1
|
Liu J, Li Y, Li J, Chen W, Pan B, Liu A, Xu ZF, Xu W, Liu C. EupDB: An integrative and comprehensive functional genomics data hub for Euphorbiaceae plants. PLANT COMMUNICATIONS 2024; 5:100683. [PMID: 37671605 PMCID: PMC10811364 DOI: 10.1016/j.xplc.2023.100683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/07/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Affiliation(s)
- Jiazhi Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen Chen
- Key Laboratory of Vascular Biology and Translational Medicine, Medical School, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Bangzhen Pan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Zeng-Fu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530003, China; Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning 530003, China
| | - Wei Xu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China.
| |
Collapse
|
2
|
Qu Z, Batz Z, Singh N, Marchal C, Swaroop A. Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids. Cell Rep 2023; 42:113543. [PMID: 38048222 PMCID: PMC10790351 DOI: 10.1016/j.celrep.2023.113543] [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: 05/12/2023] [Revised: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
We have generated a high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive stage-specific alterations in DNA topology and correlate these changes with transcription of cell-type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift toward A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression, respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages (i.e., TAD cliques) localize in active chromatin regions with binding sites for eye-field transcription factors. These genes gain chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.
Collapse
Affiliation(s)
- Zepeng Qu
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Zachary Batz
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Nivedita Singh
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Claire Marchal
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA; In silichrom Ltd, 15 Digby Road, Newbury RG14 1TS, UK
| | - Anand Swaroop
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
3
|
Conneely LJ, Berkowitz O, Lewsey MG. Emerging trends in genomic and epigenomic regulation of plant specialised metabolism. PHYTOCHEMISTRY 2022; 203:113427. [PMID: 36087823 DOI: 10.1016/j.phytochem.2022.113427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Regulation of specialised metabolism genes is multilayered and complex, influenced by an array of genomic, epigenetic and epigenomic mechanisms. Here, we review the most recent knowledge in this field, drawing from discoveries in several plant species. Our aim is to improve understanding of how plant genome structure and function influence specialised metabolism. We also highlight key areas for future exploration. Gene regulatory mechanisms influencing specialised metabolism include gene duplication and neo-functionalization, conservation of operon-like clusters of specialised metabolism genes, local chromatin modifications, and the organisation of higher order chromatin structures within the nucleus. Genomic and epigenomic research to-date in the discipline have focused on a relatively small number of plant species, primarily at whole organ or tissue level. This is largely due to the technical demands of the experimental methods needed. However, a high degree of cell-type specificity of function exists in specialised metabolism, driven by similarly specific gene regulation. In this review we focus on the genomic characteristics of genes that are found in different types of clusters within the genome. We propose that acquisition of cell-resolution epigenomic datasets in emerging models, such as the glandular trichomes of Cannabis sativa, will yield important advances. Data such as chromatin accessibility and histone modification profiles can pinpoint which regulatory sequences are active in individual cell types and at specific times in development. These could provide fundamental biological insight as well as novel targets for genetic engineering and crop improvement.
Collapse
Affiliation(s)
- Lee J Conneely
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Oliver Berkowitz
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Mathew G Lewsey
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia.
