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Ganguly A, Amin S, Al-Amin, Tasnim Chowdhury F, Khan H, Riazul Islam M. Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.). J Genet Eng Biotechnol 2024; 22:100376. [PMID: 38797551 PMCID: PMC11015510 DOI: 10.1016/j.jgeb.2024.100376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 05/29/2024]
Abstract
Jute (Corchorus sp.), a commercially important and eco-friendly crop, is widely cultivated in Bangladesh, India, and China. Some varieties of this tropical plant such as the Corchorus olitorius. Variety accession no. 2015 (acc. 2015) has been found to be low-temperature tolerant. The current study was designed to explore the genome-wide variations present in the tolerant plant acc. 2015 in comparison to the sensitive farmer popular variety Corchorus olitorius var. O9897 using the whole genome resequencing technique. Among different variations, intergenic Single Nucleotide Polymorphism (SNPs) and Insertion-Deletion (InDels) were found in the highest percentage whereas approximately 3% SNPs and 2% InDels were found in exonic regions in both plants. Gene enrichment analysis indicated the presence of acc. 2015 specific SNPs in the genes encoding peroxidase, ER lumen protein retaining receptor, and hexosyltransferase involved in stress response (GO:0006950) which were not present in sensitive variety O9897. Besides, distinctive copy number variation regions (CNVRs) comprising 120 gene loci were found in acc. 2015 with a gain of function from multiple copy numbers but absent in O9897. Gene ontology analysis revealed these gene loci to possess different receptors like kinases, helicases, phosphatases, transcription factors especially Myb transcription factors, regulatory proteins containing different binding domains, annexin, laccase, acyl carrier protein, potassium transporter, and vesicular transporter proteins that are responsible for low temperature induced adaptation pathways in plants. This work of identifying genomic variations linked to cold stress tolerance traits will help to develop successful markers that will pave the way to develop genetically modified cold-resistant jute lines for year-round cultivation to meet the demand for a sustainable fiber crop economy.
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Affiliation(s)
- Athoi Ganguly
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Shaheena Amin
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh; Department of Biochemistry and Molecular Biology, National Institute of Science and Technology, Dhaka, Bangladesh
| | - Al-Amin
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Farhana Tasnim Chowdhury
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Haseena Khan
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.
| | - Mohammad Riazul Islam
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.
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Koo H, Lee GW, Ko SR, Go S, Kwon SY, Kim YM, Shin AY. Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms. Sci Data 2023; 10:713. [PMID: 37853021 PMCID: PMC10584963 DOI: 10.1038/s41597-023-02631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Improvements in long read DNA sequencing and related techniques facilitated the generation of complex eukaryotic genomes. Despite these advances, the quality of constructed plant reference genomes remains relatively poor due to the large size of genomes, high content of repetitive sequences, and wide variety of ploidy. Here, we developed the de novo sequencing and assembly of high polyploid plant genome, Hibiscus syriacus, a flowering plant species of the Malvaceae family, using the Oxford Nanopore Technologies and Pacific Biosciences Sequel sequencing platforms. We investigated an efficient combination of high-quality and high-molecular-weight DNA isolation procedure and suitable assembler to achieve optimal results using long read sequencing data. We found that abundant ultra-long reads allow for large and complex polyploid plant genome assemblies with great recovery of repetitive sequences and error correction even at relatively low depth Nanopore sequencing data and polishing compared to previous studies. Collectively, our combination provides cost effective methods to improve genome continuity and quality compared to the previously reported reference genome by accessing highly repetitive regions. The application of this combination may enable genetic research and breeding of polyploid crops, thus leading to improvements in crop production.
