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Hayes ML, Garcia ET, Chun SO, Selke M. Crosslinking of base modified RNAs by synthetic DYW-KP base editors implicates an enzymatic lysine as the nitrogen donor for U-to-C RNA editing. J Biol Chem 2024:107454. [PMID: 38852885 DOI: 10.1016/j.jbc.2024.107454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024] Open
Abstract
Base editing mechanisms are being investigated as potential therapeutic tools to alleviate genetic diseases. Sequence specific C-to-U and A-to-I base editing tools are capable of altering RNA and DNA sequences and utilize a hydrolytic deamination mechanism requiring an active site zinc ion and a glutamate residue. In plant organelles, DYW-PG domain containing enzymes catalyze C-to-U edits and likely use the canonical deamination mechanism. Proteins developed from consensus sequences from the DYW-KP domain family catalyze what initially appeared to be U-to-C edits leading to this investigation into mechanistic insights into U-to-C editing. The synthetic DYW-KP enzyme KP6 was found sufficient for C-to-U editing activity stimulated by the addition of carboxylic acids in vitro. Despite addition of 14 different putative amine/amide donors in vitro U-to-C editing could not be observed. C-to-U editing was found not to be concomitant with U-to-C editing thus discounting a pyrimidine transaminase mechanism. RNAs containing base modifications were covalently crosslinked to KP6, KP2, and KP3 proteins. Mass spectrometry of purified KP2 and KP6 proteins revealed an additional mass of 319 Da. A U-to-C crosslinking mechanism was projected to explain the link between crosslinking, RNA base changes, and the ∼319 Da mass. In this model an enzymatic lysine attacks C4 of uridine to form a Schiff base RNA-protein conjugate. Sequenced RT-PCR products from the fern Ceratopteris richardii indicate U-to-C base edits do not preserve proteinaceous crosslinks in planta. Hydrolysis of a protonated Schiff base conjugate releasing cytidine is hypothesized to explain the completed pathway in plants.
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Affiliation(s)
- Michael L Hayes
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA.
| | - Elvin T Garcia
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
| | - Skellie O Chun
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
| | - Matthias Selke
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, California, 90032, USA
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2
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Michalak KM, Wojciechowska N, Marzec-Schmidt K, Bagniewska-Zadworna A. Conserved autophagy and diverse cell wall composition: unifying features of vascular tissues in evolutionarily distinct plants. ANNALS OF BOTANY 2024; 133:559-572. [PMID: 38324309 PMCID: PMC11037490 DOI: 10.1093/aob/mcae015] [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: 11/13/2023] [Accepted: 02/02/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND AND AIMS The formation of multifunctional vascular tissues represents a significant advancement in plant evolution. Differentiation of conductive cells is specific, involving two main pathways, namely protoplast clearance and cell wall modification. In xylogenesis, autophagy is a crucial process for complete protoplast elimination in tracheary elements, whose cell wall also undergoes strong changes. Knowledge pertaining to living sieve elements, which lose most of their protoplast during phloemogenesis, remains limited. We hypothesized that autophagy plays a crucial role, not only in complete cytoplasmic clearance in xylem but also in partial degradation in phloem. Cell wall elaborations of mature sieve elements are not so extensive. These analyses performed on evolutionarily diverse model species potentially make it possible to understand phloemogenesis to an equal extent to xylogenesis. METHODS We investigated the distribution of ATG8 protein, which is an autophagy marker, and cell wall components in the roots of ferns, gymnosperms and angiosperms (monocots, dicot herbaceous plants and trees). Furthermore, we conducted a bioinformatic analysis of complete data on ATG8 isoforms for Ceratopteris richardii. KEY RESULTS The presence of ATG8 protein was confirmed in both tracheary elements and sieve elements; however, the composition of cell wall components varied considerably among vascular tissues in the selected plants. Arabinogalactan proteins and β-1,4-galactan were detected in the roots of all studied species, suggesting their potential importance in phloem formation or function. In contrast, no evolutionary pattern was observed for xyloglucan, arabinan or homogalacturonan. CONCLUSIONS Our findings indicate that the involvement of autophagy in plants is universal during the development of tracheary elements that are dead at maturity and sieve elements that remain alive. Given the conserved nature of autophagy and its function in protoplast degradation for uninterrupted flow, autophagy might have played a vital role in the development of increasingly complex biological organizations, including the formation of vascular tissues. However, different cell wall compositions of xylem and phloem in different species might indicate diverse functionality and potential for substance transport, which is crucial in plant evolution.