| |
Collapse
|
4
|
Geng X, Zhang C, Wei L, Lin K, Xu ZF. Genome-Wide Identification and Expression Analysis of Cytokinin Response Regulator (RR) Genes in the Woody Plant Jatropha curcas and Functional Analysis of JcRR12 in Arabidopsis. Int J Mol Sci 2022; 23:ijms231911388. [PMID: 36232689 PMCID: PMC9570446 DOI: 10.3390/ijms231911388] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
The cytokinin (CK) response regulator (RR) gene family plays a pivotal role in regulating the developmental and environmental responses of plants. Axillary bud outgrowth in the perennial woody plant Jatropha curcas is regulated by the crosstalk between CK and gibberellins (GA). In this study, we first analyzed the effects of gibberellin A3 (GA3), lovastatin (a CK synthesis inhibitor), decapitation, and their interaction, on the outgrowth of axillary buds. The results indicate that lovastatin completely inhibited GA-promoted axillary bud outgrowth and partially weakened the decapitation-promoted axillary bud outgrowth. To further characterize and understand the role of CK signaling in promoting the development of female flowers and branches, we performed bioinformatics and expression analyses to characterize the CK RR gene (JcRR) family in J. curcas. A total of 14 members of the JcRR family were identified; these genes were distributed on 10 chromosomes. Phylogenetic analysis indicated that the corresponding RR proteins are evolutionarily conserved across different plant species, and the Myb-like DNA-binding domain divides the 14 members of the JcRR family into type-A and type-B proteins. Further analysis of cis-acting elements in the promoter regions of JcRRs suggests that JcRRs are expressed in response to phytohormones, light, and abiotic stress factors; thus, JcRRs may be involved in some plant development processes. Genomic sequence comparison revealed that segmental duplication may have played crucial roles in the expansion of the JcRR gene family, and five pairs of duplicated genes were all subjected to purifying selection. By analyzing RNA sequencing (RNA-seq) and quantitative reverse transcription-polymerase chain reaction (qRT–PCR) data, we characterized that the temporospatial expression patterns of JcRRs during the development of various tissues and the response of these genes to phytohormones and abiotic stress. The JcRRs were mainly expressed in the roots, while they also exhibited differential expression patterns in other tissues. The expression levels of all six type-A and one type-B JcRRs increased in response to 6-benzylaminopurine (6-BA), while the four type-B JcRRs levels decreased. The expression levels of two type-B JcRRs increased in response to exogenous GA3 treatment, while those of three type-A and three type-B JcRRs decreased. We found that type-A JcRRs may play a positive role in the continuous growth of axillary buds, while the role of type-B JcRRs might be the opposite. In response to abiotic stress, the expression levels of two type-A and three type-B JcRRs strongly increased. The overexpression of JcRR12 in Arabidopsis thaliana slightly increased the numbers of rosette branches after decapitation, but not under normal conditions. In conclusion, our results provide detailed knowledge of JcRRs for further analysis of CK signaling and JcRR functions in J. curcas.
Collapse
Affiliation(s)
- Xianchen Geng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
| | - Chun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
| | - Lida Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
| | - Kai Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
| | - Zeng-Fu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
- Correspondence:
| |
Collapse
|
5
|
Jin Q, Yang Z, Yang W, Gao X, Liu C. Genome-Wide Identification and Analysis of Lbd Transcription Factor Genes in Jatropha curcas and Related Species. PLANTS 2022; 11:plants11182397. [PMID: 36145796 PMCID: PMC9504267 DOI: 10.3390/plants11182397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022]
Abstract
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors that play important roles in organ development and stress response. However, the function of LBD genes has not been reported in Euphorbiaceae. In this paper, we used Jatropha curcas as the main study object and added rubber tree (Hevea brasiliensis), cassava (Manihot esculenta Crantz) and castor (Ricinus communis L.) to take a phylogenetic analysis of LBD genes. Of LBD, 33, 58, 54 and 30 members were identified in J. curcas, rubber tree, cassava and castor, respectively. The phylogenetic analysis showed that LBD members of Euphorbiaceae could be classified into two major classes and seven subclasses (Ia-Ie,IIa-IIb), and LBD genes of Euphorbiaceae tended to cluster in the same branch. Further analysis showed that the LBD genes of Euphorbiaceae in the same clade usually had similar protein motifs and gene structures, and tissue expression patterns showed that they also have similar expression profiles. JcLBDs in class Ia and Ie are mainly expressed in male and female flowers, and there are multiple duplication genes with similar expression profiles in these clades. It was speculated that they are likely to play important regulatory roles in flower development. Our study provided a solid foundation for further investigation of the role of LBD genes in the sexual differentiaion of J. curcas.
