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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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2
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Li Q, Chen S, Chen L, Zhuang L, Wei H, Jiang S, Wang C, Qi J, Fang P, Xu J, Tao A, Zhang L. Cloning and functional mechanism of the dwarf gene gba affecting stem elongation and cellulose biosynthesis in jute (Corchorus olitorius). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2003-2019. [PMID: 38536089 DOI: 10.1111/tpj.16724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 06/14/2024]
Abstract
Plant height (PH) is an important factor affecting bast fiber yield in jute. Here, we report the mechanism of dwarfism in the 'Guangbaai' (gba) of jute. The mutant gba had shorter internode length and cell length compared to the standard cultivar 'TaiZi 4' (TZ4). Exogenous GA3 treatment indicated that gba is a GA-insensitive dwarf mutant. Quantitative trait locus (QTL) analysis of three PH-related traits via a high-density genetic linkage map according to re-seq showed that a total of 25 QTLs were identified, including 13 QTLs for PH, with phenotypic variation explained ranging from 2.42 to 74.16%. Notably, the functional mechanism of the candidate gene CoGID1a, the gibberellic acid receptor, of the major locus qPHIL5 was evaluated by transgenic analysis and virus-induced gene silencing. A dwarf phenotype-related single nucleotide mutation in CoGID1a was identified in gba, which was also unique to the dwarf phenotype of gba among 57 cultivars. Cogid1a was unable to interact with the growth-repressor DELLA even in the presence of highly accumulated gibberellins in gba. Differentially expressed genes between transcriptomes of gba and TZ4 after GA3 treatment indicated up-regulation of genes involved in gibberellin and cellulose synthesis in gba. Interestingly, it was found that up-regulation of CoMYB46, a key transcription factor in the secondary cell wall, by the highly accumulated gibberellins in gba promoted the expression of cellulose synthase genes CoCesA4 and CoCesA7. These findings provide valuable insights into fiber development affected by endogenous gibberellin accumulation in plants.
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Affiliation(s)
- Qin Li
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siyuan Chen
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lu Chen
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingling Zhuang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huawei Wei
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shaolian Jiang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chuanyu Wang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiantang Xu
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Aifen Tao
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Li W, Chen X, Yu J, Zhu Y. Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution, lignin biosynthesis regulation, and stress tolerance. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1266-1279. [PMID: 38763999 DOI: 10.1007/s11427-024-2580-3] [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: 01/05/2024] [Accepted: 03/26/2024] [Indexed: 05/21/2024]
Abstract
Durian (Durio zibethinus) is a tropical fruit that has a unique flavor and aroma. It occupies a significant phylogenetic position within the Malvaceae family. Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling, resulting in an abundant genomic diversity. However, the ancestral karyotypes of the Malvaceae family, as well as the evolution trajectory leading to the 28 chromosomes in durian, remain poorly understood. Here, we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses. By analyzing the collinear blocks between cacao and durian, we inferred 11 Malvaceae ancestral karyotypes. These blocks were present in a single-copy form in cacao and mainly in triplicates in durian, possibly resulting from a recent whole genome triplication (WGT) event that led to hexaploidization of the durian genome around 20 (17-24) million years ago. A large proportion of the duplicated genes in durian, such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis, are derived directly from whole genome duplication, which makes it an important force in reshaping its genomic architecture. Transcriptome studies have revealed that genes involved in feruloyl-CoA formations were highly preferentially expressed in fruit peels, indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins. Among all the analyzed transcription factors (TFs), members of the heat shock factor family (HSF) were the most significantly upregulated under heat stress. All subfamilies of genes encoding heat shock proteins (HSPs) in the durian genome appear to have undergone expansion. The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified. Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome. We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.
