-11 and GFP-BnPP2-12 were predominantly located in the cytoplasm. These results provide useful information elucidating the functions of BnPP2 genes in ramie.
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Affiliation(s)
- Pingan Guo
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Yancheng Zheng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Lunjin Dai
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Cong Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
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16
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Grinshpun A, Halpern N, Granit RZ, Hubert A, Hamburger T, Laitman Y, Shacham-Shmueli E, Peerless Y, Friedman E, Peretz T. Phenotypic characteristics of colorectal cancer in BRCA1/2 mutation carriers. Eur J Hum Genet 2018; 26:382-386. [PMID: 29321669 DOI: 10.1038/s41431-017-0067-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 09/09/2017] [Accepted: 11/23/2017] [Indexed: 12/23/2022] Open
Abstract
Mutations in the BRCA1/2 genes were recently shown to be associated with an increased risk for colorectal cancer. We characterized the largest cohort available of BRCA1/2 mutation carriers with colorectal cancer. We analyzed 32 patients with lower gastrointestinal cancers and germline BRCA1/2 mutations from two large academic hospital registries; 91% of patients were of Ashkenazi ancestry, 78% were women, and 62.5% were carriers of BRCA1 gene mutations. A high percentage of colorectal tumors (34.5%) had a mucinous histology and were located atypically in the left colon. Two patients had anal cancer with unusual histology and an additional patient had mucinous small bowel carcinoma. Gene expression analysis showed significant correlation between the gene signatures of left mucinous colorectal cancer and basal-like breast cancer. Our results imply that Ashkenazi BRCA1/2 mutation carriers with colorectal cancer might have unique characteristics with a high rate of left-sided, mucinous histology colorectal cancer, and possibly anal carcinoma. This report suggests a phenotypic influence of defects in DNA repair genes on colorectal tumors.
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Affiliation(s)
- Albert Grinshpun
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
| | - Naama Halpern
- Institute of Oncology, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roy Zvi Granit
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ayala Hubert
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Hamburger
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Yael Laitman
- Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Einat Shacham-Shmueli
- Institute of Oncology, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yehudit Peerless
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eitan Friedman
- Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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17
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Guerriero G, Behr M, Legay S, Mangeot-Peter L, Zorzan S, Ghoniem M, Hausman JF. Transcriptomic profiling of hemp bast fibres at different developmental stages. Sci Rep 2017; 7:4961. [PMID: 28694530 PMCID: PMC5504027 DOI: 10.1038/s41598-017-05200-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/24/2017] [Indexed: 02/08/2023] Open
Abstract
Bast fibres are long extraxylary cells which mechanically support the phloem and they are divided into xylan- and gelatinous-type, depending on the composition of their secondary cell walls. The former, typical of jute/kenaf bast fibres, are characterized by the presence of xylan and a high degree of lignification, while the latter, found in tension wood, as well as flax, ramie and hemp bast fibres, have a high abundance of crystalline cellulose. During their differentiation, bast fibres undergo specific developmental stages: the cells initially elongate rapidly by intrusive growth, subsequently they cease elongation and start to thicken. The goal of the present study is to provide a transcriptomic close-up of the key events accompanying bast fibre development in textile hemp (Cannabis sativa L.), a fibre crop of great importance. Bast fibres have been sampled from different stem regions. The developmental stages corresponding to active elongation and cell wall thickening have been studied using RNA-Seq. The results show that the fibres sampled at each stem region are characterized by a specific transcriptomic signature and that the major changes in cell wall-related processes take place at the internode containing the snap point. The data generated also identify several interesting candidates for future functional analysis.