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Affiliation(s)
- Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Gir-Won Lee
- SML Genetree Co. Ltd., Seoul, 05855, Republic of Korea
| | - Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34113, Korea
| | - Sangjin Go
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34113, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34113, Korea
| | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
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3
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Fiallos-Salguero MS, Li J, Li Y, Xu J, Fang P, Wang Y, Zhang L, Tao A. Identification of AREB/ABF Gene Family Involved in the Response of ABA under Salt and Drought Stresses in Jute ( Corchorus olitorius L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1161. [PMID: 36904020 PMCID: PMC10005393 DOI: 10.3390/plants12051161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The abscisic acid (ABA)-responsive element binding protein/ABRE-binding factor (AREB/ABF) subfamily members are essential to ABA signaling pathways and plant adaptation to various environmental stresses. Nevertheless, there are no reports on AREB/ABF in jute (Corchorus L.). Here, eight AREB/ABF genes were identified in the C. olitorius genome and classified into four groups (A-D) based on their phylogenetic relationships. A cis-elements analysis showed that CoABFs were widely involved in hormone response elements, followed by light and stress responses. Furthermore, the ABRE response element was involved in four CoABFs, playing an essential role in the ABA reaction. A genetic evolutionary analysis indicated that clear purification selection affects jute CoABFs and demonstrated that the divergence time was more ancient in cotton than in cacao. A quantitative real-time PCR revealed that the expression levels of CoABFs were upregulated and downregulated under ABA treatment, indicating that CoABF3 and CoABF7 are positively correlated with ABA concentration. Moreover, CoABF3 and CoABF7 were significantly upregulated in response to salt and drought stress, especially with the application of exogenous ABA, which showed higher intensities. These findings provide a complete analysis of the jute AREB/ABF gene family, which could be valuable for creating novel jute germplasms with a high resistance to abiotic stresses.
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Affiliation(s)
- Manuel Sebastian Fiallos-Salguero
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Crop Breeding for Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Crop Breeding for Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunqing Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Crop Breeding for Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiantang Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Crop Breeding for Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Crop Breeding for Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yankun Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Crop Breeding for Design, 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 Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Crop Breeding for Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Aifen Tao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Crop Breeding for Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Yang Z, Tian S, Li X, Dai Z, Yan A, Chen Z, Chen J, Tang Q, Cheng C, Xu Y, Deng C, Liu C, Kang L, Xie D, Zhao J, Chen X, Zhang X, Wu Y, Li A, Su J. Multi-omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:812-829. [PMID: 36129373 DOI: 10.1111/tpj.15983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi-omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome-wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole-3-acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.
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Affiliation(s)
- Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, 100015, China
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiangkong Li
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - An Yan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 637616, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Zhong Chen
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 637616, Singapore
| | - Jiquan Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Ling Kang
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Dongwei Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Xiaojun Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiaoyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yupeng Wu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Alei Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
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5
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Sarker U, Lin YP, Oba S, Yoshioka Y, Hoshikawa K. Prospects and potentials of underutilized leafy Amaranths as vegetable use for health-promotion. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 182:104-123. [PMID: 35487123 DOI: 10.1016/j.plaphy.2022.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/31/2022] [Accepted: 04/09/2022] [Indexed: 05/23/2023]
Abstract
Climate change causes environmental variation worldwide, which is one of the most serious threats to global food security. In addition, more than 2 billion people in the world are reported to suffer from serious malnutrition, referred to as 'hidden hunger.' Dependence on only a few crops could lead to the loss of genetic diversity and high fragility of crop breeding in systems adapting to global scale climate change. The exploitation of underutilized species and genetic resources, referred to as orphan crops, could be a useful approach for resolving the issue of adaptability to environmental alteration, biodiversity preservation, and improvement of nutrient quality and quantity to ensure food security. Moreover, the use of these alternative crops will help to increase the human health benefits and the income of farmers in developing countries. In this review, we highlight the potential of orphan crops, especially amaranths, for use as vegetables and health-promoting nutritional components. This review highlights promising diversified sources of amaranth germplasms, their tolerance to abiotic stresses, and their nutritional, phytochemical, and antioxidant values for vegetable purposes. Betalains (betacyanins and betaxanthins), unique antioxidant components in amaranth vegetables, are also highlighted regarding their chemodiversity across amaranth germplasms and their stability and degradation. In addition, we discuss the physiological functions, antioxidant, antilipidemic, anticancer, and antimicrobial activities, as well as the biosynthesis pathway, molecular, biochemical, genetics, and genomic mechanisms of betalains in detail.