Collapse
Affiliation(s)
- Qi Jin
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Zitian Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Wenjing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaoyang Gao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Changning Liu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- Correspondence:
| |
Collapse
|
6
|
Zhao ML, Zhou ZF, Chen MS, Xu CJ, Xu ZF. An ortholog of the MADS-box gene SEPALLATA3 regulates stamen development in the woody plant Jatropha curcas. PLANTA 2022; 255:111. [PMID: 35478059 DOI: 10.1007/s00425-022-03886-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Overexpression of JcSEP3 causes defective stamen development in Jatropha curcas, in which brassinosteroid and gibberellin signaling pathways may be involved. SEPALLATAs (SEPs), the class E genes of the ABCE model, are required for floral organ determination. In this study, we investigated the role of the JcSEP3 gene in floral organ development in the woody plant Jatropha curcas. Transgenic Jatropha plants overexpressing JcSEP3 displayed abnormal phenotypes such as deficient anthers and pollen, as well as free stamen filaments, whereas JcSEP3-RNA interference (RNAi) transgenic plants had no obvious phenotypic changes, suggesting that JcSEP3 is redundant with other JcSEP genes in Jatropha. Moreover, we compared the transcriptomes of wild-type plants, JcSEP3-overexpressing, and JcSEP3-RNAi transgenic plants. In the JcSEP3-overexpressing transgenic plants, we discovered 25 upregulated genes involved in anther and pollen development, as well as 12 induced genes in brassinosteroid (BR) and gibberellin (GA) signaling pathways. These results suggest that JcSEP3 directly or indirectly regulates stamen development, concomitant with the regulation of BR and GA signaling pathways. Our findings help to understand the roles of SEP genes in stamen development in perennial woody plants.
Collapse
Affiliation(s)
- Mei-Li Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Zhi-Fang Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
| | - Chuan-Jia Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, 530004, Guangxi, China.
| |
Collapse
|
7
|
Xu Q, Niu SC, Li KL, Zheng PJ, Zhang XJ, Jia Y, Liu Y, Niu YX, Yu LH, Chen DF, Zhang GQ. Chromosome-Scale Assembly of the Dendrobium nobile Genome Provides Insights Into the Molecular Mechanism of the Biosynthesis of the Medicinal Active Ingredient of Dendrobium. Front Genet 2022; 13:844622. [PMID: 35299950 PMCID: PMC8921531 DOI: 10.3389/fgene.2022.844622] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 01/07/2023] Open
Abstract
Orchids constitute approximately 10% of flowering plant species. However, only about 10 orchid genomes have been published. Metabolites are the main way through which orchids respond to their environment. Dendrobium nobile, belonging to Dendrobium, the second largest genus in Orchidaceae, has high ornamental, medicinal, and ecological value. D. nobile is the source of many popular horticultural varieties. Among the Dendrobium species, D. nobile has the highest amount of dendrobine, which is regarded as one of the criteria for evaluating medicinal quality. Due to lack of data and analysis at the genomic level, the biosynthesis pathways of dendrobine and other related medicinal ingredients in D. nobile are unknown. In this paper, we report a chromosome-scale reference genome of D. nobile to facilitate the investigation of its genomic characteristics for comparison with other Dendrobium species. The assembled genome size of D. nobile was 1.19 Gb. Of the sequences, 99.45% were anchored to 19 chromosomes. Furthermore, we identified differences in gene number and gene expression patterns compared with two other Dendrobium species by integrating whole-genome sequencing and transcriptomic analysis [e.g., genes in the polysaccharide biosynthesis pathway and upstream of the alkaloid (dendrobine) biosynthesis pathway]. Differences in the TPS and CYP450 gene families were also found among orchid species. All the above differences might contribute to the species-specific medicinal ingredient biosynthesis pathways. The metabolic pathway-related analysis will provide further insight into orchid responses to the environment. Additionally, the reference genome will provide important insights for further molecular elucidation of the medicinal active ingredients of Dendrobium and enhance the understanding of orchid evolution.
