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Ojosnegros S, Alvarez JM, Gagliardini V, Quintanilla LG, Grossniklaus U, Fernández H. Transcriptomic analyses in the gametophytes of the apomictic fern Dryopteris affinis. PLANTA 2024; 260:111. [PMID: 39356333 PMCID: PMC11447071 DOI: 10.1007/s00425-024-04540-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 09/21/2024] [Indexed: 10/03/2024]
Abstract
MAIN CONCLUSION A novel genomic map of the apogamous gametophyte of the fern Dryopteris affinis unlocks oldest hindrance with this complex plant group, to gain insight into evo-devo approaches. The gametophyte of the fern Dryopteris affinis ssp. affinis represents a good model to explore the molecular basis of vegetative and reproductive development, as well as stress responses. Specifically, this fern reproduces asexually by apogamy, a peculiar case of apomixis whereby a sporophyte forms directly from a gametophytic cell without fertilization. Using RNA-sequencing approach, we have previously annotated more than 6000 transcripts. Here, we selected 100 of the inferred proteins homolog to those of Arabidopsis thaliana, which were particularly interesting for a detailed study of their potential functions, protein-protein interactions, and distance trees. As expected, a plethora of proteins associated with gametogenesis and embryogenesis in angiosperms, such as FERONIA (FER) and CHROMATING REMODELING 11 (CHR11) were identified, and more than a dozen candidates potentially involved in apomixis, such as ARGONAUTE family (AGO4, AGO9, and AGO 10), BABY BOOM (BBM), FASCIATED STEM4 (FAS4), FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), and MATERNAL EFFECT EMBRYO ARREST29 (MEE29). In addition, proteins involved in the response to biotic and abiotic stresses were widely represented, as shown by the enrichment of heat-shock proteins. Using the String platform, the interactome revealed that most of the protein-protein interactions were predicted based on experimental, database, and text mining datasets, with MULTICOPY SUPPRESSOR OF IRA4 (MSI4) showing the highest number of interactions: 16. Lastly, some proteins were studied through distance trees by comparing alignments with respect to more distantly or closely related plant groups. This analysis identified DCL4 as the most distant protein to the predicted common ancestor. New genomic information in relation to gametophyte development, including apomictic reproduction, could expand our current vision of evo-devo approaches.
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Affiliation(s)
- Sara Ojosnegros
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071, Oviedo, Spain
| | - José Manuel Alvarez
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071, Oviedo, Spain
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
| | - Luis G Quintanilla
- Global Change Research Institute, University Rey Juan Carlos, 28933, Móstoles, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071, Oviedo, Spain.
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Ambrose BA, Stevenson DW. The evolution and development of sporangia-The fundamental reproductive organ of land plant sporophytes. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102563. [PMID: 38838582 DOI: 10.1016/j.pbi.2024.102563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
A key innovation of land plants is the origin and evolution of the sporangium, the fundamental reproductive structure of the diploid sporophyte. In vascular plants, whether the structure is a cone, fertile leaf, or flower-all are clusters of sporangia. The evolution of morphologically distinct sporangia (heterospory) and retention of the gametophyte evolved three times independently as a prerequisite for the evolution of seeds. This review summarizes the development of vascular plant sporangia, molecular genetics of angiosperm sporangia, and provides a framework to investigate evolution and development in vascular plant sporangia.
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Affiliation(s)
- Barbara A Ambrose
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, NY, 10458, USA.
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Chang N, Yang X, Wang X, Chen C, Wang C, Xu Y, Huang H, Wang Y. Epiphytic Patterns Impacting Metabolite Diversity of Drynaria roosii Rhizomes Based on Widely Targeted Metabolomics. Metabolites 2024; 14:409. [PMID: 39195505 DOI: 10.3390/metabo14080409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
Drynaria roosii Nakaike, a fern widely distributed in China and some countries in Southeast Asia, is a commonly used herbal medicine in tonic diets and Chinese patented medicine. The metabolites of its dried rhizomes are easily affected by the epiphytic pattern, whether on rock tunnels (RTs) or tree trunks (TTs). The current research focused on rhizomes from these two patterns, RTs and TTs (further divided into subclasses TA, TB, TC, and TD, based on trunk differences) and conducted a widely targeted metabolomics analysis. A total of 1435 components were identified across 13 categories, with flavonoids, amino acids, and their derivative, lipids, identified as the main components. They accounted for 19.96%, 12.07%, and 12.14% of all metabolites, respectively. The top five flavonoids in TB were eriodicty-ol-7-O-(6″-acetyl)glucoside, quercetin-3-O-sophoroside (baimaside), dihydrochar-cone-4'-O-glucoside, morin, and hesperetin-7-O-glucoside, with relative contents 76.10, 24.20, 17.02, 15.84, and 14.64 times higher than in RTs. Principal component analysis revealed that samples with different epiphytic patterns clustered into five groups. The RT patterns revealed unique metabolites that were not detected in the other four epiphytic species (TA, TB, TC, and TD), including 16 authenticated metabolites: 1 alkaloid, 1 amino acid derivative, 7 flavonoids, 2 lignans, 1 lipid, 1 alcohol, 1 aldehyde, and 2 phenolic acids. These differences in epiphytic patterns considerably affected the accumulation of both primary and secondary metabolites. The comparison of diversity between RTs and TTs can guide the selection of a cultivation substance and the grading of collective rhizomes in the wild. This comprehensive analysis of D. roosii rhizome metabolites also offers fundamental insights for identifying active components and understanding the mechanisms underlying their potential pharmacological activities.