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Affiliation(s)
- Umakanta Sarker
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - Ya-Ping Lin
- World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan
| | - Shinya Oba
- Faculty of Applied Biological Science, Gifu University, Gifu, 501-1193, Japan
| | - Yosuke Yoshioka
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Ibaraki, Japan; Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Ken Hoshikawa
- World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan; Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan; Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ohwashi 1-1, Tsukuba, Ibaraki, 305-8686, Japan.
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6
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Wang Z, Xue JY, Hu SY, Zhang F, Yu R, Chen D, Van de Peer Y, Jiang J, Song A, Ni L, Hua J, Lu Z, Yu C, Yin Y, Gu C. The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat. HORTICULTURE RESEARCH 2022; 9:uhac067. [PMID: 35480957 PMCID: PMC9039499 DOI: 10.1093/hr/uhac067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Hibiscus hamabo is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms. Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number (107 309 genes). Comparison of the H. hamabo genome with that of its close relative Hibiscus cannabinus, which has not experienced a recent WGT, indicated that genes associated with high stress resistance have been preferentially preserved in the H. hamabo genome, suggesting an underlying association between polyploidy and stronger stress resistance. Transcriptomic data indicated that genes in the roots and leaves responded differently to stress. In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas no such rapid response was observed from genes in leaves. Using co-expression networks, potential stress resistance genes were identified for use in future functional investigations. The genome sequence, along with several transcriptome datasets, provide insights into genome evolution and the mechanism of salt and waterlogging tolerance in H. hamabo, suggesting the importance of polyploidization for environmental adaptation.
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Affiliation(s)
- Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Longjie Ni
- College of Forest Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhiguo Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
- College of Forest Sciences, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Utilization of Agricultural Germplasm, Nanjing, 210014, China
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7
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Zhang L, Ma X, Zhang X, Xu Y, Ibrahim AK, Yao J, Huang H, Chen S, Liao Z, Zhang Q, Niyitanga S, Yu J, Liu Y, Xu X, Wang J, Tao A, Xu J, Chen S, Yang X, He Q, Lin L, Fang P, Zhang L, Ming R, Qi J, Zhang L. Reference genomes of the two cultivated jute species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2235-2248. [PMID: 34170619 PMCID: PMC8541789 DOI: 10.1111/pbi.13652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/08/2021] [Accepted: 06/17/2021] [Indexed: 05/10/2023]
Abstract
Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome-level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo-chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole-genome resequencing resulted in post-domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker-trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome-wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.
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Affiliation(s)
- Lilan Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaokai Ma
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xingtan Zhang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yi Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aminu Kurawa Ibrahim
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiayu Yao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Huaxing Huang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shuai Chen
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhenyang Liao
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qing Zhang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiaxin Yu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yi Liu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiuming Xu
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jingjing Wang
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aifen Tao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiantang Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Siyuan Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xin Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qingyao He
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lihui Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liemei Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ray Ming
- Department of Plant Biologythe University of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast ChinaFujian Public Platform for Germplasm Resources of Bast Fibre CropsFujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and BiotechnologyHaixia Institue of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
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Zhang Y, Zheng C, Islam S, Kim YM, Sankoff D. Branching Out to Speciation in a Model of Fractionation: The Malvaceae. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1875-1884. [PMID: 31869797 DOI: 10.1109/tcbb.2019.2955649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fractionation is the genome-wide process of losing one gene per duplicate pair following whole genome doubling (WGD). An important type of evidence for duplicate gene loss is the frequency distribution of similarities between paralogous gene pairs in a genome or orthologous gene pairs in two species. We extend a previous branching process model for fractionation, originally accounting for paralog similarities, to encompass the distribution of ortholog similarities, after multiple rounds of whole genome doubling and fractionation, with the speciation event occurring at any point. We estimate the fractionation rates during all the inter-event periods in each lineage of the plant family Malvaceae. We suggest a major correction of the phylogenetic position of the durian sub-family, and discover a new triplication event in this lineage.