Collapse
Affiliation(s)
- Qing Xu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
| | - Shan-Ce Niu
- College of Horticulture, Hebei Agricultural University, Baoding, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Kang-Li Li
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Pei-Ji Zheng
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiao-Jing Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yin Jia
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yang Liu
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yun-Xia Niu
- School of Vocational Education, Tianjin University of Technology and Education, Tianjin, China
| | - Li-Hong Yu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Duan-Fen Chen
- College of Horticulture, Hebei Agricultural University, Baoding, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
| | - Guo-Qiang Zhang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
- Laboratory for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, The National Orchid Conservation Center of China, Shenzhen, China
- *Correspondence: Qing Xu, ; Duan-Fen Chen, ; Guo-Qiang Zhang,
| |
Collapse
|
8
|
Kumar S, Kaur S, Seem K, Kumar S, Mohapatra T. Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective. Front Cell Dev Biol 2021; 9:774719. [PMID: 34957106 PMCID: PMC8692796 DOI: 10.3389/fcell.2021.774719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/23/2021] [Indexed: 01/17/2023] Open
Abstract
The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.
Collapse
Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | |
Collapse
|
9
|
Wang M, Gu Z, Fu Z, Jiang D. High-quality genome assembly of an important biodiesel plant, Euphorbia lathyris L. DNA Res 2021; 28:6402006. [PMID: 34664644 PMCID: PMC8545615 DOI: 10.1093/dnares/dsab022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
Caper spurge, Euphorbia lathyris L., is an important energy crop and medicinal crop. Here, we generated a high-quality, chromosome-level genome assembly of caper spurge using Oxford Nanopore sequencing, Illumina sequencing, and Hi-C technology. The final genome assembly was ∼988.9 Mb in size, 99.8% of which could be grouped into 10 pseudochromosomes, with contig and scaffold N50 values of 32.6 and 95.7 Mb, respectively. A total of 651.4 Mb repetitive sequences and 36,342 protein-coding genes were predicted in the genome assembly. Comparative genomic analysis showed that caper spurge and castor bean clustered together. We found that no independent whole-genome duplication event had occurred in caper spurge after its split from castor bean, and recent substantial amplification of LTR retrotransposons (LTR-RTs) has contributed significantly to its genome expansion. Furthermore, based on gene homology searching, we identified a number of candidate genes involved in the biosynthesis of fatty acids and triacylglycerols. The reference genome presented here will be highly useful for the further study of the genetics, genomics, and breeding of this high-value crop, as well as for evolutionary studies of spurge family and angiosperms.
Collapse
Affiliation(s)
- Mingcheng Wang
- Institute for Advanced Study, Chengdu University, No. 2025 Chengluo Road, Chengdu, 610106, China
| | - Zhijia Gu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhixi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Dechun Jiang
- CAS Key laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| |
Collapse
|
10
|
Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes. Sci Rep 2021; 11:13797. [PMID: 34226617 PMCID: PMC8257616 DOI: 10.1038/s41598-021-93257-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/16/2021] [Indexed: 01/27/2023] Open
Abstract
Genome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.
Collapse
|
11
|
Wang Z, Zhu J, Yuan W, Wang Y, Hu P, Jiao C, Xia H, Wang D, Cai Q, Li J, Wang C, Zhang X, Chen Y, Wang Z, Ou Z, Xu Z, Shi J, Chen J. Genome-wide characterization of bZIP transcription factors and their expression patterns in response to drought and salinity stress in Jatropha curcas. Int J Biol Macromol 2021; 181:1207-1223. [PMID: 33971233 DOI: 10.1016/j.ijbiomac.2021.05.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 11/18/2022]
Abstract
The basic leucine zipper (bZIP) family is one of the largest families of transcription factors (TFs) in plants and is responsible for various functions, including regulating development and responses to abiotic/biotic stresses. However, the roles of bZIPs in the regulation of responses to drought stress and salinity stress remain poorly understood in Jatropha curcas L., a biodiesel crop. In the present study, 50 JcbZIP genes were identified and classified into ten groups. Cis-element analysis indicated that JcbZIP genes are associated with abiotic stress. Gene expression patterns and quantitative real-time PCR (qRT-PCR) showed that four JcbZIP genes (JcbZIPs 34, 36, 49 and 50) are key resistance-related genes under both drought and salinity stress conditions. On the basis of the results of cis-element and phylogenetic analyses, JcbZIP49 and JcbZIP50 are likely involved in responses to drought and salinity stress; moreover, JcbZIP34 and JcbZIP36 might also play important roles in seed development and response to abiotic stress. These findings advance our understanding of the comprehensive characteristics of JcbZIP genes and provide new insights for functional validation in the further.
