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Saha S, Hooda Y, Malavige GN, Nisar MI. Overcoming colonialism in pathogen genomics. Lancet Digit Health 2024; 6:e520-e525. [PMID: 38906617 DOI: 10.1016/s2589-7500(24)00091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 03/15/2024] [Accepted: 04/25/2024] [Indexed: 06/23/2024]
Abstract
Historical legacies of colonialism affect the distribution and control of scientific knowledge today, including within the pathogen genomics field, which remains dominated by high-income countries (HICs). We discuss the imperatives for decolonising pathogen genomics, including the need for more equitable representation, collaboration, and capacity-strengthening, and the shared responsibilities that both low-income and middle-income countries (LMICs) and HICs have in this endeavour. By highlighting examples from LMICs, we illuminate the pathways and challenges that researchers in LMICs face in the bid to gain autonomy in this crucial domain. Recognising the inherent value of local expertise and resources, we argue for a more inclusive, globally collaborative approach to pathogen genomics. Such an approach not only fosters scientific growth and innovation, but also strengthens global health security by equipping all nations with the tools needed to respond to health crises.
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Affiliation(s)
- Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh.
| | - Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Gathsaurie Neelika Malavige
- Allergy lmmunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Muhammad Imran Nisar
- Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan; CITRIC Centre for Bioinformatics and Computational Biology, The Aga Khan University, Karachi, Pakistan
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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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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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Sun P, Lu Z, Wang Z, Wang S, Zhao K, Mei D, Yang J, Yang Y, Renner SS, Liu J. Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family. Proc Natl Acad Sci U S A 2024; 121:e2313921121. [PMID: 38568968 PMCID: PMC11009661 DOI: 10.1073/pnas.2313921121] [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: 08/12/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies and include economically important species, such as cacao, cotton, durian, and jute, with cotton an important model system for studying the domestication of polyploids. Here, we use chromosome-level genome assemblies from representatives of five or six subfamilies (depending on the placement of Ochroma) to differentiate coexisting subgenomes and their evolution during the family's deep history. The results reveal that the allohexaploid Helicteroideae partially derive from an allotetraploid Sterculioideae and also form a component of the allodecaploid Bombacoideae and Malvoideae. The ancestral Malvaceae karyotype consists of 11 protochromosomes. Four subfamilies share a unique reciprocal chromosome translocation, and two other subfamilies share a chromosome fusion. DNA alignments of single-copy nuclear genes do not yield the same relationships as inferred from chromosome structural traits, probably because of genes originating from different ancestral subgenomes. These results illustrate how chromosome-structural data can unravel the evolutionary history of groups with ancient hybrid genomes.
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Affiliation(s)
- Pengchuan Sun
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Zhiqiang Lu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan666303, China
| | - Zhenyue Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Shang Wang
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Kexin Zhao
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Dong Mei
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Jiao Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yongzhi Yang
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | | | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
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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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Ahmed B, Hasan F, Tabassum A, Ahmed R, Hassan R, Amin MR, Alam M. Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis. J Genet Eng Biotechnol 2023; 21:5. [PMID: 36652035 PMCID: PMC9849630 DOI: 10.1186/s43141-022-00453-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation and stress-mediated expression profiling of jute SnRK2 is available. Recent whole-genome sequencing of two Corchorus species prompted to identify and characterize this SnRK2 gene family. RESULT We identified seven SnRK2 genes of each of Corchorus olitorius (Co) and C. capsularis (Cc) genomes, with similar physico-molecular properties and sub-group patterns of other models and related crops. In both species, the SnRK2 gene family showed an evolutionarily distinct trend. Highly variable C-terminal and conserved N-terminal regions were observed. Co- and CcSnRK2.3, Co- and CcSnRk2.5, Co- and CcSnRk2.7, and Co- and CcSnRK2.8 were upregulated in response to drought and salinity stresses. In waterlogging conditions, Co- and CcSnRk2.6 and Co- and CcSnRK2.8 showed higher activity when exposed to hypoxic conditions. Expression analysis in different plant parts showed that SnRK2.5 in both Corchorus species is highly expressed in fiber cells providing evidence of the role of fiber formation. CONCLUSION This is the first comprehensive study of SnRK2 genes in both Corchorus species. All seven genes identified in this study showed an almost similar pattern of gene structures and molecular properties. Gene expression patterns of these genes varied depending on the plant parts and in response to abiotic stresses.
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Affiliation(s)
- Borhan Ahmed
- grid.482525.c0000 0001 0699 8850Basic and Applied Research On Jute Project, Bangladesh Jute Research Institute, Dhaka, 1207 Bangladesh
| | - Fakhrul Hasan
- grid.443108.a0000 0000 8550 5526Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur, 1706 Bangladesh
| | - Anika Tabassum
- grid.442972.e0000 0001 2218 5390American International University of Bangladesh, Dhaka, 1229 Bangladesh
| | - Rasel Ahmed
- grid.482525.c0000 0001 0699 8850Basic and Applied Research On Jute Project, Bangladesh Jute Research Institute, Dhaka, 1207 Bangladesh
| | - Rajnee Hassan
- grid.24434.350000 0004 1937 0060Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Md. Ruhul Amin
- grid.482525.c0000 0001 0699 8850Basic and Applied Research On Jute Project, Bangladesh Jute Research Institute, Dhaka, 1207 Bangladesh
| | - Mobashwer Alam
- grid.1003.20000 0000 9320 7537Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, 47 Mayers Rd, Nambour, QLD 4560 Australia
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Mukul M. Genetic analyses of morphological traits, and phenotypic screening of tossa jute germplasm grown under salinity stress. Heliyon 2022; 9:e12448. [PMID: 36820182 PMCID: PMC9938408 DOI: 10.1016/j.heliyon.2022.e12448] [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: 09/24/2022] [Revised: 10/30/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
Corchorus olitorius L. jute is a natural fiber crop that is very susceptible to salinity stress. Salinity in soil is a serious threat to tossa jute cultivation in salt-prone regions of Bangladesh. Development of salinity stress tolerant tossa jute variety is a crying need in Bangladesh. Hence, 22 tossa jute genotypes were investigated in an augmented design against 7.86-7.93 dSm-1 salinity stress at coastal regions of Bangladesh during 2017-2019. Salt-tolerant jute genotypes were phenotypically screened out based on survivability, vegetative growth, plant height, base diameter, and fiber yield capacity. Among all genotypes, Acc. 4160 and Acc. 2311 showed good fiber yield (18.0 and 13.8 g plant-1, respectively) with the lowest mortality rate (5.67 and 8.0%, respectively). Acc. 1381, Acc. 2307, Acc. 1334, Acc. 1381 and the pre-released varieties, namely O-9897, BJRI Tossa Pat 5, JRO-524 (Green) were also found good for the aforesaid traits. Among the studied characters, high heritability in a broad sense, genetic advance (%) of mean and significant associations were found which contribute to fiber yield significantly. According to the Clustering and principal component analyses, the relatively salt-tolerant genotypes of cluster II (Acc. 4160, Acc. 2311, Acc. 2307, JRO-524 (Green), Acc. 4327, BJRI Tossa Pat 5, Acc. 1334 & Acc. 1381) could be used as breeding materials and sources of salt-tolerant genes to develop salt-tolerant tossa jute variety.