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9
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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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Djemiel C, Goulas E, Badalato N, Chabbert B, Hawkins S, Grec S. Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota. Front Genet 2020; 11:581664. [PMID: 33193706 PMCID: PMC7652851 DOI: 10.3389/fgene.2020.581664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
The mechanical and chemical properties of natural plant fibers are determined by many different factors, both intrinsic and extrinsic to the plant, during growth but also after harvest. A better understanding of how all these factors exert their effect and how they interact is necessary to be able to optimize fiber quality for use in different industries. One important factor is the post-harvest process known as retting, representing the first step in the extraction of bast fibers from the stem of species such as flax and hemp. During this process microorganisms colonize the stem and produce hydrolytic enzymes that target cell wall polymers thereby facilitating the progressive destruction of the stem and fiber bundles. Recent advances in sequencing technology have allowed researchers to implement targeted metagenomics leading to a much better characterization of the microbial communities involved in retting, as well as an improved understanding of microbial dynamics. In this paper we review how our current knowledge of the microbiology of retting has been improved by targeted metagenomics and discuss how related '-omics' approaches might be used to fully characterize the functional capability of the retting microbiome.
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Affiliation(s)
- Christophe Djemiel
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Estelle Goulas
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Nelly Badalato
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Brigitte Chabbert
- Université de Reims Champagne Ardenne, INRAE, UMR FARE A 614, Reims, France
| | - Simon Hawkins
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Grec
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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Shafqat W, Jaskani MJ, Maqbool R, Sattar Khan A, Abbas Naqvi S, Ali Z, Ahmad Khan I. Genome Wide Analysis of Citrus sinensis Heat Shock Proteins. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2529. [PMID: 34056019 PMCID: PMC8148642 DOI: 10.30498/ijb.2020.2529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Plant and animal cells possess a ubiquitous protein known as heat shock proteins (HSPs). Hsps were originally described in relation to heat shock and against abiotic and biotic stresses. Heat shock protein was classified in other crops on the bases of single classes or all classes but in Citrus sinensis Hsps groups, classes, subfamilies and members were not classified and characterized up to our knowledge. Objectives Present study was focused on the identification and grouping of C. sinensis Hsps (CsHsps) classes, members among classes, their phylogenetic relationship, gene structure, conserved motifs and identification of proteins by using bioinformatics tools and analyses. Materials and Methods Genomic, Peptide and CDS sequences of CsHsps were downloaded from phytozome. MEGA 7 used for the phylogenetic analysis, GSDS for gene structure, UGENE for the multiple sequence alignment and MEME suite for the conserved motif analysis. Results The genome size of C. sinensis was 367 Mb, Chromosome number (2n)18, having 151 Hsps with six groups CsHsp10, 20, 40, 60,70 and 90. CsHsp20 was the largest group having 54 members, followed by CsHsp60 and CsHsp70 both having 30 members respectively. Conclusion CsHsps members within a class shared more similar gene and protein structure. CsHsp 60, CsHsp 70 and CsHsp90 shared more conserved and similar amino acid pattern. Each class had some important proteins such as Cpn in CsHsp10, Hypothetical proteins in CsHsp20 and 40, Dnak in CsHsp60, Molecular chaperone in CsHsp70 and Hsp90 in CsHsp90. These proteins are produced by cells in response to stresses in citrus. Chaperonins and some hypothetical proteins identified in CsHsps, help in ATP synthesis and protein degradation. This is genome wide analysis and classification sets the groundwork for future investigations to fully characterize functionally the Citrus Hsps families and underscores the relevance of Hsps response to abiotic and biotic stresses in Citrus.