Collapse
Affiliation(s)
- Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jin Zhu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Wenya Yuan
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Ying Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Peipei Hu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Chunyan Jiao
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Haimeng Xia
- School of Biosciences, University of Nottingham, Sutton Bonington 999020, UK
| | - Dandan Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qianwen Cai
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Jie Li
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Chenchen Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Xie Zhang
- Institute of Botany, Hunan Academy of Forestry, Changsha 410004, China
| | - Yansong Chen
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zhaoxia Wang
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zulan Ou
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Zhongdong Xu
- College of Life Sciences, Hefei Normal University, Hefei 230601, China
| | - Jisen Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jinhui Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
12
|
Xia WX, Li HR, Ge JH, Liu YW, Li HH, Su YH, Wang HZ, Guo HF, Dai YX, Liu YW, Gou XC. High-continuity genome assembly of the jellyfish Chrysaora quinquecirrha. Zool Res 2021; 42:130-134. [PMID: 33377334 PMCID: PMC7840447 DOI: 10.24272/j.issn.2095-8137.2020.258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Atlantic sea nettle (Chrysaora quinquecirrha) has an important evolutionary position due to its high ecological value. However, due to limited sequencing technologies and complex jellyfish genomic sequences, the current C. quinquecirrha genome assembly is highly fragmented. Here, we used the most advanced high-throughput chromosome conformation capture (Hi-C) technology to obtain high-coverage sequencing data of the C. quinquecirrha genome. We then anchored these data to the previously published contig-level assembly to improve the genome. Finally, a high-continuity genome sequence of C. quinquecirrha was successfully assembled, which contained 1 882 scaffolds with a N50 length of 3.83 Mb. The N50 length of the genome assembly was 5.23 times longer than the previously released one, and additional analysis revealed that it had a high degree of genomic continuity and accuracy. Acquisition of the high-continuity genome sequence of C. quinquecirrha not only provides a basis for the study of jellyfish evolution through comparative genomics but also provides an important resource for studies on jellyfish growth and development.
Collapse
Affiliation(s)
- Wang-Xiao Xia
- Shaanxi Key Laboratory of Brain Disorders, Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi 710021, China
| | - Hao-Rong Li
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Jing-Hao Ge
- Shaanxi Key Laboratory of Brain Disorders, Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi 710021, China
| | - Yao-Wu Liu
- ZhiQiao Research Institute, Changsha, Hunan 410000, China
| | - Hong-Hui Li
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yan-Hua Su
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Hai-Zhen Wang
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Hui-Fang Guo
- Shaanxi Key Laboratory of Infection and Immune Disorders, School of Basic Medical Science, Xi'an Medical University, Xi'an, Shaanxi 710021, China
| | - Yu-Xuan Dai
- Shaanxi Key Laboratory of Brain Disorders, Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi 710021, China
| | - Yao-Wen Liu
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan 650201, China. E-mail:
| | - Xing-Chun Gou
- Shaanxi Key Laboratory of Brain Disorders, Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an, Shaanxi 710021, China. E-mail:
| |
Collapse
|
13
|
Xu CJ, Zhao ML, Chen MS, Xu ZF. Silencing of the Ortholog of DEFECTIVE IN ANTHER DEHISCENCE 1 Gene in the Woody Perennial Jatropha curcas Alters Flower and Fruit Development. Int J Mol Sci 2020; 21:ijms21238923. [PMID: 33255510 PMCID: PMC7727821 DOI: 10.3390/ijms21238923] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/17/2020] [Accepted: 11/21/2020] [Indexed: 01/12/2023] Open
Abstract
DEFECTIVE IN ANTHER DEHISCENCE 1 (DAD1), a phospholipase A1, utilizes galactolipids (18:3) to generate α-linolenic acid (ALA) in the initial step of jasmonic acid (JA) biosynthesis in Arabidopsis thaliana. In this study, we isolated the JcDAD1 gene, an ortholog of Arabidopsis DAD1 in Jatropha curcas, and found that it is mainly expressed in the stems, roots, and male flowers of Jatropha. JcDAD1-RNAi transgenic plants with low endogenous jasmonate levels in inflorescences exhibited more and larger flowers, as well as a few abortive female flowers, although anther and pollen development were normal. In addition, fruit number was increased and the seed size, weight, and oil contents were reduced in the transgenic Jatropha plants. These results indicate that JcDAD1 regulates the development of flowers and fruits through the JA biosynthesis pathway, but does not alter androecium development in Jatropha. These findings strengthen our understanding of the roles of JA and DAD1 in the regulation of floral development in woody perennial plants.