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Islam T, Afroz N, Koh C, Hoque MN, Rahman MJ, Gupta DR, Mahmud NU, Nahid AA, Islam R, Bhowmik PK, Sharpe AG. Whole-genome sequencing of a year-round fruiting jackfruit ( Artocarpus heterophyllus Lam.) reveals high levels of single nucleotide variation. FRONTIERS IN PLANT SCIENCE 2022; 13:1044420. [PMID: 36605965 PMCID: PMC9809283 DOI: 10.3389/fpls.2022.1044420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Jackfruit (Artocarpus heterophyllus Lam.) is the national fruit of Bangladesh and produces fruit in the summer season only. However, jackfruit is not commercially grown in Bangladesh because of an extremely high variation in fruit quality, short seasonal fruiting (June-August) and susceptibility to abiotic stresses. Conversely, a year-round high yielding (ca. 4-fold higher than the seasonal variety) jackfruit variety, BARI Kanthal-3 developed by the Bangladesh Agricultural Research Institute (BARI) derived from a wild accession found in Ramgarh of Chattogram Hiltracts of Bangladesh, provides fruits from September to June. This study aimed to generate a draft whole-genome sequence (WGS) of BARI Kanthal-3 to obtain molecular insights including genes associated with year-round fruiting trait of this important unique variety. The estimated genome size of BARI Kanthal-3 was 1.04-gigabase-pair (Gbp) with a heterozygosity rate of 1.62%. De novo assembly yielded a scaffolded 817.7 Mb genome while a reference-guided approach, yielded 843 Mb of genome sequence. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 included 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are in inter-genic regions. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing identified orthologous gene groups in BARI Kanthal-3 with five closely and one distantly related species of 10,092 common orthogroups were found across the genomes of the six species. The phylogenetic analysis of the shared orthogroups showed that A. heterophyllus was the closest species to BARI Kanthal-3 and orthogroups related to flowering time were found to be more highly prevalent in BARI Kanthal-3 compared to the other Arctocarpus spp. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting of this highly nutritious fruit crop as well as providing a resource for molecular breeding.
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Affiliation(s)
- Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nadia Afroz
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - ChuShin Koh
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Md. Jillur Rahman
- Pomology Division, Horticultural Research Center, Bangladesh Agricultural Research Institute, Gazipur, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nur Uddin Mahmud
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Abdullah Al Nahid
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Rashedul Islam
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Pankaj K. Bhowmik
- Cell Technologies and Trait Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
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Zhao M, Li Y, Zhang X, You X, Yu H, Guo R, Zhao X. Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress. Int J Mol Sci 2022; 23:ijms232315225. [PMID: 36499551 PMCID: PMC9736363 DOI: 10.3390/ijms232315225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/08/2022] Open
Abstract
Juglans mandshurica has strong freezing resistance, surviving temperatures as low as -40 °C, making it an important freeze tolerant germplasm resource of the genus Juglans. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific superfamily of transcription factors that regulates plant development, growth, and the response to biotic and abiotic stress. In this study, phylogenetic analysis was used to identify 184 AP2/ERF genes in the J. mandshurica genome, which were classified into five subfamilies (JmAP2, JmRAV, JmSoloist, JmDREB, and JmERF). A significant amount of discordance was observed in the 184 AP2/ERF genes distribution of J. mandshurica throughout its 16 chromosomes. Duplication was found in 14 tandem and 122 segmental gene pairs, which indicated that duplications may be the main reason for JmAP2/ERF family expansion. Gene structural analysis revealed that 64 JmAP2/ERF genes contained introns. Gene evolution analysis among Juglandaceae revealed that J. mandshurica is separated by 14.23 and 15 Mya from Juglans regia and Carya cathayensis, respectively. Based on promoter analysis in J. mandshurica, many cis-acting elements were discovered that are related to light, hormones, tissues, and stress response processes. Proteins that may contribute to cold resistance were selected for further analysis and were used to construct a cold regulatory network based on GO annotation and JmAP2/ERF protein interaction network analysis. Expression profiling using qRT-PCR showed that 14 JmAP2/ERF genes were involved in cold resistance, and that seven and five genes were significantly upregulated under cold stress in female flower buds and phloem tissues, respectively. This study provides new light on the role of the JmAP2/ERF gene in cold stress response, paving the way for further functional validation of JmAP2/ERF TFs and their application in the genetic improvement of Juglans and other tree species.
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Affiliation(s)
- Minghui Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Yan Li
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Xinxin Zhang
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Xiangling You
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Haiyang Yu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Ruixue Guo
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (R.G.); (X.Z.)
| | - Xiyang Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (R.G.); (X.Z.)
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10
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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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11
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Comparative genomic analysis of Echinococcus multilocularis with other tapeworms. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01120-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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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: 13] [Impact Index Per Article: 6.5] [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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13
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Genome-Wide Identification, Characterization, and Expression Profiling of AP2/ERF Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan ( Carya illinoinensis). Int J Mol Sci 2022; 23:ijms23062920. [PMID: 35328341 PMCID: PMC8950532 DOI: 10.3390/ijms23062920] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
The ethylene-responsive element (AP2/ERF) is one of the keys and conserved transcription factors (TFs) in plants that play a vital role in regulating plant growth, development, and stress response. A total of 202 AP2/ERF genes were identified from the pecan genome and renamed according to the chromosomal distribution of the CiAP2/ERF genes. They were divided into four subfamilies according to the domain and phylogenetic analysis, including 26 AP2, 168 ERF, six RAV, and two Soloist gene family members. These genes were distributed randomly across the 16 chromosomes, and we found 19 tandem and 146 segmental duplications which arose from ancient duplication events. The gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements, which were related to light responsiveness, stress, and defense responses, were identified in the promoter regions of AP2/ERFs. The expression profiling of 202 CiAP2/ERF genes was assessed by using RNA-Seq data and qRT-PCR during development (pistillate flowering development, graft union development, and kernel development) and under abiotic stresses (waterlogging, drought). Moreover, the results suggested that the ERF-VII members may play a critical role in waterlogging stress. These findings provided new insights into AP2/ERF gene evolution and divergence in pecan and can be considered a valuable resource for further functional validation, as well as for utilization in a stress-resistance-variety development program.