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Affiliation(s)
- Waqar Shafqat
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Jafar Jaskani
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Rizwana Maqbool
- Center for Advanced Studies, University of Agriculture, Faisalabad, Pakistan.,Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Ahmad Sattar Khan
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Summar Abbas Naqvi
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Zulfiqar Ali
- Plant Breeding and Genetics, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Iqrar Ahmad Khan
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
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Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven legume species. Genetica 2020; 148:253-268. [PMID: 32949338 DOI: 10.1007/s10709-020-00103-5] [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: 05/29/2019] [Accepted: 09/02/2020] [Indexed: 10/23/2022]
Abstract
Availability of genome sequence of different legume species has provided an opportunity to characterize the abundance, distribution, and divergence of canonical intact long terminal retrotransposons (In-LTR-RT) superfamilies. Among seven legume species, Arachis ipaensis (Aip) showed the highest number of full-length canonical In-LTR-RTs (3325), followed by Glycine max (Gma, 2328), Vigna angularis (Van, 1625), Arachis durensis (Adu, 1348), Lotus japonicus (Lja, 1294), Medicago truncatula (Mtr, 788), and Circer arietinum (Car, 124). Divergence time analysis demonstrated that the amplification timeframe of LTR-RTs dramatically varied in different families. The average insertion time of Copia element varied from 0.51 (Van) to 1.37 million years ago (Mya) (Adu, and Aip), whereas that of Gypsy was between 0.22 (Mtr) and 1.82 Mya (Adu). Bayesian phylogenetic tree analysis suggested that the 1397 and 1917 reverse transcriptase (RT) domains of Copia and Gypsy families of the seven legume species were clustered into 7 and 14 major groups, respectively. The highest proportion (approximately 94.79-100%) of transposable element (TE)-associated genes assigned to pathways was mapped to metabolism-related pathways in all species. The results enabled the structural understanding of full-length In-LTR-RTs and will be valuable resource for the further study of the impact of TEs on gene structure and expression in legume species.
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Martin SL, Parent JS, Laforest M, Page E, Kreiner JM, James T. Population Genomic Approaches for Weed Science. PLANTS (BASEL, SWITZERLAND) 2019; 8:E354. [PMID: 31546893 PMCID: PMC6783936 DOI: 10.3390/plants8090354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.
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Affiliation(s)
- Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Jean-Sebastien Parent
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
| | - Eric Page
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON N0R 1G0, Canada.
| | - Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Tracey James
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
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Hossain MS, Ahmed R, Haque MS, Alam MM, Islam MS. Identification and validation of reference genes for real-time quantitative RT-PCR analysis in jute. BMC Mol Biol 2019; 20:13. [PMID: 31035927 PMCID: PMC6489354 DOI: 10.1186/s12867-019-0130-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/16/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene expression profiles of a target gene can provide valuable clues towards the understanding of its biological function. Reverse transcription quantitative real-time PCR (qRT-PCR) is the best method for targeted gene expression analysis due to its sensitivity and reproducibility. However, calculating relative expression requires reference genes, which must be stable across various biological conditions. For this purposes, 11 prospective genes namely, 28S RNA, ACT7, CYP, EF1A, EF2, ETIF3E, GAPDH, PP2Ac, PTB, UBC2 and UBI1 were evaluated for their potential use as reference genes in jute. RESULTS The expression stabilities of eleven prospective genes were analyzed in various jute plant tissues, such as the root, stick, bark, leaf, flower, seed and fiber, as well as under abiotic (waterlogged, drought and salinity) and biotic stress (infestation with Macrophomina phaseolina) conditions with different time points. All 11 genes were variably expressed in different tissues and stress conditions. To find suitable reference genes in different sample sets, a comprehensive approach based on four statistical algorithms such as GeNorm, BestKeeper, NormFinder the ΔCt was used. The PP2Ac and EF2 genes were the most stably expressed across the different tissues. ACT7 and UBC2 were suitable reference genes under drought stress, and CYP and PP2Ac were the most appropriate after inoculation with Macrophomina phaseolina. Under salinity stress, PP2Ac and UBC2 were the best genes, and ACT7 and PP2Ac were the most suitable under waterlogged conditions. CONCLUSION Expression stability of reference genes from jute varied in different tissues and selected experimental conditions. Our results provide a valuable resource for the accurate normalization of gene expression experiments in fiber research for important bast fiber crops.