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Affiliation(s)
- Nana Chang
- Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences, Nanchang 330115, China
- Jiangxi Institute of Traditional Chinese Medicine Health Industry, Nanchang 330115, China
| | - Xianping Yang
- Dexing Research and Training Center, Dexing Academy of Traditional Chinese Medicine, Dexing 334213, China
| | - Xiaoqing Wang
- Jiangxi Provincial Institute of Traditional Chinese Medicine, Nanchang 330046, China
| | - Chao Chen
- Jiangxi Provincial Institute of Traditional Chinese Medicine, Nanchang 330046, China
| | - Chu Wang
- Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences, Nanchang 330115, China
- Jiangxi Institute of Traditional Chinese Medicine Health Industry, Nanchang 330115, China
| | - Yang Xu
- Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences, Nanchang 330115, China
- Jiangxi Institute of Traditional Chinese Medicine Health Industry, Nanchang 330115, China
| | - Hengyu Huang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Ye Wang
- Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences, Nanchang 330115, China
- Jiangxi Institute of Traditional Chinese Medicine Health Industry, Nanchang 330115, China
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4
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Xu P, Zhang L, Lu L, Zhu Y, Gao D, Liu S. Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns. Genes (Basel) 2024; 15:887. [PMID: 39062666 PMCID: PMC11276031 DOI: 10.3390/genes15070887] [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: 05/11/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
The latest research shows that ferns and lycophytes have distinct evolutionary lineages. The codon usage patterns of lycophytes and ferns have not yet been documented. To investigate the gene expression profiles across various plant lineages with respect to codon usage, analyze the disparities and determinants of gene evolution in primitive plant species, and identify appropriate exogenous gene expression platforms, the whole-genome sequences of four distinct species were retrieved from the NCBI database. The findings indicated that Ceratopteris richardii, Adiantum capillus-veneris, and Selaginella moellendorffii exhibited an elevated A/U content in their codon base composition and a tendency to end with A/U. Additionally, S. capillus-veneris had more C/G in its codons and a tendency to end with C/G. The ENC values derived from both ENC-plot and ENC-ratio analyses deviated significantly from the standard curves, suggesting that the codon usage preferences of these four species were primarily influenced by genetic mutations and natural selection, with natural selection exerting a more prominent influence. This finding was further supported by PR2-Plot, neutrality plot analysis, and COA. A combination of RSCU and ENC values was used as a reference criterion to rank the codons and further identify the optimal codons. The study identified 24 high-frequency codons in C. richardii, A. capillus-veneris, and Diphasiastrum complanatum, with no shared optimal codons among the four species. Arabidopsis thaliana and Ginkgo biloba exhibited similar codon preferences to the three species, except for S. moellendorffii. This research offers a theoretical framework at the genomic codon level for investigating the phylogenetic relationships between lycophytes and ferns, shedding light on gene codon optimization and its implications for genetic engineering in breeding.
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Affiliation(s)
- Piaoran Xu
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Liping Lu
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Yanli Zhu
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
| | - Dandan Gao
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
| | - Shanshan Liu
- China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China; (P.X.); (L.L.); (Y.Z.)
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China;
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Gazzarrini S, Song L. LAFL Factors in Seed Development and Phase Transitions. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:459-488. [PMID: 38657282 DOI: 10.1146/annurev-arplant-070623-111458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Development is a chain reaction in which one event leads to another until the completion of a life cycle. Phase transitions are milestone events in the cycle of life. LEAFY COTYLEDON1 (LEC1), ABA INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 proteins, collectively known as LAFL, are master transcription factors (TFs) regulating seed and other developmental processes. Since the initial characterization of the LAFL genes, more than three decades of active research has generated tremendous amounts of knowledge about these TFs, whose roles in seed development and germination have been comprehensively reviewed. Recent advances in cell biology with genetic and genomic tools have allowed the characterization of the LAFL regulatory networks in previously challenging tissues at a higher throughput and resolution in reference species and crops. In this review, we provide a holistic perspective by integrating advances at the epigenetic, transcriptional, posttranscriptional, and protein levels to exemplify the spatiotemporal regulation of the LAFL networks in Arabidopsis seed development and phase transitions, and we briefly discuss the evolution of these TF networks.
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Affiliation(s)
- Sonia Gazzarrini
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada;
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada;
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Zhang G, Wang H, Ren X, Xiao Y, Liu D, Meng W, Qiu Y, Hu B, Xie Q, Chu C, Tong H. Brassinosteroid-dependent phosphorylation of PHOSPHATE STARVATION RESPONSE2 reduces its DNA-binding ability in rice. THE PLANT CELL 2024; 36:2253-2271. [PMID: 38416876 PMCID: PMC11132879 DOI: 10.1093/plcell/koae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/06/2024] [Accepted: 02/22/2024] [Indexed: 03/01/2024]
Abstract
Brassinosteroids (BRs) are widely used as plant growth regulators in modern agriculture. Understanding how BRs regulate nutrient signaling is crucial for reducing fertilizer usage. Here we elucidate that the central BR signaling inhibitor GSK3/SHAGGY-LIKE KINASE2 (GSK2) interacts directly with and phosphorylates PHOSPHATE STARVATION RESPONSE2 (OsPHR2), the key regulator of phosphate (Pi) signaling, to suppress its transcription factor activity in rice (Oryza sativa). We identify a critical phosphorylation site at serine residue S269 of OsPHR2 and demonstrate that phosphorylation by GSK2 or phosphor-mimic mutation of S269 substantially impairs the DNA-binding activity of OsPHR2, and thus diminishes expression of OsPHR2-induced genes and reduces Pi levels. Like BRs, Pi starvation noticeably induces GSK2 instability. We further show that this site-specific phosphorylation event is conserved in Arabidopsis (Arabidopsis thaliana), but varies among the PHR-family members, being present only in most land plants. These results unveil a distinctive post-transcriptional regulatory mechanism in Pi signaling by which BRs promote Pi acquisition, with a potential contribution to the environmental adaptability of plants during their evolution.