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Affiliation(s)
- Wanwan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xin Chen
- The State Key Laboratory of Protein and Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
| | - Yuxian Zhu
- The Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
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4
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Shao L, Jin S, Chen J, Yang G, Fan R, Zhang Z, Deng Q, Han J, Ma X, Dong Z, Lu H, Hu W, Wang K, Hu L, Shen Z, Huang S, Zhao T, Guan X, Hu Y, Zhang T, Fang L. High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development. PLANT COMMUNICATIONS 2024; 5:100832. [PMID: 38321741 PMCID: PMC11121743 DOI: 10.1016/j.xplc.2024.100832] [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: 08/07/2023] [Revised: 09/15/2023] [Accepted: 02/01/2024] [Indexed: 02/08/2024]
Abstract
Members of the Malvaceae family, including Corchorus spp., Gossypium spp., Bombax spp., and Ceiba spp., are important sources of natural fibers. In the past decade, the genomes of several Malvaceae species have been assembled; however, the evolutionary history of Malvaceae species and the differences in their fiber development remain to be clarified. Here, we report the genome assembly and annotation of two natural fiber plants from the Malvaceae, Bombax ceiba and Ceiba pentandra, whose assembled genome sizes are 783.56 Mb and 1575.47 Mb, respectively. Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number (2n = 14 to 2n = 96) and genome size (234 Mb to 2676 Mb) among Malvaceae species. We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromosomes, providing new insights into the evolutionary trajectories of Malvaceae species. MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions in fiber cell-fate determination in the epidermis. It appears to perform this function in any tissue where it is expressed, i.e. in fibers on the endocarp of B. ceiba and in ovule fibers of cotton. We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of the finer, less spinnable, weaker fibers of B. ceiba. Our study provides two high-quality genomes of natural fiber plants and offers insights into the evolution of Malvaceae species and differences in their natural fiber formation and development through multi-omics analysis.
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Affiliation(s)
- Lei Shao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guangsui Yang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Rui Fan
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhiyuan Zhang
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Qian Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaowei Ma
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeyu Dong
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hejun Lu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wanying Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lisong Hu
- Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China
| | - Zhen Shen
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Surong Huang
- Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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5
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Arafat MY, Narula K, Kumar M, Chakraborty N, Chakraborty S. Proteo-metabolomic Dissection of Extracellular Matrix Reveals Alterations in Cell Wall Integrity and Calcium Signaling Governs Wall-Associated Susceptibility during Stem Rot Disease in Jute. J Proteome Res 2024. [PMID: 38572503 DOI: 10.1021/acs.jproteome.3c00781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The plant surveillance system confers specificity to disease and immune states by activating distinct molecular pathways linked to cellular functionality. The extracellular matrix (ECM), a preformed passive barrier, is dynamically remodeled at sites of interaction with pathogenic microbes. Stem rot, caused by Macrophomina phaseolina, adversely affects fiber production in jute. However, how wall related susceptibility affects the ECM proteome and metabolome remains undetermined in bast fiber crops. Here, stem rot responsive quantitative temporal ECM proteome and metabolome were developed in jute upon M. phaseolina infection. Morpho-histological examination revealed that leaf shredding was accompanied by reactive oxygen species production in patho-stressed jute. Electron microscopy showed disease progression and ECM architecture remodeling due to necrosis in the later phase of fungal attack. Using isobaric tags for relative and absolute quantitative proteomics and liquid chromatography-tandem mass spectrometry, we identified 415 disease-responsive proteins involved in wall integrity, acidification, proteostasis, hydration, and redox homeostasis. The disease-related correlation network identified functional hubs centered on α-galactosidase, pectinesterase, and thaumatin. Gas chromatography-mass spectrometry analysis pointed toward enrichment of disease-responsive metabolites associated with the glutathione pathway, TCA cycle, and cutin, suberin, and wax metabolism. Data demonstrated that wall-degrading enzymes, structural carbohydrates, and calcium signaling govern rot responsive wall-susceptibility. Proteomics data were deposited in Pride (PXD046937; PXD046939).