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14
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Sadat MA, Ullah MW, Hossain MS, Ahmed B, Bashar KK. Genome-wide in silico identification of phospholipase D (PLD) gene family from Corchorus capsularis and Corchorus olitorius: reveals their responses to plant stress. J Genet Eng Biotechnol 2022; 20:28. [PMID: 35147846 PMCID: PMC8837719 DOI: 10.1186/s43141-022-00311-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/30/2022] [Indexed: 11/17/2022]
Abstract
Background Plant grows in nature facing various types of abiotic stresses for their normal growth and development. During abiotic stress, plants evolve different types of mechanisms to survive in a hostile environment. Phospholipase D (PLD) plays important role in the regulation of diverse cellular processes including stress responses in plants. Member of PLD genes are well studied in different model plants; however, their functions in the jute are not clear yet. Result In the present study, a total of 12 and 11 PLD genes were identified in the genome of C. capsularis and C. olitorius, respectively. The presence of the two conserved HKD motifs in PLD genes except for CoPLDδ-2 in jute suggests their strong lipase activity. Twenty different motifs were found in the identified PLD genes, and PLD-β1, PLD-γ1, and all members of PLD-δ1 of both jute species contained the highest number of motifs. Phylogenetic analysis showed the close evolutionary relationship among the five groups of jute PLD proteins along with the PLD proteins from Arabidopsis. Tissue-specific expression pattern of PLDα1-2, PLD-α2, PLDβ1, PLDγ1, and PLDδ1 of two jute species suggested their involvement in plant growth and development. However, the expression pattern of PLDα1-2, PLDα1-3, PLD-α4, PLDδ1, and PLDδ3 indicated their association during waterlogging stress. In addition, PLD-α2, PLDβ1, and PLDδ2 seemed to be involved in drought stress as well as salinity stress. Conclusion This genome-wide identification of jute PLD genes from C. capsularis and C. olitorius will help to further functional characterization of the PLD genes for developing stress-tolerant jute variety.
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Affiliation(s)
- Md Abu Sadat
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh.
| | - Md Wali Ullah
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Md Sabbir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Borhan Ahmed
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Kazi Khayrul Bashar
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
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15
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Di Marsico M, Paytuvi Gallart A, Sanseverino W, Aiese Cigliano R. GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. Nucleic Acids Res 2022; 50:D1442-D1447. [PMID: 34723326 PMCID: PMC8728176 DOI: 10.1093/nar/gkab1014] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 02/04/2023] Open
Abstract
The Green Non-Coding Database (GreeNC) is one of the reference databases for the study of plant long non-coding RNAs (lncRNAs). Here we present our most recent update where 16 species have been updated, while 78 species have been added, resulting in the annotation of more than 495 000 lncRNAs. Moreover, sequence clustering was applied providing information about sequence conservation and gene families. The current version of the database is available at: http://greenc.sequentiabiotech.com/wiki2/Main_Page.
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Affiliation(s)
- Marco Di Marsico
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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16
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Tello-Ruiz MK, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol 2022; 2443:101-131. [PMID: 35037202 DOI: 10.1007/978-1-0716-2067-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end-users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.
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Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, USA.
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17
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Xu Q, Zhang X, Zhang Y, Zheng C, Leebens-Mack JH, Jin L, Sankoff D. The monoploid chromosome complement of reconstructed ancestral genomes in a phylogeny. J Bioinform Comput Biol 2021; 19:2140008. [PMID: 34806950 DOI: 10.1142/s0219720021400084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Using RACCROCHE, a method for reconstructing gene content and order of ancestral chromosomes from a phylogeny of extant genomes represented by the gene orders on their chromosomes, we study the evolution of three orders of woody plants. The method retrieves the monoploid complement of each Ancestor in a phylogeny, consisting a complete set of distinct chromosomes, despite some of the extant genomes being recently or historically polyploidized. The three orders are the Sapindales, the Fagales and the Malvales. All of these are independently estimated to have ancestral monoploid number [Formula: see text].
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Affiliation(s)
- Qiaoji Xu
- Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada
| | - Xiaomeng Zhang
- Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada
| | - Yue Zhang
- Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada
| | | | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5C9, Canada
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, 150 Louis Pasteur Pvt, Ottawa, Ontario, Canada K1N 6NP, Canada
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18
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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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Jute Responses and Tolerance to Abiotic Stress: Mechanisms and Approaches. PLANTS 2021; 10:plants10081595. [PMID: 34451640 PMCID: PMC8398869 DOI: 10.3390/plants10081595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 11/16/2022]
Abstract
Jute (Corchorus spp.) belongs to the Malvaceae family, and there are two species of jute, C. capsularis and C. olitorious. It is the second-largest natural bast fiber in the world according to production, which has diverse uses not only as a fiber but also as multiple industrial materials. Because of climate change, plants experience various stressors such as salt, drought, heat, cold, metal/metalloid toxicity, and flooding. Although jute is particularly adapted to grow in hot and humid climates, it is grown under a wide variety of climatic conditions and is relatively tolerant to some environmental adversities. However, abiotic stress often restricts its growth, yield, and quality significantly. Abiotic stress negatively affects the metabolic activities, growth, physiology, and fiber yield of jute. One of the major consequences of abiotic stress on the jute plant is the generation of reactive oxygen species, which lead to oxidative stress that damages its cellular organelles and biomolecules. However, jute’s responses to abiotic stress mainly depend on the plant’s age and type and duration of stress. Therefore, understanding the abiotic stress responses and the tolerance mechanism would help plant biologists and agronomists in developing climate-smart jute varieties and suitable cultivation packages for adverse environmental conditions. In this review, we summarized the best possible recent literature on the plant abiotic stress factors and their influence on jute plants. We described the possible approaches for stress tolerance mechanisms based on the available literature.
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21
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Wang Y, Li F, He Q, Bao Z, Zeng Z, An D, Zhang T, Yan L, Wang H, Zhu S, Liu T. Genomic analyses provide comprehensive insights into the domestication of bast fiber crop ramie (Boehmeria nivea). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:787-800. [PMID: 33993558 DOI: 10.1111/tpj.15346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 05/27/2023]
Abstract
Ramie (Boehmeria nivea) is an economically important natural fiber-producing crop that has been cultivated for thousands of years in China; however, the evolution of this crop remains largely unknown. Here, we report a ramie domestication analysis based on genome assembly and resequencing of cultivated and wild accessions. Two chromosome-level genomes representing wild and cultivated ramie were assembled de novo. Numerous structural variations between two assemblies, together with the genetic variations from population resequencing, constituted a comprehensive genomic variation map for ramie. Domestication analysis identified 71 high-confidence selective sweeps comprising 320 predicted genes, and 29 genes from sweeps were associated with fiber growth in the expression. In addition, we identified seven genetic loci associated with the fiber yield trait in the segregated population derived from the crossing of two assembled accessions, and two of which showed an overlap with the selective sweeps. These findings indicated that bast fiber traits were focused on during the domestication history of ramie. This study sheds light on the domestication of ramie and provides a valuable resource for biological and breeding studies of this important crop.