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Affiliation(s)
- Guoxia Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xiangle Ren
- Division of Hematology/Oncology, Department of Pediatrics, Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02138, USA
| | - Yunhua Xiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dapu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenjing Meng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yahong Qiu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingjun Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Chengcai Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongning Tong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Khan Q, Wang Y, Xia G, Yang H, Luo Z, Zhang Y. Deleterious Effects of Heat Stress on the Tomato, Its Innate Responses, and Potential Preventive Strategies in the Realm of Emerging Technologies. Metabolites 2024; 14:283. [PMID: 38786760 PMCID: PMC11122942 DOI: 10.3390/metabo14050283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/28/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The tomato is a fruit vegetable rich in nutritional and medicinal value grown in greenhouses and fields worldwide. It is severely sensitive to heat stress, which frequently occurs with rising global warming. Predictions indicate a 0.2 °C increase in average surface temperatures per decade for the next three decades, which underlines the threat of austere heat stress in the future. Previous studies have reported that heat stress adversely affects tomato growth, limits nutrient availability, hammers photosynthesis, disrupts reproduction, denatures proteins, upsets signaling pathways, and damages cell membranes. The overproduction of reactive oxygen species in response to heat stress is toxic to tomato plants. The negative consequences of heat stress on the tomato have been the focus of much investigation, resulting in the emergence of several therapeutic interventions. However, a considerable distance remains to be covered to develop tomato varieties that are tolerant to current heat stress and durable in the perspective of increasing global warming. This current review provides a critical analysis of the heat stress consequences on the tomato in the context of global warming, its innate response to heat stress, and the elucidation of domains characterized by a scarcity of knowledge, along with potential avenues for enhancing sustainable tolerance against heat stress through the involvement of diverse advanced technologies. The particular mechanism underlying thermotolerance remains indeterminate and requires further elucidatory investigation. The precise roles and interplay of signaling pathways in response to heat stress remain unresolved. The etiology of tomato plants' physiological and molecular responses against heat stress remains unexplained. Utilizing modern functional genomics techniques, including transcriptomics, proteomics, and metabolomics, can assist in identifying potential candidate proteins, metabolites, genes, gene networks, and signaling pathways contributing to tomato stress tolerance. Improving tomato tolerance against heat stress urges a comprehensive and combined strategy including modern techniques, the latest apparatuses, speedy breeding, physiology, and molecular markers to regulate their physiological, molecular, and biochemical reactions.
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Affiliation(s)
| | | | | | | | | | - Yan Zhang
- Department of Landscape and Horticulture‚ Ecology College‚ Lishui University‚ Lishui 323000‚ China; (Q.K.); (Y.W.); (G.X.); (H.Y.); (Z.L.)
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8
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Xiang DL, Li GS. Control of leaf development in the water fern Ceratopteris richardii by the auxin efflux transporter CrPINMa in the CRISPR/Cas9 analysis. BMC PLANT BIOLOGY 2024; 24:322. [PMID: 38654173 PMCID: PMC11040788 DOI: 10.1186/s12870-024-05009-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND PIN-FORMED genes (PINs) are crucial in plant development as they determine the directionality of auxin flow. They are present in almost all land plants and even in green algae. However, their role in fern development has not yet been determined. This study aims to investigate the function of CrPINMa in the quasi-model water fern Ceratopteris richardii. RESULTS CrPINMa possessed a long central hydrophilic loop and characteristic motifs within it, which indicated that it belonged to the canonical rather than the non-canonical PINs. CrPINMa was positioned in the lineage leading to Arabidopsis PIN6 but not that to its PIN1, and it had undergone numerous gene duplications. CRISPR/Cas9 genome editing had been performed in ferns for the first time, producing diverse mutations including local frameshifts for CrPINMa. Plants possessing disrupted CrPINMa exhibited retarded leaf emergence and reduced leaf size though they could survive and reproduce at the same time. CrPINMa transcripts were distributed in the shoot apical meristem, leaf primordia and their vasculature. Finally, CrPINMa proteins were localized to the plasma membrane rather than other cell parts. CONCLUSIONS CRISPR/Cas9 genome editing is feasible in ferns, and that PINs can play a role in fern leaf development.
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Affiliation(s)
- De-Liang Xiang
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Gui-Sheng Li
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, 416000, China.
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9
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Nomura T, Seto Y, Kyozuka J. Unveiling the complexity of strigolactones: exploring structural diversity, biosynthesis pathways, and signaling mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1134-1147. [PMID: 37877933 DOI: 10.1093/jxb/erad412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023]
Abstract
Strigolactone is the collective name for compounds containing a butenolide as a part of their structure, first discovered as compounds that induce seed germination of root parasitic plants. They were later found to be rhizosphere signaling molecules that induce hyphal branching of arbuscular mycorrhizal fungi, and, finally, they emerged as a class of plant hormones. Strigolactones are found in root exudates, where they display a great variability in their chemical structure. Their structure varies among plant species, and multiple strigolactones can exist in one species. Over 30 strigolactones have been identified, yet the chemical structure of the strigolactone that functions as an endogenous hormone and is found in the above-ground parts of plants remains unknown. We discuss our current knowledge of the synthetic pathways of diverse strigolactones and their regulation, as well as recent progress in identifying strigolactones as plant hormones. Strigolactone is perceived by the DWARF14 (D14), receptor, an α/β hydrolase which originated by gene duplication of KARRIKIN INSENSITIVE 2 (KAI2). D14 and KAI2 signaling pathways are partially overlapping paralogous pathways. Progress in understanding the signaling mechanisms mediated by two α/β hydrolase receptors as well as remaining challenges in the field of strigolactone research are reviewed.