Collapse
Affiliation(s)
- Chuan-Jia Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovative Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China; (C.-J.X.); (M.-L.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei-Li Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovative Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China; (C.-J.X.); (M.-L.Z.)
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovative Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China; (C.-J.X.); (M.-L.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China
- Correspondence: (M.-S.C.); (Z.-F.X.)
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovative Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China; (C.-J.X.); (M.-L.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China
- Correspondence: (M.-S.C.); (Z.-F.X.)
| |
Collapse
|
14
|
Chen MS, Niu L, Zhao ML, Xu C, Pan BZ, Fu Q, Tao YB, He H, Hou C, Xu ZF. De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas. Gigascience 2020; 9:giaa009. [PMID: 32048715 PMCID: PMC7014976 DOI: 10.1093/gigascience/giaa009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/04/2019] [Accepted: 01/19/2020] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Chromatin architecture is an essential factor regulating gene transcription in different cell types and developmental phases. However, studies on chromatin architecture in perennial woody plants and on the function of chromatin organization in sex determination have not been reported. RESULTS Here, we produced a chromosome-scale de novo genome assembly of the woody plant Jatropha curcas with a total length of 379.5 Mb and a scaffold N50 of 30.7 Mb using Pacific Biosciences long reads combined with genome-wide chromosome conformation capture (Hi-C) technology. Based on this high-quality reference genome, we detected chromatin architecture differences between monoecious and gynoecious inflorescence buds of Jatropha. Differentially expressed genes were significantly enriched in the changed A/B compartments and topologically associated domain regions and occurred preferentially in differential contact regions between monoecious and gynoecious inflorescence buds. Twelve differentially expressed genes related to flower development or hormone synthesis displayed significantly different genomic interaction patterns in monoecious and gynoecious inflorescence buds. These results demonstrate that chromatin organization participates in the regulation of gene transcription during the process of sex differentiation in Jatropha. CONCLUSIONS We have revealed the features of chromatin architecture in perennial woody plants and investigated the possible function of chromatin organization in Jatropha sex differentiation. These findings will facilitate understanding of the regulatory mechanisms of sex determination in higher plants.
Collapse
Affiliation(s)
- Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Longjian Niu
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Rd., Shenzhen, Guangdong 518055, China
- Department of Biology, Nankai University, 94 Weijing Rd., Tianjin 660885, China
| | - Mei-Li Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- College of Life Sciences, University of Chinese Academy of Sciences, 19(A) Yuquan Rd., Beijing 100049, China
| | - Chuanjia Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- College of Life Sciences, University of Chinese Academy of Sciences, 19(A) Yuquan Rd., Beijing 100049, China
| | - Bang-Zhen Pan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Qiantang Fu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Yan-Bin Tao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Huiying He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Chunhui Hou
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Rd., Shenzhen, Guangdong 518055, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| |
Collapse
|