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Affiliation(s)
- Gea Guerriero
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg.
| | - Marc Behr
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
- Université catholique de Louvain, Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Louvain-la-Neuve, B-1348, Belgium
| | - Sylvain Legay
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Lauralie Mangeot-Peter
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
- Institut National de la Recherche Agronomique, Université de Lorraine, UMR 1136, Interactions Arbres-Microorganismes, Champenoux, F-54280, France
| | - Simone Zorzan
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Mohammad Ghoniem
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Jean-Francois Hausman
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
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18
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HUANG XING, BAO YANING, WANG BO, LIU LIJUN, CHEN JIE, DAI LUNJIN, BALOCH SANAULLAH, PENG DINGXIANG. Identification of small auxin-up RNA (SAUR) genes in Urticales plants: mulberry (Morus notabilis), hemp (Cannabis sativa) and ramie (Boehmeria nivea). J Genet 2016; 95:119-29. [DOI: 10.1007/s12041-016-0622-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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19
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Transcriptome Analysis of Ramie (Boehmeria nivea L. Gaud.) in Response to Ramie Moth (Cocytodes coerulea Guenée) Infestation. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3702789. [PMID: 27034936 PMCID: PMC4789370 DOI: 10.1155/2016/3702789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/13/2015] [Accepted: 02/01/2016] [Indexed: 11/27/2022]
Abstract
The ramie moth Cocytodes coerulea Guenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore, de novo assembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.
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20
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Zhang L, Ming R, Zhang J, Tao A, Fang P, Qi J. De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.). BMC Genomics 2015; 16:1062. [PMID: 26666317 PMCID: PMC4678609 DOI: 10.1186/s12864-015-2256-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Jute fiber, extracted from stem bast, is called golden fiber. It is essential for fiber improvement to discover the genes associated with jute development at the vegetative growth stage. However, only 858 EST sequences of jute were deposited in the GenBank database. Obviously, the public available data is far from sufficient to understand the molecular mechanism of the fiber biosynthesis. It is imperative to conduct transcriptomic sequence for jute, which can be used for the discovery of a number of new genes, especially genes involved in cellulose biosynthesis. RESULTS A total of 79,754,600 clean reads (7.98 Gb) were generated using Illumina paired-end sequencing. De novo assembly yielded 48,914 unigenes with an average length of 903 bp. By sequence similarity searching for known proteins, 27,962 (57.16 %) unigenes were annotated for their function. Out of these annotated unigenes, 21,856 and 11,190 unigenes were assigned to gene ontology (GO) and euKaryotic Ortholog Groups (KOG), respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 14,216 unigenes were mapped to 268 KEGG pathways. Moreover, 5 Susy, 3 UGPase, 9 CesA, 18 CSL, 2 Kor (Korrigan), and 12 Cobra unigenes involving in cellulose biosynthesis were identified. Among these unigenes, the unigenes of comp11264_c0 (SuSy), comp24568_c0 (UGPase), comp11363_c0 (CesA), comp11363_c1 (CesA), comp24217_c0 (CesA), and comp23531_c0 (CesA), displayed relatively high expression level in stem bast using FPKM and RT-qPCR, indicating that they may have potential value of dissecting mechanism on cellulose biosynthesis in jute. In addition, a total of 12,518 putative gene-associate SNPs were called from these assembled uingenes. CONCLUSION We characterized the transcriptome of jute, discovered a broad survey of unigenes associated with vegetative growth and development, developed large-scale SNPs, and analyzed the expression patterns of genes involved in cellulose biosynthesis for bast fiber. All these provides a valuable genomics resource, which will accelerate the understanding of the mechanism of fiber development in jute.
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Affiliation(s)
- Liwu Zhang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Aifen Tao
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Pingping Fang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jianmin Qi
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Chen J, Yu R, Liu L, Wang B, Peng D. Large-scale developing of simple sequence repeat markers and probing its correlation with ramie (Boehmeria nivea L.) fiber quality. Mol Genet Genomics 2015; 291:753-61. [PMID: 26577947 DOI: 10.1007/s00438-015-1143-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
Marker-assisted selection is an important component of the discipline of molecular breeding. Using DNA markers to assist in plant breeding, the efficiency and precision could be greatly increased. However, the scarcity number of identified DNA markers has hindered the research and the breeding process of ramie (Boehmeria nivea L.) in many aspects, especially fiber quality, one of the top-priority breeding objectives of ramie. In this study, 4230 SSR loci were identified in 3969 unigenes (6.80 % of 58,369), which were de novo assembled from the transcriptome involving different ramie fiber developmental stages. Among these SSRs, the dinucleotides (1599, 37.80 %) and trinucleotides (772, 18.25 %) were most abundant; the motifs AG/CT (1140, 26.94 %), AT/AT (407, 9.62 %) and AGA/TCT (246, 8.31 %) comprised the three most abundant repeats. A total of 2431 primer pairs were designed flanking the SSRs and 1050 of them were employed in PCR amplification for their usefulness using three ramie cultivars. The results showed that 88.10 % of these primers could generate positive PCR bands in any of the three cultivars. Further phylogenetic analysis that conducted from the PCR amplification of 52 specifically sifted SSR primers within 17 cultivars approved that the possible correlation may exist between the primers and ramie fiber quality. These developed SSR markers could be applied in downstream studies, like genetic and physical maps, quantitative trait loci mapping, genetic diversity studies and cultivar fingerprinting, and breeding processes of ramie with better fiber quality under further confirmation of the correlation with ramie fiber quality.