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Affiliation(s)
- Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Yoshiya Seto
- School of Agriculture, Meiji University, Kawasaki, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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10
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Li C, Wickell D, Kuo LY, Chen X, Nie B, Liao X, Peng D, Ji J, Jenkins J, Williams M, Shu S, Plott C, Barry K, Rajasekar S, Grimwood J, Han X, Sun S, Hou Z, He W, Dai G, Sun C, Schmutz J, Leebens-Mack JH, Li FW, Wang L. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. Proc Natl Acad Sci U S A 2024; 121:e2312607121. [PMID: 38236735 PMCID: PMC10823260 DOI: 10.1073/pnas.2312607121] [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: 07/31/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.
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Affiliation(s)
- Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - David Wickell
- Boyce Thompson Institute, Ithaca, NY14853
- Plant Biology Section, Cornell University, Ithaca, NY14853
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Xueqing Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Mellissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ85721
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
| | - Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Weijun He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Guanhua Dai
- Research Station of Changbai Mountain Forest Ecosystems, Chinese Academy of Sciences, Yanji133000, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing100048, China
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL35806
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY14853
- Plant Biology Section, Cornell University, Ithaca, NY14853
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing100700, China
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11
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Katayama N, Yamamoto T, Aiuchi S, Watano Y, Fujiwara T. Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales). FRONTIERS IN PLANT SCIENCE 2024; 14:1286320. [PMID: 38264021 PMCID: PMC10803465 DOI: 10.3389/fpls.2023.1286320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern-Phegopteris decursivepinnata-and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.
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Affiliation(s)
- Natsu Katayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Takuya Yamamoto
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Sakura Aiuchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Tao Fujiwara
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
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12
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Castel B, El Mahboubi K, Jacquet C, Delaux PM. Immunobiodiversity: Conserved and specific immunity across land plants and beyond. MOLECULAR PLANT 2024; 17:92-111. [PMID: 38102829 DOI: 10.1016/j.molp.2023.12.005] [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: 10/16/2023] [Revised: 11/20/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Angiosperms represent most plants that humans cultivate, grow, and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature, and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defense pathways. Exploring diversity at the genomic and functional levels demonstrates the conservation of these pathways across land plants, some of which are beyond plants. On basis of the conserved mechanisms, lineage-specific variations have occurred, leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species by integration of wild immune receptors or engineering of novel forms of receptors for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.
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Affiliation(s)
- Baptiste Castel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Karima El Mahboubi
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France.
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13
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Zhang Y, Van de Peer Y, Lu B, Zhang S, Che J, Chen J, Marchal K, Yang X. Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii. BMC Biol 2023; 21:244. [PMID: 37926805 PMCID: PMC10626718 DOI: 10.1186/s12915-023-01743-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Sterile-fertile heteroblasty is a common phenomenon observed in ferns, where the leaf shape of a fern sporophyll, responsible for sporangium production, differs from that of a regular trophophyll. However, due to the large size and complexity of most fern genomes, the molecular mechanisms that regulate the formation of these functionally different heteroblasty have remained elusive. To shed light on these mechanisms, we generated a full-length transcriptome of Ceratopteris chingii with PacBio Iso-Seq from five tissue samples. By integrating Illumina-based sequencing short reads, we identified the genes exhibiting the most significant differential expression between sporophylls and trophophylls. RESULTS The long reads were assembled, resulting in a total of 24,024 gene models. The differential expressed genes between heteroblasty primarily involved reproduction and cell wall composition, with a particular focus on expansin genes. Reconstructing the phylogeny of expansin genes across 19 plant species, ranging from green algae to seed plants, we identified four ortholog groups for expansins. The observed high expression of expansin genes in the young sporophylls of C. chingii emphasizes their role in the development of heteroblastic leaves. Through gene coexpression analysis, we identified highly divergent expressions of expansin genes both within and between species. CONCLUSIONS The specific regulatory interactions and accompanying expression patterns of expansin genes are associated with variations in leaf shapes between sporophylls and trophophylls.
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Affiliation(s)
- Yue Zhang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bei Lu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Jingru Che
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- Department of Information Technology, IDLab, IMEC, Ghent University, 9052, Ghent, Belgium.
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China.
- Hubei Ecology Polytechnic College, Wuhan, 430200, China.