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Affiliation(s)
- Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Zhigui Bao
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Dong An
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Ting Zhang
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Li Yan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Hengyun Wang
- Shanghai OE Biotech. Co., Ltd, No. 138, Road of Xinjun, Shanghai, 201100, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, Western Road of Xiajiahu, Changsha, 410205, China
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22
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Hong S, Lim YP, Kwon SY, Shin AY, Kim YM. Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:702243. [PMID: 34290729 PMCID: PMC8288248 DOI: 10.3389/fpls.2021.702243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/14/2021] [Indexed: 05/03/2023]
Abstract
In polyploids, whole genome duplication (WGD) played a significant role in genome expansion, evolution and diversification. Many gene families are expanded following polyploidization, with the duplicated genes functionally diversified by neofunctionalization or subfunctionalization. These mechanisms may support adaptation and have likely contributed plant survival during evolution. Flowering time is an important trait in plants, which affects critical features, such as crop yields. The flowering-time gene family is one of the largest expanded gene families in plants, with its members playing various roles in plant development. Here, we performed genome-wide identification and comparative analysis of flowering-time genes in three palnt families i.e., Malvaceae, Brassicaceae, and Solanaceae, which indicate these genes were expanded following the event/s of polyploidization. Duplicated genes have been retained during evolution, although genome reorganization occurred in their flanking regions. Further investigation of sequence conservation and similarity network analyses provide evidence for functional diversification of duplicated genes during evolution. These functionally diversified genes play important roles in plant development and provide advantages to plants for adaptation and survival in response to environmental changes encountered during evolution. Collectively, we show that flowering-time genes were expanded following polyploidization and retained as large gene family by providing advantages from functional diversification during evolution.
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Affiliation(s)
- Seongmin Hong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yong-Min Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
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23
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Niyitanga S, Yang X, Guerriero G, Jin S, Qi J, Zhang L, Zhang L. Editorial: Applied Genetics of Natural Fiber Plants. Front Genet 2021; 12:647225. [PMID: 33927750 PMCID: PMC8078908 DOI: 10.3389/fgene.2021.647225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/19/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.,Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China/Public Platform of Fujian for Germplasm Resources of Bast Fiber Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.,Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China/Public Platform of Fujian for Germplasm Resources of Bast Fiber Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Hautcharage, Luxembourg
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liemei Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.,Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China/Public Platform of Fujian for Germplasm Resources of Bast Fiber Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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24
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In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis. Heliyon 2021; 7:e06705. [PMID: 33869875 PMCID: PMC8045047 DOI: 10.1016/j.heliyon.2021.e06705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/02/2021] [Accepted: 03/31/2021] [Indexed: 11/24/2022] Open
Abstract
Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre alongside lower environmental threat. Small noncoding ~21 to 24 nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including functional annotation of specific gene targets. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 non-redundant ESTs of jute genome, resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were composed of 18 nucleotides having a range of -0.49 to -1.56 MFEI values and 55%–61% of (A + U) content in their pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. Five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, S-adenosyl-L-Met–dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation. The present study might accelerate the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.
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Zhang G, Huang S, Zhang C, Wu Y, Li D, Deng J, Shan S, Qi J. Comparative transcriptome sequencing analysis and functional identification of a NAM-2-like gene in jute (Corchorus capsularis L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:25-35. [PMID: 33561658 DOI: 10.1016/j.plaphy.2021.01.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Jute (Corchorus capsularis L.) is one of the most important sources of natural fibre. Drought is among the main factors affecting the production of jute. It is essential for drought tolerance improvement to discover the genes associated with jute development during drought stress. In this study, we analyzed the transcriptome of jute under drought stress and identified new genes involved in drought stress response. In total, 120,219 transcripts with an average length of 764 bp were obtained, these transcripts included 94,246 unigenes (average length, 622 bp). Differentially expressed genes (DEGs) were discovered in drought stress (1329), among which 903 genes showed up-regulated expression, while 426 genes showed down-regulated expression. GO enrichment analyses indicated most of the enriched biological pathways were biosynthesis pathways of organic ring compounds and cellular nitrogen compounds. KEGG enrichment analyses indicated 573 DEGs were involved in 157 metabolic pathways. RT-qPCR experiments indicated that the expression trends were consistent with the results of the high-throughput sequencing. Over-expression of no apical meristem (NAM) -2-like gene increased drought tolerance and knockdown plants were drought sensitive. It has expression peaks after 6 h of drought stress and regulate 3-ketoacyl-CoA synthase gene expression. Yeast-2-Hybrid assays validated the physical interaction between NAM-2-like protein and KCS. The results provide relatively comprehensive information regarding genes and metabolic pathways that lays the foundation for the breeding of drought-resistant varieties, and represent the first identification of NAM-2-like gene and provides new insight into the regulatory network of drought tolerance in Corchorus capsularis L.
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Affiliation(s)
- Gaoyang Zhang
- Shangrao Normal University, Shangrao, China; Chinese Academy of Agricultural Sciences Institute of Bast Fiber Crops, Changsha, China
| | - Siqi Huang
- Chinese Academy of Agricultural Sciences Institute of Bast Fiber Crops, Changsha, China
| | - Chao Zhang
- Shangrao Normal University, Shangrao, China
| | - Yingbao Wu
- Shangrao Normal University, Shangrao, China
| | - Defang Li
- Chinese Academy of Agricultural Sciences Institute of Bast Fiber Crops, Changsha, China.
| | | | | | - Jianmin Qi
- Fujian Agriculture and Forestry University, Fuzhou, China.
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Genome-wide identification of fasciclin-like arabinogalactan proteins in jute and their expression pattern during fiber formation. Mol Biol Rep 2020; 47:7815-7829. [PMID: 33011893 DOI: 10.1007/s11033-020-05858-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/23/2020] [Indexed: 10/23/2022]
Abstract
Fasciclin-like arabinogalactan proteins (FLAs), a class of arabinogalactan proteins (AGPs) are involved in plant growth and development via cell communication and adhesion. FLAs were also associated with fiber and wood formation in plants but no information is available about the roles of FLA proteins during fibre development of jute. Here, we performed molecular characterization, evolutionary relationship and expression profiling of FLAs proteins in jute (Corchorus olitorius). In total, nineteen CoFLA genes have been identified in jute genome, which were divided into four classes like FLAs of other species based on protein structure and similarity. All CoFLAs have N-terminal signal peptide and one or two FAS domain while two FLAs lack well defined AGP region and eight FLAs were devoid of C-terminal glycosylphosphatidylinositol (GPI) anchor. Expression analysis of different regions of jute stem suggested their involvement in different fiber development stages. Four genes CoFLA 11, 12, 20, and 23 were highly or predominately expressed in fiber containing bark tissues while the expression levels of six CoFLA genes 02, 03, 04, 06, 14 and 19 were comparatively higher in stick. Higher transcripts levels of CoFLA 12 and 20 in the middle bark tissues suggest their involvement in fiber elongation. In contrast, the CoFLA 11 and 23 were more expressed in bottom bark tissues suggesting their potential involvement in secondary cell wall synthesis. Our study can serve as solid foundation for further functional exploration of FLAs and in future breeding program of jute aiming fiber improvement.