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Affiliation(s)
- Md. Sabbir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Samiul Haque
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Monjurul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md. Shahidul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
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15
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Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in tossa jute (Corchorus olitorius L.). Mol Genet Genomics 2019; 294:479-492. [DOI: 10.1007/s00438-018-1526-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022]
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16
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Majumder S, Datta K, Sarkar C, Saha SC, Datta SK. The Development of Macrophomina phaseolina (Fungus) Resistant and Glufosinate (Herbicide) Tolerant Transgenic Jute. FRONTIERS IN PLANT SCIENCE 2018; 9:920. [PMID: 30042772 PMCID: PMC6048421 DOI: 10.3389/fpls.2018.00920] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/11/2018] [Indexed: 05/10/2023]
Abstract
The worldwide demand for natural bast fibers is met aptly by the long, golden and silky fibers of jute. This highest bast fiber producing crop is of great applicability and is extensively used in paper and textile industry. Macrophomina phaseolina (Tassi) Goid is a severely devastating necrotrophic fungal pathogen causing stem rot, root rot, and charcoal rot diseases in both the cultivated species of jute - Corchorus capsularis and Corchorus olitorius. Another major problem faced in jute cultivation is profuse weed infestation in the fields. Huge losses in quality fiber production is caused by this pathogenic fungi and cultivation cost increases as well due to weed management expenditure during cropping season. To solve these long persisting jute cultivation challenges, the chitinase (chi11) gene (to provide fungus resistance) and the bar gene (to provide herbicide tolerance) have been incorporated in C. capsularis JRC-321 via Agrobacterium transformation and analyzed up to T2 generation. Stable integration and expression of these two genes in the jute genome was confirmed upon extensive analyses. Transgenic plants showed higher chitinase expression and chitin degrading activity than non-transgenic control plants. Antifungal activity significantly increased in transgenic plants as confirmed by detached leaf and whole plant M. phaseolina bioassay. Herbicide tolerance was analyzed by growing transgenic plants in 10 mg/l glufosinate ammonium containing media and by spraying 0.25% (v/v) glufosinate herbicide Basta® on them. Assessment of residual phytotoxicity effects of Basta® on soil confirmed no negative impact on growth of indicator plants corn and cucumber. Transgenic jute plants were at par with non-transgenic (control) jute plants in all phenotypic aspects. Non-transgenic (control) jute plants suffered significant losses in fiber yield and quality due to M. phaseolina infection whereas the transgenic lines maintained the quality of fiber even after the infection.
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Affiliation(s)
- Shuvobrata Majumder
- Laboratory of Translational Research on Transgenic Crops, Department of Botany, University of Calcutta, Kolkata, India
| | - Karabi Datta
- Laboratory of Translational Research on Transgenic Crops, Department of Botany, University of Calcutta, Kolkata, India
| | - Chirabrata Sarkar
- Laboratory of Translational Research on Transgenic Crops, Department of Botany, University of Calcutta, Kolkata, India
| | - Subhas C. Saha
- Quality Assurance Section, ICAR-National Institute of Research on Jute and Allied Fibre Technology, Kolkata, India
| | - Swapan K. Datta
- Laboratory of Translational Research on Transgenic Crops, Department of Botany, University of Calcutta, Kolkata, India
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Key Stages of Fiber Development as Determinants of Bast Fiber Yield and Quality. FIBERS 2018. [DOI: 10.3390/fib6020020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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