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14
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Liu W, Cai G, Zhai N, Wang H, Tang T, Zhang Y, Zhang Z, Sun L, Zhang Y, Beeckman T, Xu L. Genome and transcriptome of Selaginella kraussiana reveal evolution of root apical meristems in vascular plants. Curr Biol 2023; 33:4085-4097.e5. [PMID: 37716350 DOI: 10.1016/j.cub.2023.08.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/30/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The evolution of roots allowed vascular plants to adapt to land environments. Fossil evidence indicates that roots evolved independently in euphyllophytes (ferns and seed plants) and lycophytes, the two lineages of extant vascular plants. Based on a high-quality genome assembly, mRNA sequencing (mRNA-seq) data, and single-cell RNA-seq data for the lycophyte Selaginella kraussiana, we show that the two root origin events in lycophytes and euphyllophytes adopted partially similar molecular modules in the regulation of root apical meristem (RAM) development. In S. kraussiana, the RAM initiates from the rhizophore primordium guided by auxin and duplicates itself by dichotomous branching. The auxin signaling pathway directly upregulates euAINTEGUMENTAb (SkeuANTb), and then SkeuANTb directly promotes the expression of SkeuANTa and the WUSCHEL-RELATED HOMEOBOX13b (SkWOX13b) for RAM maintenance, partially similar to the molecular pathway involving the euANT-branch PLETHORA (AtPLT) genes and AtWOX5 in root initiation in the seed plant Arabidopsis thaliana. Other molecular modules, e.g., SHORT-ROOT and SCARECROW, also have partially similar expression patterns in the RAMs of S. kraussiana and A. thaliana. Overall, our study not only provides genome and transcriptome tools of S. kraussiana but also indicates the employment of some common molecular modules in RAMs during root origins in lycophytes and euphyllophytes.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Tengfei Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhiyao Zhang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lijun Sun
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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15
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Withers KA, Falls K, Youngstrom CE, Nguyen T, DeWald A, Yarvis RM, Simons GP, Flanagan R, Bui LT, Irish EE, Cheng CL. A Ceratopteris EXCESS MICROSPOROCYTES1 suppresses reproductive transition in the fern vegetative leaves. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111812. [PMID: 37532002 DOI: 10.1016/j.plantsci.2023.111812] [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: 03/10/2023] [Revised: 06/28/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Land plant sexual reproduction involves the transition of cells from somatic to reproductive identity during post-embryonic development. In Arabidopsis, the leucine-rich repeat receptor-like kinase EXCESS MICROSPOROCYTES1 (EXS/EMS1) restricts the number of sporogenous cells during the transition from diploid tissue to haploid spore production by promoting the formation of the tapetum cell layer within the anther. Although all land plants studied contain EMS1 genes, its function is unknown beyond a few angiosperms. In the model fern Ceratopteris (Ceratopteris richardii), we discovered an EMS1 homolog (CrEMS1) that functions to suppress formation of reproductive structures on vegetative leaves of the fern sporophyte, a role not found in angiosperms. Suppression of CrEMS1 by RNAi did not affect sporogenesis on reproductive leaves but did affect antheridium production of the fern gametophyte. Expression patterns of CrEMS1 across developmental stages suggest threshold levels of CrEMS1 control the specification of reproductive organs during both generations of the fern. Additional EMS1 homologs present in the fern genome suggest a dynamic role of EMS1 receptors in the evolution of reproductive development in vascular plants.
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Affiliation(s)
- Kelley A Withers
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA
| | - Kevin Falls
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA
| | | | - Tommy Nguyen
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA
| | - Anika DeWald
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA
| | - Rebekah M Yarvis
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA
| | - Gabriel P Simons
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA
| | - Robert Flanagan
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA
| | - Linh T Bui
- The Translational Genomics Research Institute, 445 N. Fifth St., Phoenix, AZ 85004, USA
| | - Erin E Irish
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA
| | - Chi-Lien Cheng
- Department of Biology, University of Iowa, 129 E. Jefferson St., Iowa City, IA 52242, USA.
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16
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Yu JG, Tang JY, Wei R, Lan MF, Xiang RC, Zhang XC, Xiang QP. The first homosporous lycophyte genome revealed the association between the recent dynamic accumulation of LTR-RTs and genome size variation. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01366-0. [PMID: 37380791 DOI: 10.1007/s11103-023-01366-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023]
Abstract
The contrasting genome size between homosporous and heterosporous plants is fascinating. Different from the heterosporous seed plants and mainly homosporous ferns, the lycophytes are either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). Many lycophytes are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimer's disease. For the seed-free vascular plants, several high-quality genomes of heterosporous Selaginella, homosporous ferns (maidenhair fern, monkey spider tree fern), and heterosporous ferns (Azolla) have been published and provided important insights into the origin and evolution of early land plants. However, the homosporous lycophyte genome has not been decoded. Here, we assembled the first homosporous lycophyte genome and conducted comparative genomic analyses by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size of Lycopodium clavatum is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is long terminal repeat (LTR). This study disclosed a high birth rate and a low death rate of the LTR-RTs in homosporous lycophytes, but the opposite occurs in heterosporous lycophytes. we propose that the recent activity of LTR-RT is responsible for the immense genome size variation between homosporous and heterosporous lycophytes. By combing Ks analysis with a phylogenetic approach, we discovered two whole genome duplications (WGD). Morover, we identified all the five recognized key enzymes for the HupA biosynthetic pathway in the L. clavatum genome, but found this pathway incomplete in other major lineages of land plants. Overall, this study is of great importance for the medicinal utilization of lycophytes and the decoded genome data will be a key cornerstone to elucidate the evolution and biology of early vascular land plants.
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Affiliation(s)
- Ji-Gao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Jun-Yong Tang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, China
| | - Mei-Fang Lan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Rui-Chen Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, China.
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, China.
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17
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Roychowdhury R, Das SP, Gupta A, Parihar P, Chandrasekhar K, Sarker U, Kumar A, Ramrao DP, Sudhakar C. Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses. Genes (Basel) 2023; 14:1281. [PMID: 37372461 PMCID: PMC10298225 DOI: 10.3390/genes14061281] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.