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Natural arrangement of fiber-like aragonites and its impact on mechanical behavior of mollusk shells: A review. J Mech Behav Biomed Mater 2020; 110:103940. [PMID: 32957234 DOI: 10.1016/j.jmbbm.2020.103940] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/13/2020] [Accepted: 06/15/2020] [Indexed: 11/20/2022]
Abstract
During billions of years of evolution, creatures in nature have possessed nearly perfect structures and functions for survival. Multiscale structures in biological materials over several length scales play a pivotal role in achieving structural and functional integrity. Fiber, as a common principal structural element in nature, can be easily constructed in different ways, thus resulting in various natural structures. In this review, we summarized the decades of investigations on a typical biological structure constructed by fiber aragonites in mollusk shells. Crossed-lamellar structure, as one of the most widespread structures in mollusk shells, reconciles the strength-toughness trade-off dilemma successfully due to the presence of highly-hierarchical architectures. This distinctive structure includes several orders of sub-lamellae, and the different order lamellae present a cross-ply feature in one macro crossed-lamellar layer. When a mollusk shell has more than one macro-layer, the crossed-lamellar structure exhibits various forms of architectures including 0°/90°, 0°/90°/0° typical-sandwich, 15°/75°/0° quasi-sandwich, and 0°/90°/0°/90° arranged modes. The fracture resistance and the relevant toughening mechanisms are directly related to the highly-hierarchical crossed-lamellar structures on different length scales. This article is aimed to review the different arranged modes of crossed-lamellar structures existing in nature, with special attention to their impact on the mechanical behavior and salient toughening mechanisms over several length scales, for seeking the design guidelines for the fabrication of bio-inspired advanced engineering materials that are adaptive to different loading conditions.
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Zhang L, Wan X, Xu Y, Niyitanga S, Qi J, Zhang L. De novo assembly of transcriptome and genome-wide identification reveal GA 3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis). BMC PLANT BIOLOGY 2020; 20:403. [PMID: 32867682 PMCID: PMC7460746 DOI: 10.1186/s12870-020-02617-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 08/23/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis. RESULTS A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress. CONCLUSIONS A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.
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Affiliation(s)
- Lilan Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xuebei Wan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Yi Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Zhang L, Xu Y, Zhang X, Ma X, Zhang L, Liao Z, Zhang Q, Wan X, Cheng Y, Zhang J, Li D, Zhang L, Xu J, Tao A, Lin L, Fang P, Chen S, Qi R, Xu X, Qi J, Ming R. The genome of kenaf (Hibiscus cannabinus L.) provides insights into bast fibre and leaf shape biogenesis. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1796-1809. [PMID: 31975524 PMCID: PMC7336286 DOI: 10.1111/pbi.13341] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/30/2019] [Accepted: 01/03/2020] [Indexed: 05/03/2023]
Abstract
Kenaf is an annual crop that is widely cultivated as a source of bast (phloem) fibres, the phytoremediation of heavy metal-contaminated farmlands and textile-relevant compounds. Leaf shape played a unique role in kenaf improvement, due to the inheritance as a single locus and the association with fibre development in typical lobed-leaf varieties. Here we report a high-quality genome assembly and annotation for var. 'Fuhong 952' with 1078 Mbp genome and 66 004 protein-coding genes integrating single-molecule real-time sequencing, a high-density genetic map and high-throughput chromosome conformation capture techniques. Gene mapping assists the identification of a homeobox transcription factor LATE MERISTEM IDENTITY 1 (HcLMI1) gene controlling lobed-leaf. Virus-induced gene silencing (VIGS) of HcLMI1 in a lobed-leaf variety was critical to induce round (entire)-like leaf formation. Candidate genes involved in cell wall formation were found in quantitative trait loci (QTL) for fibre yield and quality-related traits. Comparative genomic and transcriptome analyses revealed key genes involved in bast fibre formation, among which there are twice as many cellulose synthase A (CesA) genes due to a recent whole-genome duplication after divergence from Gossypium. Population genomic analysis showed two recent population bottlenecks in kenaf, suggesting domestication and improvement process have led to an increase in fibre biogenesis and yield. This chromosome-scale genome provides an important framework and toolkit for sequence-directed genetic improvement of fibre crops.
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Affiliation(s)
- Liwu Zhang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yi Xu
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xingtan Zhang
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaokai Ma
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lilan Zhang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhenyang Liao
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qing Zhang
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xuebei Wan
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yan Cheng
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jisen Zhang
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Dongxu Li
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liemei Zhang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiantang Xu
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aifen Tao
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lihui Lin
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Pingping Fang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shuai Chen
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Rui Qi
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiuming Xu
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jianmin Qi
- Key Laboratory for Genetics, Breeding and Multiple Utilization of CropsMinistry of Education/Fujian Provincial Key Laboratory of Crop Breeding by Design/College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Experiment Station of Jute and Kenaf in Southeast China of Ministry of Agriculture and Rural Affairs/Public Platform for Germplasm Resources of Bast Fiber Crops of Fujian/Fujian International Cooperation Base of Science and Technology for Genetics, Breeding and Multiple Utilization Development of Southern Economic CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ray Ming
- Center for Genomics and Biotechnology of Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhouChina
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
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Honi U, Amin MR, Kabir SMT, Bashar KK, Moniruzzaman M, Jahan R, Jahan S, Haque MS, Islam S. Genome-wide identification, characterization and expression profiling of gibberellin metabolism genes in jute. BMC PLANT BIOLOGY 2020; 20:306. [PMID: 32611317 PMCID: PMC7329397 DOI: 10.1186/s12870-020-02512-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/22/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Gibberellin (GA) is one of the most essential phytohormones that modulate plant growth and development. Jute (Corchorus sp.) is the second most important source of bast fiber. Our result has shown that exogenous GA can positively regulate jute height and related characteristics which mean increasing endogenous GA production will help to get a jute variety with improved characteristics. However, genes involved in jute GA biosynthesis have not been analyzed precisely. RESULTS Genome-wide analysis identified twenty-two candidate genes involved in jute GA biosynthesis pathway. Among them, four genes- CoCPS, CoKS, CoKO and CoKAO work in early steps. Seven CoGA20oxs, three CoGA3oxs, and eight GA2oxs genes work in the later steps. These genes were characterized through phylogenetic, motif, gene structure, and promoter region analysis along with chromosomal localization. Spatial gene expression analysis revealed that 11 GA oxidases were actively related to jute GA production and four of them were marked as key regulators based on their expression level. All the biosynthesis genes both early and later steps showed tissue specificity. GA oxidase genes were under feedback regulation whereas early steps genes were not subject to such regulation. CONCLUSION Enriched knowledge about jute GA biosynthesis pathway and genes will help to increase endogenous GA production in jute by changing the expression level of key regulator genes. CoGA20ox7, CoGA3ox2, CoGA2ox3, and CoGA2ox5 may be the most important genes for GA production.