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Affiliation(s)
- Jie Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Runqing Yu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China.
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China.
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Chen J, Dai L, Wang B, Liu L, Peng D. Cloning of expansin genes in ramie (Boehmeria nivea L.) based on universal fast walking. Gene 2015; 569:27-33. [PMID: 25481635 DOI: 10.1016/j.gene.2014.11.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
Abstract
Gene cloning is the first step to study the expression profiles and functions of a particular gene; considerable cloning methods have been developed. Expansin, thought to involve in the cell-wall modification events, was not cloned in ramie (Boehmeria nivea L.), which is one of the most important bast fiber crops with little conducted molecular research, especially on its fiber development. Studying the expansin gene family will uncover its possible relationship with ramie fiber development and other growth events. As a result, five expansin genes were cloned with full-length and their sequence information was investigated. Additionally, the phylogenetic analysis was conducted, which suggested that the cloned genes belong to the α-subfamily, and these genes expressed differently during ramie fiber developmental process. In this study, we aimed to apply a strategy for cloning novel full-length genes from genomic DNA of ramie, based on using degenerate primers, touchdown polymerase chain reaction and universal fast walking protocols. By cloning five full-length expansin genes, we believe the polymerase chain reaction-based gene cloning strategy could be applied to general gene studies in ramie and other crops.
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Affiliation(s)
- Jie Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China.
| | - Lunjin Dai
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China.
| | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China.
| | - Lijun Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China.
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, #1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China.
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Arun-Chinnappa KS, McCurdy DW. De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research. FRONTIERS IN PLANT SCIENCE 2015; 6:217. [PMID: 25914703 PMCID: PMC4391045 DOI: 10.3389/fpls.2015.00217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/17/2015] [Indexed: 05/20/2023]
Abstract
Vicia faba (L.) is an important cool-season grain legume species used widely in agriculture but also in plant physiology research, particularly as an experimental model to study transfer cell (TC) development. TCs are specialized nutrient transport cells in plants, characterized by invaginated wall ingrowths with amplified plasma membrane surface area enriched with transporter proteins that facilitate nutrient transfer. Many TCs are formed by trans-differentiation from differentiated cells at apoplasmic/symplasmic boundaries in nutrient transport. Adaxial epidermal cells of isolated cotyledons can be induced to form functional TCs, thus providing a valuable experimental system to investigate genetic regulation of TC trans-differentiation. The genome of V. faba is exceedingly large (ca. 13 Gb), however, and limited genomic information is available for this species. To provide a resource for future transcript profiling of epidermal TC differentiation, we have undertaken de novo assembly of a genome-wide transcriptome map for V. faba. Illumina paired-end sequencing of total RNA pooled from different tissues and different stages, including isolated cotyledons induced to form epidermal TCs, generated 69.5 M reads, of which 65.8 M were used for assembly following trimming and quality control. Assembly using a De-Bruijn graph-based approach generated 21,297 contigs, of which 80.6% were successfully annotated against GO terms. The assembly was validated against known V. faba cDNAs held in GenBank, including transcripts previously identified as being specifically expressed in epidermal cells across TC trans-differentiation. This genome-wide transcriptome map therefore provides a valuable tool for future transcript profiling of epidermal TC trans-differentiation, and also enriches the genetic resources available for this important legume crop species.
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Affiliation(s)
| | - David W. McCurdy
- Centre for Plant Science, School of Environmental and Life Sciences, The University of NewcastleNewcastle, NSW, Australia
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