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Affiliation(s)
- Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)—The Volcani Institute, Rishon Lezion 7505101, Israel
| | - Soumya Prakash Das
- School of Bioscience, Seacom Skills University, Bolpur 731236, West Bengal, India
| | - Amber Gupta
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Parul Parihar
- Department of Biotechnology and Bioscience, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India
| | - Kottakota Chandrasekhar
- Department of Plant Biochemistry and Biotechnology, Sri Krishnadevaraya College of Agricultural Sciences (SKCAS), Affiliated to Acharya N.G. Ranga Agricultural University (ANGRAU), Guntur 522034, Andhra Pradesh, India
| | - Umakanta Sarker
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Ajay Kumar
- Department of Botany, Maharshi Vishwamitra (M.V.) College, Buxar 802102, Bihar, India
| | - Devade Pandurang Ramrao
- Department of Biotechnology, Mizoram University, Pachhunga University College Campus, Aizawl 796001, Mizoram, India
| | - Chinta Sudhakar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, Andhra Pradesh, India
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18
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Wang X, Chen Y, Liu S, Fu W, Zhuang Y, Xu J, Lou Y, Baldwin IT, Li R. Functional dissection of rice jasmonate receptors involved in development and defense. THE NEW PHYTOLOGIST 2023; 238:2144-2158. [PMID: 36869435 DOI: 10.1111/nph.18860] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 02/26/2023] [Indexed: 05/04/2023]
Abstract
The phytohormones, jasmonates (JAs), mediate many plant developmental processes and their responses to important environmental stresses, such as herbivore attack. Bioactive JAs are perceived by CORONATINE INSENSITIVE (COI)-receptors, and associated JAZ proteins, to activate downstream responses. To date, the JA receptors of the important monocot crop plant, rice, remain to be explored. Here, we studied all three rice COI proteins, OsCOI1a, OsCOI1b, and OsCOI2, by ligand binding, genome editing, and phenotyping and examining some of the responsible mechanisms for the different responses. OsCOI2 binds to most individual OsJAZs in the presence of endogenous JA ligands, as OsCOI1a /1b do, albeit with greater partner selectivity. Single mutants of each OsCOI and OsCOI1a/1b double mutants were constructed by CRIPSR-Cas9-based genome editing and used to phenotype developmental and defense responses. OsCOI1b is involved in root growth and grain-size control and plays overlapping roles with OsCOI1a in spikelet development, while OsCOI2 regulates leaf senescence, male sterility, root growth, and grain size. All OsCOIs mediated resistance to the devastating rice pest, the brown planthopper. However, the defense sectors regulated by OsCOI1a/1b and OsCOI2 clearly differed. Our results revealed that all three OsCOIs are functional JA receptors that play diverse roles in regulating downstream JA responses.
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Affiliation(s)
- Xinjue Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yumeng Chen
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shuting Liu
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenjie Fu
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunqi Zhuang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jie Xu
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yonggen Lou
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, D-07745, Germany
| | - Ran Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
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19
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Mueller KK, Pfeifer L, Schuldt L, Szövényi P, de Vries S, de Vries J, Johnson KL, Classen B. Fern cell walls and the evolution of arabinogalactan proteins in streptophytes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:875-894. [PMID: 36891885 DOI: 10.1111/tpj.16178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 05/27/2023]
Abstract
Significant changes have occurred in plant cell wall composition during evolution and diversification of tracheophytes. As the sister lineage to seed plants, knowledge on the cell wall of ferns is key to track evolutionary changes across tracheophytes and to understand seed plant-specific evolutionary innovations. Fern cell wall composition is not fully understood, including limited knowledge of glycoproteins such as the fern arabinogalactan proteins (AGPs). Here, we characterize the AGPs from the leptosporangiate fern genera Azolla, Salvinia, and Ceratopteris. The carbohydrate moiety of seed plant AGPs consists of a galactan backbone including mainly 1,3- and 1,3,6-linked pyranosidic galactose, which is conserved across the investigated fern AGPs. Yet, unlike AGPs of angiosperms, those of ferns contained the unusual sugar 3-O-methylrhamnose. Besides terminal furanosidic arabinose, Ara (Araf), the main linkage type of Araf in the ferns was 1,2-linked Araf, whereas in seed plants 1,5-linked Araf is often dominating. Antibodies directed against carbohydrate epitopes of AGPs supported the structural differences between AGPs of ferns and seed plants. Comparison of AGP linkage types across the streptophyte lineage showed that angiosperms have rather conserved monosaccharide linkage types; by contrast bryophytes, ferns, and gymnosperms showed more variability. Phylogenetic analyses of glycosyltransferases involved in AGP biosynthesis and bioinformatic search for AGP protein backbones revealed a versatile genetic toolkit for AGP complexity in ferns. Our data reveal important differences across AGP diversity of which the functional significance is unknown. This diversity sheds light on the evolution of the hallmark feature of tracheophytes: their elaborate cell walls.
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Affiliation(s)
- Kim-Kristine Mueller
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Lukas Pfeifer
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Lina Schuldt
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstr. 107, 8008, Zurich, Switzerland
- Zurich-Basel Plant Science Center (PSC), ETH Zürich, Tannenstrasse 1, 8092, Zürich, Switzerland
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- Department of Applied Bioinformatics, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtsr. 1, 37077, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstr. 1, 37077, Goettingen, Germany
| | - Kim L Johnson
- Department of Animal, Plant and Soil Science, La Trobe Institute for Agriculture & Food, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Birgit Classen
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118, Kiel, Germany
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20
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Xie P, Ke Y, Kuo L. Modified CTAB protocols for high-molecular-weight DNA extractions from ferns. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11526. [PMID: 37342164 PMCID: PMC10278929 DOI: 10.1002/aps3.11526] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 06/22/2023]
Abstract
Premise Efficient protocols for extracting high-molecular-weight (HMW) DNA from ferns facilitate the long-read sequencing of their large and complex genomes. Here, we perform two cetyltrimethylammonium bromide (CTAB)-based protocols to extract HMW DNA and evaluate their applicability in diverse fern taxa for the first time. Methods and Results We describe two modified CTAB protocols, with key adjustments to minimize mechanical disruption during lysis to prevent DNA shearing. One of these protocols uses a small amount of fresh tissue but yields a considerable quantity of HMW DNA with high efficiency. The other accommodates a large amount of input tissue, adopts an initial step of nuclei isolation, and thus ensures a high yield in a short period of time. Both methods were proven to be robust and effective in obtaining HMW DNA from diverse fern lineages, including 33 species in 19 families. The DNA extractions mostly had high DNA integrity, with mean sizes larger than 50 kbp, as well as high purity (A260/A230 and A260/A280 > 1.8). Conclusions This study provides HMW DNA extraction protocols for ferns in the hope of facilitating further attempts to sequence their genomes, which will bridge our genomic understanding of land plant diversity.