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Affiliation(s)
- Ummay Honi
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Md Ruhul Amin
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Shah Md Tamim Kabir
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Kazi Khayrul Bashar
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Md Moniruzzaman
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Rownak Jahan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Sharmin Jahan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Md Samiul Haque
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
- Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh
| | - Shahidul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh.
- Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh.
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Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.). BMC Genomics 2020; 21:406. [PMID: 32546133 PMCID: PMC7298812 DOI: 10.1186/s12864-020-06805-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenced by many factors. Therefore, to understand the molecular mechanisms of tissue development, it is necessary to study tissue-specific gene expression and regulation. We used weighted gene coexpression network analysis, to predict the functional roles of gene coexpression modules and individual genes, including those underlying the development of different tissue types. Although several transcriptome studies have been conducted on C. capsularis, there have not yet been any systematic and comprehensive transcriptome analyses for this species. RESULTS There was significant variation in gene expression between plant tissues. Comparative transcriptome analysis and weighted gene coexpression network analysis were performed for different C. capsularis tissues at different developmental stages. We identified numerous tissue-specific differentially expressed genes for each tissue, and 12 coexpression modules, comprising 126 to 4203 genes, associated with the development of various tissues. There was high consistency between the genes in modules related to tissues, and the candidate upregulated genes for each tissue. Further, a gene network including 21 genes directly regulated by transcription factor OMO55970.1 was discovered. Some of the genes, such as OMO55970.1, OMO51203.1, OMO50871.1, and OMO87663.1, directly involved in the development of stem bast tissue. CONCLUSION We identified genes that were differentially expressed between tissues of the same developmental stage. Some genes were consistently up- or downregulated, depending on the developmental stage of each tissue. Further, we identified numerous coexpression modules and genes associated with the development of various tissues. These findings elucidate the molecular mechanisms underlying the development of each tissue, and will promote multipurpose molecular breeding in jute and other fiber crops.
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Huang G, Wu Z, Percy RG, Bai M, Li Y, Frelichowski JE, Hu J, Wang K, Yu JZ, Zhu Y. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nat Genet 2020; 52:516-524. [PMID: 32284579 PMCID: PMC7203013 DOI: 10.1038/s41588-020-0607-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/04/2020] [Indexed: 12/13/2022]
Abstract
Upon assembling the first Gossypium herbaceum (A1) genome and substantially improving the existing Gossypium arboreum (A2) and Gossypium hirsutum ((AD)1) genomes, we showed that all existing A-genomes may have originated from a common ancestor, referred to here as A0, which was more phylogenetically related to A1 than A2. Further, allotetraploid formation was shown to have preceded the speciation of A1 and A2. Both A-genomes evolved independently, with no ancestor-progeny relationship. Gaussian probability density function analysis indicates that several long-terminal-repeat bursts that occurred from 5.7 million years ago to less than 0.61 million years ago contributed compellingly to A-genome size expansion, speciation and evolution. Abundant species-specific structural variations in genic regions changed the expression of many important genes, which may have led to fiber cell improvement in (AD)1. Our findings resolve existing controversial concepts surrounding A-genome origins and provide valuable genomic resources for cotton genetic improvement.
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Affiliation(s)
- Gai Huang
- Institute for Advanced Studies, Wuhan University, Wuhan, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Richard G Percy
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, TX, USA
| | | | - Yang Li
- College of Life Sciences, Wuhan University, Wuhan, China
| | - James E Frelichowski
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, TX, USA
| | - Jiang Hu
- Nextomics Biosciences Institute, Wuhan, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - John Z Yu
- Crop Germplasm Research Unit, Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), College Station, TX, USA.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, China.
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Comparison of Phytochemical Profile, Mineral Content, and In VitroAntioxidant Activities of Corchorus capsularisand Corchorus olitoriusLeaf Extracts from Different Populations. J FOOD QUALITY 2020. [DOI: 10.1155/2020/2931097] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In addition to fiber,Corchorus(jute) leaf is also rich in secondary metabolites and is used in folk medicine in jute-producing communities. It has been reported that jute halts progression of and helps manage different chronic diseases like tumors, obesity, diabetes, and cardiovascular diseases. Various phytochemical, mineral, and antioxidant potency properties of 30 genotypes belonging toCorchorus capsularisandCorchorus olitoriuswere evaluated in the current study. The results demonstrate that the range of total flavonoids and polyphenols was 3.04 to 13.66 mg rutin equivalent (RE)/g and 5.12 to 7.78 mg gallic acid equivalent (GAE)/g DW, respectively. Total tannin and saponin content in both species was 13.08 to 26.95 mg tannic acid (TAE)/g and 34.45 to 114.59 mg tea saponin (TSE)/g DW, respectively, when analyzed for the first time. Moreover, this study sincerely establishes that jute leaf is a great source of mineral elements (magnesium, zinc, and selenium) and could also be a good energy source. The antioxidant properties of samples were examined with three unique strategies, including DPPH, FRAP, and ABTS values of leaf extract ranging from 206.42 to 351.77 μg/ml (IC50), 16.69 to 94.69 mmol Fe (II)/g DW, and 50.27 to 149.90 mmol trolox equivalent (TE)/g DW, respectively. A principle component analysis (PCA) explained 58.52% of the variance, while a hierarchical cluster analysis (HCA) was performed to construct five distinct groups based on their secondary compound metabolites content and antioxidant activities. Therefore, this study facilitates selection of the high genotypes that might be used as new materials for developing industrial and medicinal uses in addition to sorting genotypes for future genetic engineering purposes in order to enhance a particular bioactive compound and its natural antioxidants that are beneficial for human health.