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Affiliation(s)
- Md Yasir Arafat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Mohit Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Liu D, Tian X, Shao S, Ma Y, Zhang R. Haplotype-resolved chromosomal-level genome assembly of Buzhaye (Microcos paniculata). Sci Data 2023; 10:901. [PMID: 38102170 PMCID: PMC10724166 DOI: 10.1038/s41597-023-02821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Microcos paniculata is a shrub used traditionally as folk medicine and to make herbal teas. Previous research into this species has mainly focused on its chemical composition and medicinal value. However, the lack of a reference genome limits the study of the molecular mechanisms of active compounds in this species. Here, we assembled a haplotype-resolved chromosome-level genome of M. paniculata based on PacBio HiFi and Hi-C data. The assembly contains two haploid genomes with sizes 399.43 Mb and 393.10 Mb, with contig N50 lengths of 43.44 Mb and 30.17 Mb, respectively. About 99.93% of the assembled sequences could be anchored to 18 pseudo-chromosomes. Additionally, a total of 482 Mb repeat sequences were identified, accounting for 60.76% of the genome. A total of 49,439 protein-coding genes were identified, of which 48,979 (99%) were functionally annotated. This haplotype-resolved chromosome-level assembly and annotation of M. paniculata will serve as a valuable resource for investigating the biosynthesis and genetic basis of active compounds in this species, as well as advancing evolutionary phylogenomic studies in Malvales.
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Affiliation(s)
- Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaoling Tian
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China
| | - Shicheng Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- University of Chinese Academy of Sciences, Beijing, 101408, China.
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7
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Yao J, Jiang S, Li H, Li Q, Qiu Z, Tao A, Fang P, Xu J, Lin L, Qi J, Zhang L. Genome-wide association study reveals loci and candidate genes of flowering time in jute ( Corchorus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:85. [PMID: 38009098 PMCID: PMC10667207 DOI: 10.1007/s11032-023-01435-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Suitable flowering time can improve fiber yield and quality, which is of great significance for jute biological breeding. In this study, 242 jute accessions were planted in Fujian for 2 consecutive years, and 244,593 SNPs distributed in jute genome were used for genome-wide association analysis of flowering time. A total of 19 candidate intervals (P < 0.0001) were identified by using GLM and FaST-LMM and were significantly associated with flowering time, with phenotypic variation explained (PVE) ranging from 5.8 to 18.61%. Six stable intervals that were repeatedly detected in different environments were further identified by the linkage disequilibrium heatmap. The most likely 7 candidate genes involved to flowering time were further predicted according to the gene functional annotations. Notably, functional analysis of the candidate gene CcPRR7 of the major loci qFT-3-1, a key factor in circadian rhythm in the photoperiodic pathway, was evaluated by linkage, haplotype, and transgenic analysis. β-glucuronidase (GUS) and luciferase (LUC) activity assay of the promoters with two specific haplotypes confirmed that the flowering time can be controlled by regulating the expression of CcPRR7. The model of CcPRR7 involved in the photoperiod regulation pathway under different photoperiods was proposed. These findings provide insights into genetic loci and genes for molecular marker-assisted selection in jute and valuable information for genetically engineering PRR7 homologs in plants. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01435-8.
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Affiliation(s)
- Jiayu Yao
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shaolian Jiang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hu Li
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qin Li
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhaowei Qiu
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Aifen Tao
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Pingping Fang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jiantang Xu
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lihui Lin
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetic Breeding and Multiple Utilization of Crops / Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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8
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Zhang H, Ding X, Wang H, Chen H, Dong W, Zhu J, Wang J, Peng S, Dai H, Mei W. Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP14 and AsbZIP41 in Aquilaria sinensis. FRONTIERS IN PLANT SCIENCE 2023; 14:1243323. [PMID: 37719219 PMCID: PMC10499555 DOI: 10.3389/fpls.2023.1243323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 09/19/2023]
Abstract
Introduction Agarwood, the dark-brown resin produced by Aquilaria trees, has been widely used as incense, spice, perfume or traditional medicine and 2-(2-phenethyl) chromones (PECs) are the key markers responsible for agarwood formation. But the biosynthesis and regulatory mechanism of PECs were still not illuminated. The transcription factor of basic leucine zipper (bZIP) presented the pivotal regulatory roles in various secondary metabolites biosynthesis in plants, which might also contribute to regulate PECs biosynthesis. However, molecular evolution and function of bZIP are rarely reported in Malvales plants, especially in Aquilaria trees. Methods and results Here, 1,150 bZIPs were comprehensively identified from twelve Malvales and model species genomes and the evolutionary process were subsequently analyzed. Duplication types and collinearity indicated that bZIP is an ancient or conserved TF family and recent whole genome duplication drove its evolution. Interesting is that fewer bZIPs in A. sinensis than that species also experienced two genome duplication events in Malvales. 62 AsbZIPs were divided into 13 subfamilies and gene structures, conservative domains, motifs, cis-elements, and nearby genes of AsbZIPs were further characterized. Seven AsbZIPs in subfamily D were significantly regulated by ethylene and agarwood inducer. As the typical representation of subfamily D, AsbZIP14 and AsbZIP41 were localized in nuclear and potentially regulated PECs biosynthesis by activating or suppressing type III polyketide synthases (PKSs) genes expression via interaction with the AsPKS promoters. Discussion Our results provide a basis for molecular evolution of bZIP gene family in Malvales and facilitate the understanding the potential functions of AsbZIP in regulating 2-(2-phenethyl) chromone biosynthesis and agarwood formation.