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Affiliation(s)
- Pei‐Jun Xie
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Ya‐Ting Ke
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Li‐Yaung Kuo
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
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21
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Zumkeller S, Polsakiewicz M, Knoop V. Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis. Commun Biol 2023; 6:296. [PMID: 36941328 PMCID: PMC10027690 DOI: 10.1038/s42003-023-04659-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Plant mitochondrial genomes can be complex owing to highly recombinant structures, lack of gene syntenies, heavy RNA editing and invasion of chloroplast, nuclear or even foreign DNA by horizontal gene transfer (HGT). Leptosporangiate ferns remained the last major plant clade without an assembled mitogenome, likely owing to a demanding combination of the above. We here present both organelle genomes now for Haplopteris ensiformis. More than 1,400 events of C-to-U RNA editing and over 500 events of reverse U-to-C edits affect its organelle transcriptomes. The Haplopteris mtDNA is gene-rich, lacking only the ccm gene suite present in ancestral land plant mitogenomes, but is highly unorthodox, indicating extraordinary recombinogenic activity. Although eleven group II introns known in disrupted trans-splicing states in seed plants exist in conventional cis-arrangements, a particularly complex structure is found for the mitochondrial rrnL gene, which is split into two parts needing reassembly on RNA level by a trans-splicing group I intron. Aside from ca. 80 chloroplast DNA inserts that complicated the mitogenome assembly, the Haplopteris mtDNA features as an idiosyncrasy 30 variably degenerated protein coding regions from Rickettiales bacteria indicative of heavy bacterial HGT on top of tRNA genes of chlamydial origin.
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Affiliation(s)
- Simon Zumkeller
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Monika Polsakiewicz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany.
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22
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Rahmatpour N, Kuo LY, Kang J, Herman E, Lei L, Li M, Srinivasan S, Zipper R, Wolniak SM, Delwiche CF, Mount S, Li FW. Analyses of Marsilea vestita genome and transcriptomes do not support widespread intron retention during spermatogenesis. THE NEW PHYTOLOGIST 2023; 237:1490-1494. [PMID: 36451524 DOI: 10.1111/nph.18652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Affiliation(s)
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Jessica Kang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Eliana Herman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Lily Lei
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Sruthi Srinivasan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Richard Zipper
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Stephen M Wolniak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Stephen Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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23
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Salino A, Rouhan G, Kuo LY, Almeida TE. Editorial: Biology, systematics, and evolution of ferns and lycophytes in the omics era. FRONTIERS IN PLANT SCIENCE 2023; 14:1146829. [PMID: 36909387 PMCID: PMC9996449 DOI: 10.3389/fpls.2023.1146829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Alexandre Salino
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, Sorbonne Université, EPHE, UA, CNRS, Paris, France
| | - Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Thaís Elias Almeida
- Universidade Federal de Pernambuco, Departamento de Botânica, Centro de Biociências, Recife, Brazil
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24
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Chen H, Fang Y, Zwaenepoel A, Huang S, Van de Peer Y, Li Z. Revisiting ancient polyploidy in leptosporangiate ferns. THE NEW PHYTOLOGIST 2023; 237:1405-1417. [PMID: 36349406 PMCID: PMC7614084 DOI: 10.1111/nph.18607] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/30/2022] [Indexed: 05/31/2023]
Abstract
Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building KS -age distributions and applying substitution rate corrections and by conducting statistical gene tree-species tree reconciliation analyses. Our integrative analyses not only identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree-species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.
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Affiliation(s)
- Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Yuhan Fang
- Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sanwen Huang
- Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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25
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Giant Fern Genomes Show Complex Evolution Patterns: A Comparative Analysis in Two Species of Tmesipteris (Psilotaceae). Int J Mol Sci 2023; 24:ijms24032708. [PMID: 36769031 PMCID: PMC9916801 DOI: 10.3390/ijms24032708] [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: 12/16/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Giant genomes are rare across the plant kingdom and their study has focused almost exclusively on angiosperms and gymnosperms. The scarce genetic data that are available for ferns, however, indicate differences in their genome organization and a lower dynamism compared to other plant groups. Tmesipteris is a small genus of mainly epiphytic ferns that occur in Oceania and several Pacific Islands. So far, only two species with giant genomes have been reported in the genus, T. tannensis (1C = 73.19 Gbp) and T. obliqua (1C = 147.29 Gbp). Low-coverage genome skimming sequence data were generated in these two species and analyzed using the RepeatExplorer2 pipeline to identify and quantify the repetitive DNA fraction of these genomes. We found that both species share a similar genomic composition, with high repeat diversity compared to taxa with small (1C < 10 Gbp) genomes. We also found that, in general, characterized repetitive elements have relatively high heterogeneity scores, indicating ancient diverging evolutionary trajectories. Our results suggest that a whole genome multiplication event, accumulation of repetitive elements, and recent activation of those repeats have all played a role in shaping these genomes. It will be informative to compare these data in the future with data from the giant genome of the angiosperm Paris japonica, to determine if the structures observed here are an emergent property of massive genomic inflation or derived from lineage specific processes.