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Ding X, Mei W, Lin Q, Wang H, Wang J, Peng S, Li H, Zhu J, Li W, Wang P, Chen H, Dong W, Guo D, Cai C, Huang S, Cui P, Dai H. Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family. Gigascience 2020; 9:giaa013. [PMID: 32118265 PMCID: PMC7050300 DOI: 10.1093/gigascience/giaa013] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/01/2019] [Accepted: 02/03/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUD Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information. FINDINGS We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18-84.37 million years ago. CONCLUSIONS Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.
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Affiliation(s)
- Xupo Ding
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Wenli Mei
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Qiang Lin
- Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Rd. Pengfei No. 7, Shenzhen 518120, China
| | - Hao Wang
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Jun Wang
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Shiqing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology; Chinese Academy of Tropical Agriculture Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Huiliang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology; Chinese Academy of Tropical Agriculture Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Jiahong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology; Chinese Academy of Tropical Agriculture Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Wei Li
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Pei Wang
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Huiqin Chen
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Wenhua Dong
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology; Chinese Academy of Tropical Agriculture Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Caihong Cai
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Shengzhuo Huang
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
| | - Peng Cui
- Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Rd. Pengfei No. 7, Shenzhen 518120, China
| | - Haofu Dai
- Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China
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Tang CY, Li S, Wang YT, Wang X. Comparative genome/transcriptome analysis probes Boraginales' phylogenetic position, WGDs in Boraginales, and key enzyme genes in the alkannin/shikonin core pathway. Mol Ecol Resour 2019; 20:228-241. [PMID: 31625679 DOI: 10.1111/1755-0998.13104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 12/27/2022]
Abstract
Boraginales (the forget-me-not order) is a core group within the lamiids clade. However, until now, no genome from Boraginales has been reported, and published transcriptomes are also rare. Here, we report the first Boraginales species de novo genome (i.e. Echium plantagineum genome) and seven other Boraginales species transcriptomes to probe three issues: (i) Boraginales' phylogenetic position within the lamiids clade; (ii) potential whole genome duplications (WGDs) in Boraginales; and (iii) candidate key enzyme genes in the alkannin/shikonin core pathway. The results showed that: (i) Boraginales was most probably closer to the Solanales/Gentianales clade than the Lamiales clade, at least based on the single-copy orthologous genes from genome/transcriptome data; (ii) after the gamma (γ) event, Boraginaceae (classified into the Boraginales I clade) probably underwent at least two rounds of WGD, whereas Heliotropiaceae and Ehretiaceae (classified into the Boraginales II clade) probably underwent only one round of WGD; and (iii) several candidate key enzyme genes in the alkannin/shikonin core pathway were inferred, e.g. genes corresponding to geranyl cyclase, naphthol hydroxylase and O-acyl transferase.
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Affiliation(s)
- Cheng-Yi Tang
- School of the Environment, Nanjing University, Nanjing, China
| | - Song Li
- School of the Environment, Nanjing University, Nanjing, China.,Biomarker Technologies Corporation, Beijing, China
| | | | - Xi Wang
- Biomarker Technologies Corporation, Beijing, China
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Yang Z, Yang Y, Dai Z, Xie D, Tang Q, Cheng C, Xu Y, Liu C, Deng C, Chen J, Su J. Construction of a high-resolution genetic map and identification of quantitative trait loci for salt tolerance in jute (Corchous spp.). BMC PLANT BIOLOGY 2019; 19:391. [PMID: 31500566 PMCID: PMC6734509 DOI: 10.1186/s12870-019-2004-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Salt stress greatly restricts plant development and growth. A high-density genetic linkage map is the basis of quantitative trait locus (QTLs) mapping. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. However, such studies are rare for jute. Only several low-density genetic maps have been constructed and no salt tolerance-related QTL has been mapped in jute to date. RESULTS We developed a high-density genetic map with 4839 single nucleotide polymorphism markers spanning 1375.41 cM and an average distance of 0.28 cM between adjacent markers on seven linkage groups (LGs) using an F2 jute population, LGs ranged from LG2 with 299 markers spanning 113.66 cM to LG7 with 1542 markers spanning 350.18 cM. In addition, 99.57% of gaps between adjacent markers were less than 5 cM. Three obvious and 13 minor QTLs involved in salt tolerance were identified on four LGs explaining 0.58-19.61% of the phenotypic variance. The interval length of QTL mapping varied from 1.3 to 20.2 cM. The major QTL, qJST-1, was detected under two salt stress conditions that explained 11.81 and 19.61% of the phenotypic variation, respectively, and peaked at 19.3 cM on LG4. CONCLUSIONS We developed the first high-density and the most complete genetic map of jute to date using a genotyping-by-sequencing approach. The first QTL mapping related to salt tolerance was also carried out in jute. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.
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Affiliation(s)
- Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
| | - Youxin Yang
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
| | - Dongwei Xie
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150000 People’s Republic of China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
| | - Jiquan Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, 410205 People’s Republic of China
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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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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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Satya P, Chakraborty A, Sarkar D, Karan M, Das D, Mandal NA, Saha D, Datta S, Ray S, Kar CS, Karmakar PG, Mitra J, Singh NK. Transcriptome profiling uncovers β-galactosidases of diverse domain classes influencing hypocotyl development in jute (Corchorus capsularis L.). PHYTOCHEMISTRY 2018; 156:20-32. [PMID: 30172937 DOI: 10.1016/j.phytochem.2018.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/21/2018] [Accepted: 08/21/2018] [Indexed: 05/25/2023]
Abstract
Enzyme β-galactosidase (EC 3.2.1.23) is known to influence vascular differentiation during early vegetative growth of plants, but its role in hypocotyl development is not yet fully understood. We generated the hypocotyl transcriptome data of a hypocotyl-defect jute (Corchorus capsularis L.) mutant (52,393 unigenes) and its wild-type (WT) cv. JRC-212 (44,720 unigenes) by paired-end RNA-seq and identified 11 isoforms of β-galactosidase, using a combination of sequence annotation, domain identification and structural-homology modeling. Phylogenetic analysis classified the jute β-galactosidases into six subfamilies of glycoside hydrolase-35 family, which are closely related to homologs from Malvaceous species. We also report here the expression of a β-galactosidase of glycoside hydrolase-2 family that was earlier considered to be absent in higher plants. Comparative analysis of domain structure allowed us to propose a domain-centric evolution of the five classes of plant β-galactosidases. Further, we observed 1.8-12.2-fold higher expression of nine β-galactosidase isoforms in the mutant hypocotyl, which was characterized by slower growth, undulated shape and deformed cell wall. In vitro and in vivo β-galactosidase activities were also higher in the mutant hypocotyl. Phenotypic analysis supported a significant (P ≤ 0.01) positive correlation between enzyme activity and undulated hypocotyl. Taken together, our study identifies the complete set of β-galactosidases expressed in the jute hypocotyl, and provides compelling evidence that they may be involved in cell wall degradation during hypocotyl development.