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Affiliation(s)
- Hao Zhang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xupo Ding
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Hao Wang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Huiqin Chen
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenhua Dong
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiahong Zhu
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jian Wang
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan, College of Forestry, Hainan University, Haikou, China
| | - Shiqing Peng
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Haofu Dai
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenli Mei
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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9
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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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Akhter S, Sami AA, Toma TI, Jahan B, Islam T. Caffeoyl-CoA 3-O-methyltransferase gene family in jute: Genome-wide identification, evolutionary progression and transcript profiling under different quandaries. FRONTIERS IN PLANT SCIENCE 2022; 13:1035383. [PMID: 36589126 PMCID: PMC9798919 DOI: 10.3389/fpls.2022.1035383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Jute (Corchorus sp.), is a versatile, naturally occurring, biodegradable material that holds the promising possibility of diminishing the extensive use of plastic bags. One of the major components of the cell wall, lignin plays both positive and negative roles in fiber fineness and quality. Although it gives mechanical strength to plants, an excess amount of it is responsible for the diminution of fiber quality. Among various gene families involved in the lignin biosynthesis, Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is the most significant and has remained mostly unexplored. In this study, an extensive in-silico characterization of the CCoAOMT gene family was carried out in two jute species (C. capsularis L. and C. olitoroius L.) by analyzing their structural, functional, molecular and evolutionary characteristics. A total of 6 CCoAOMT gene members were identified in each of the two species using published reference genomes. These two jute species showed high syntenic conservation and the identified CCoAOMT genes formed four clusters in the phylogenetic tree. Histochemical assay of lignin in both jute species could shed light on the deposition pattern in stems and how it changes in response to abiotic stresses. Furthermore, expression profiling using qPCR showed considerable alteration of CCoAOMT transcripts under various abiotic stresses and hormonal treatment. This study will lay a base for further analysis and exploration of target candidates for overexpression of gene silencing using modern biotechnological techniques to enhance the quality of this economically important fiber crop.
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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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Sourav MSU, Wang H. Intelligent Identification of Jute Pests Based on Transfer Learning and Deep Convolutional Neural Networks. Neural Process Lett 2022; 55:1-18. [PMID: 35990859 PMCID: PMC9376051 DOI: 10.1007/s11063-022-10978-4] [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] [Accepted: 07/20/2022] [Indexed: 11/10/2022]
Abstract
Pest attacks pose a substantial threat to jute production and other significant crop plants. Jute farmers in Bangladesh generally distinguish between different pests that appear to be the same using their eyes and expertise, which isn't always accurate. We developed an intelligent model for jute pests identification based on transfer learning (TL) and deep convolutional neural networks (DCNN) to solve this practical problem. The proposed DCNN model can realize fast and accurate automatic identification of jute pests based on photographs. Specifically, the VGG19 CNN model was trained by TL on the ImageNet database. A well-structured image dataset of four dominant jute pests is also established. Our model shows a final accuracy of 95.86% on the four most vital jute pest classes. The model's performance is further demonstrated by the precision, recall, F1-score, and confusion matrix results. The proposed model is integrated into Android and IOS applications for practical uses.
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Affiliation(s)
- Md Sakib Ullah Sourav
- School of Management Science and Engineering, Shandong University of Finance and Economics, Jinan, China
| | - Huidong Wang
- School of Management Science and Engineering, Shandong University of Finance and Economics, Jinan, China
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