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26
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Jiang M, Jian J, Zhou C, Li L, Wang Y, Zhang W, Song Z, Yang J. Does integument arise de novo or from pre-existing structures? ── Insights from the key regulatory genes controlling integument development. FRONTIERS IN PLANT SCIENCE 2023; 13:1078248. [PMID: 36714739 PMCID: PMC9880897 DOI: 10.3389/fpls.2022.1078248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
The origin of seeds is one of the key innovations in land plant evolution. Ovules are the developmental precursors of seeds. The integument is the envelope structure surrounding the nucellus within the ovule and developing into the seed coat when ovules mature upon fertilization. The question of whether the integument arise de novo or evolve from elaboration of pre-existing structures has caused much debate. By exploring the origin and evolution of the key regulatory genes controlling integument development and their functions during both individual and historical developmental processes, we showed the widespread presence of the homologs of ANT, CUC, BEL1, SPL, C3HDZ, INO, ATS, and ETT in seedless plant genomes. All of these genes have undergone duplication-divergence events in their evolutionary history, with most of the descendant paralogous suffering motif gain and/or loss in the coding regions. Expression and functional characterization have shown that these genes are key components of the genetic program that patterns leaf-like lateral organs. Serial homology can thus be postulated between integuments and other lateral organs in terms of the shared master regulatory genes. Given that the genetic program patterning leaf-like lateral organs formed in seedless plants, and was reused during seed origin, the integument is unlikely to arise de novo but evolved from the stem segment-specific modification of pre-existing serially homologous structures. The master 'switches' trigging the modification to specify the integument identity remain unclear. We propose a successive transformation model of integument origin.
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Affiliation(s)
- Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jinjing Jian
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Chengchuan Zhou
- Institute of Tree Genetics Breeding and Cultivation, Jiangxi Academy of Forestry, Nanchang, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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27
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Luo R, Pan W, Liu W, Tian Y, Zeng Y, Li Y, Li Z, Cui L. The barley DIR gene family: An expanded gene family that is involved in stress responses. Front Genet 2022; 13:1042772. [PMID: 36406120 PMCID: PMC9667096 DOI: 10.3389/fgene.2022.1042772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/24/2022] [Indexed: 09/09/2023] Open
Abstract
Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.
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Affiliation(s)
- Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenqiang Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yuan Tian
- Xintai Urban and Rural Development Group Co., Ltd., Taian, Shandong, China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhimin Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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28
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Shen L, Tian F, Cheng Z, Zhao Q, Feng Q, Zhao Y, Han B, Fang Y, Lin Y, Chen R, Wang D, Sun W, Sun J, Zeng H, Yao N, Gao G, Luo J, Xu Z, Bai S. OsMADS58 Stabilizes Gene Regulatory Circuits during Rice Stamen Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:2899. [PMID: 36365352 PMCID: PMC9658454 DOI: 10.3390/plants11212899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Rice (Oryza sativa) OsMADS58 is a C-class MADS box protein, and characterization of a transposon insertion mutant osmads58 suggested that OsMADS58 plays a role in stamen development. However, as no null mutation has been obtained, its role has remained unclear. Here, we report that the CRISPR knockout mutant osmads58 exhibits complex altered phenotypes, including anomalous diploid germ cells, aberrant meiosis, and delayed tapetum degeneration. This CRISPR mutant line exhibited stronger changes in expression of OsMADS58 target genes compared with the osmads58 dSpm (transposon insertion) line, along with changes in multiple pathways related to early stamen development. Notably, transcriptional regulatory circuits in young panicles covering the stamen at stages 4-6 were substantially altered in the CRISPR line compared to the dSpm line. These findings strongly suggest that the pleiotropic effects of OsMADS58 on stamen development derive from a potential role in stabilizing gene regulatory circuits during early stamen development. Thus, this work opens new avenues for viewing and deciphering the regulatory mechanisms of early stamen development from a network perspective.
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Affiliation(s)
- Liping Shen
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Feng Tian
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
- Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Zhukuan Cheng
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Qiang Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yan Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yuhan Fang
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
| | - Yanan Lin
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
| | - Rui Chen
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
| | - Donghui Wang
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
| | | | - Jiaqi Sun
- School of Life Science, Sun Yat-sen University, Guangzhou 510260, China
| | - Hongyun Zeng
- School of Life Science, Sun Yat-sen University, Guangzhou 510260, China
| | - Nan Yao
- School of Life Science, Sun Yat-sen University, Guangzhou 510260, China
| | - Ge Gao
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
- Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Jingchu Luo
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Zhihong Xu
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
| | - Shunong Bai
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- Center of Quantitative Biology, Peking University, Beijing 100871, China
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Bai SN, Rao GY, Yang J. Origins of the seed: The "golden-trio hypothesis". FRONTIERS IN PLANT SCIENCE 2022; 13:965000. [PMID: 36105705 PMCID: PMC9465013 DOI: 10.3389/fpls.2022.965000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
The seed is an evolutionary innovation in the plant kingdom. While human civilization depends heavily on seed production, how the seed trait emerged remains elusive. In this opinion article, a "golden-trio hypothesis" is proposed based on our investigations of LEC1 gene functions in Adiantum capillus-veneris. This hypothesis posits that a "seed program" arose from spatiotemporal integration of three key components: assimilate flow, ABA-mediated stress responses, and stress-induced LEC1 expression. Thus, the evolutionary innovation of seeds should be considered not a simple event resulting from new genes; rather, it represents the outcome of a series of physiological and morphological innovations that emerged prior to and regardless of the origin of the seed program. This new perspective could help us tackle some long-standing questions around the puzzling origin of seeds.
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Affiliation(s)
- Shu-Nong Bai
- College of Life Sciences, Peking University, Beijing, China
| | - Guang-Yuan Rao
- College of Life Sciences, Peking University, Beijing, China
| | - Ji Yang
- School of Life Sciences, Fudan University, Shanghai, China
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