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Affiliation(s)
- Pratik Satya
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India.
| | - Avrajit Chakraborty
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Debabrata Sarkar
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Maya Karan
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Debajeet Das
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Nur Alam Mandal
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Dipnarayan Saha
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Subhojit Datta
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Soham Ray
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Chandan Sourav Kar
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Pran Gobinda Karmakar
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Jiban Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Nilganj, Barrackpore, Kolkata, 700 120, West Bengal, India
| | - Nagendra Kumar Singh
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110 012, India
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Expression Analysis of Cell Wall-Related Genes in Cannabis sativa: The “Ins and Outs” of Hemp Stem Tissue Development. FIBERS 2018. [DOI: 10.3390/fib6020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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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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Luan MB, Jian JB, Chen P, Chen JH, Chen JH, Gao Q, Gao G, Zhou JH, Chen KM, Guang XM, Chen JK, Zhang QQ, Wang XF, Fang L, Sun ZM, Bai MZ, Fang XD, Zhao SC, Xiong HP, Yu CM, Zhu AG. Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich. Mol Ecol Resour 2018; 18:639-645. [PMID: 29423997 DOI: 10.1111/1755-0998.12766] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/27/2017] [Accepted: 01/22/2018] [Indexed: 12/01/2022]
Abstract
Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae.
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Affiliation(s)
- Ming-Bao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | | | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | | | - Jian-Hua Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | | | - Kun-Mei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | | | - Ji-Kang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | | | - Xiao-Fei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Long Fang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhi-Min Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | | | | | | | - He-Ping Xiong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Chun-Ming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Ai-Guo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
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Yang Z, Dai Z, Xie D, Chen J, Tang Q, Cheng C, Xu Y, Wang T, Su J. Development of an InDel polymorphism database for jute via comparative transcriptome analysis. Genome 2018; 61:323-327. [PMID: 29420906 DOI: 10.1139/gen-2017-0191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31. Further, we found 94 InDel types, varying from 1 to 159 bp; the most common were single-nucleotide (23 028), binucleotide (9824), and trinucleotide (9182). In total, 49 563 InDels in 18 445 transcripts were discovered in the comparison between TC and YG, followed by 48 934 InDels in 18 408 transcripts between NY and YG, and 3570 InDels in 2701 unigenes between NY and TC. Additionally, there were 1273 InDel sites in 1129 unigenes with polymorphisms between any two of the three accessions. Twenty-nine (58%) primer pairs represented polymorphisms when compared to the jute accessions, and PIC varied from 0.340 to 0.680, with an average of 0.491.
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Affiliation(s)
- Zemao Yang
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Zhigang Dai
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Dongwei Xie
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Jiquan Chen
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Qing Tang
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Chaohua Cheng
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Ying Xu
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Tingzhang Wang
- b Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jianguang Su
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
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Transcriptome Analysis of Two Species of Jute in Response to Polyethylene Glycol (PEG)- induced Drought Stress. Sci Rep 2017; 7:16565. [PMID: 29185475 PMCID: PMC5707433 DOI: 10.1038/s41598-017-16812-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/16/2017] [Indexed: 11/08/2022] Open
Abstract
Drought stress results in significant crop yield losses. Comparative transcriptome analysis between tolerant and sensitive species can provide insights into drought tolerance mechanisms in jute. We present a comprehensive study on drought tolerance in two jute species-a drought tolerant species (Corchorus olitorius L., GF) and a drought sensitive species (Corchorus capsularis L., YY). In total, 45,831 non-redundant unigenes with average sequence length of 1421 bp were identified. Higher numbers of differentially expressed genes (DEGs) were discovered in YY (794) than in GF (39), implying that YY was relatively more vulnerable or hyper-responsive to drought stress at the molecular level; the two main pathways, phenylpropanoid biosynthesis and peroxisome pathway, significantly involved in scavenging of reactive oxygen species (ROS) and 14 unigenes in the two pathways presented a significant differential expression in response to increase of superoxide. Our classification analysis showed that 1769 transcription factors can be grouped into 81 families and 948 protein kinases (PKs) into 122 families. In YY, we identified 34 TF DEGs from and 23 PK DEGs, including 19 receptor-like kinases (RLKs). Most of these RLKs were downregulated during drought stress, implying their role as negative regulators of the drought tolerance mechanism in jute.
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Saha D, Rana RS, Chakraborty S, Datta S, Kumar AA, Chakraborty AK, Karmakar PG. Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.02.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Guerriero G, Behr M, Legay S, Mangeot-Peter L, Zorzan S, Ghoniem M, Hausman JF. Transcriptomic profiling of hemp bast fibres at different developmental stages. Sci Rep 2017; 7:4961. [PMID: 28694530 PMCID: PMC5504027 DOI: 10.1038/s41598-017-05200-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/24/2017] [Indexed: 02/08/2023] Open
Abstract
Bast fibres are long extraxylary cells which mechanically support the phloem and they are divided into xylan- and gelatinous-type, depending on the composition of their secondary cell walls. The former, typical of jute/kenaf bast fibres, are characterized by the presence of xylan and a high degree of lignification, while the latter, found in tension wood, as well as flax, ramie and hemp bast fibres, have a high abundance of crystalline cellulose. During their differentiation, bast fibres undergo specific developmental stages: the cells initially elongate rapidly by intrusive growth, subsequently they cease elongation and start to thicken. The goal of the present study is to provide a transcriptomic close-up of the key events accompanying bast fibre development in textile hemp (Cannabis sativa L.), a fibre crop of great importance. Bast fibres have been sampled from different stem regions. The developmental stages corresponding to active elongation and cell wall thickening have been studied using RNA-Seq. The results show that the fibres sampled at each stem region are characterized by a specific transcriptomic signature and that the major changes in cell wall-related processes take place at the internode containing the snap point. The data generated also identify several interesting candidates for future functional analysis.
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Affiliation(s)
- Gea Guerriero
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg.
| | - Marc Behr
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
- Université catholique de Louvain, Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Louvain-la-Neuve, B-1348, Belgium
| | - Sylvain Legay
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Lauralie Mangeot-Peter
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
- Institut National de la Recherche Agronomique, Université de Lorraine, UMR 1136, Interactions Arbres-Microorganismes, Champenoux, F-54280, France
| | - Simone Zorzan
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Mohammad Ghoniem
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
| | - Jean-Francois Hausman
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette, L-4362, Luxembourg
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The draft genome of Corchorus olitorius cv. JRO-524 (Navin). GENOMICS DATA 2017; 12:151-154. [PMID: 28540183 PMCID: PMC5432662 DOI: 10.1016/j.gdata.2017.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 11/23/2022]
Abstract
Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000).
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