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Affiliation(s)
- Kornel M Michalak
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Natalia Wojciechowska
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | | | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
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3
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Xiao YL, Li GS. Differential expression and co-localization of transcriptional factors during callus transition to differentiation for shoot organogenesis in the water fern Ceratopteris richardii. ANNALS OF BOTANY 2024; 133:495-507. [PMID: 38206867 PMCID: PMC11006541 DOI: 10.1093/aob/mcae006] [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: 10/23/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND AND AIMS In flowering plants, regeneration can be achieved by a variety of approaches, and different sets of transcriptional factors are involved in these processes. However, regeneration in taxa other than flowering plants remains a mystery. Ceratopteris richardii is a representative fern capable of both direct and indirect organogenesis, and we aimed to investigate the genetics underlying the transition from callus proliferation to differentiation. METHODS Morphological and histological analyses were used to determine the type of regeneration involved. RNA sequencing and differential gene expression were used to investigate how the callus switches from proliferation to differentiation. Phylogenetic analysis and RNA in situ hybridization were used to understand whether transcriptional factors are involved in this transition. KEY RESULTS The callus formed on nascent leaves and subsequently developed the shoot pro-meristem and shoot meristem, thus completing indirect de novo shoot organogenesis in C. richardii. Genes were differentially expressed during the callus transition from proliferation to differentiation, indicating a role for photosynthesis, stimulus response and transmembrane signalling in this transition and the involvement of almost all cell layers that make up the callus. Transcriptional factors were either downregulated or upregulated, which were generally in many-to-many orthology with genes known to be involved in callus development in flowering plants, suggesting that the genetics of fern callus development are both conserved and divergent. Among them, an STM-like, a PLT-like and an ethylene- and salt-inducible ERF gene3-like gene were expressed simultaneously in the vasculature but not in the other parts of the callus, indicating that the vasculature played a role in the callus transition from proliferation to differentiation. CONCLUSIONS Indirect de novo shoot organogenesis could occur in ferns, and the callus transition from proliferation to differentiation required physiological changes, differential expression of transcriptional factors and involvement of the vasculature.
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Affiliation(s)
- Yuan-Le Xiao
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou 416000, China
| | - Gui-Sheng Li
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou 416000, China
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4
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Arnoux-Courseaux M, Coudert Y. Re-examining meristems through the lens of evo-devo. TRENDS IN PLANT SCIENCE 2024; 29:413-427. [PMID: 38040554 DOI: 10.1016/j.tplants.2023.11.003] [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: 07/26/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023]
Abstract
The concept of the meristem was introduced in 1858 to characterize multicellular, formative, and proliferative tissues that give rise to the entire plant body, based on observations of vascular plants. Although its original definition did not encompass bryophytes, this concept has been used and continuously refined over the past 165 years to describe the diverse apices of all land plants. Here, we re-examine this matter in light of recent evo-devo research and show that, despite displaying high anatomical diversity, land plant meristems are unified by shared genetic control. We also propose a modular view of meristem function and highlight multiple evolutionary mechanisms that are likely to have contributed to the assembly and diversification of the varied meristems during the course of plant evolution.
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Affiliation(s)
- Moïra Arnoux-Courseaux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France; Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des Martyrs, F-38054, Grenoble, France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France.
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Li H, Akella S, Engstler C, Omini JJ, Rodriguez M, Obata T, Carrie C, Cerutti H, Mower JP. Recurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida. Nat Commun 2024; 15:1548. [PMID: 38378784 PMCID: PMC10879542 DOI: 10.1038/s41467-024-45813-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Mitochondrial cytochrome c maturation (CCM) requires heme attachment via distinct pathways termed systems I and III. The mosaic distribution of these systems in Archaeplastida raises questions about the genetic mechanisms and evolutionary forces promoting repeated evolution. Here, we show a recurrent shift from ancestral system I to the eukaryotic-specific holocytochrome c synthase (HCCS) of system III in 11 archaeplastid lineages. Archaeplastid HCCS is sufficient to rescue mutants of yeast system III and Arabidopsis system I. Algal HCCS mutants exhibit impaired growth and respiration, and altered biochemical and metabolic profiles, likely resulting from deficient CCM and reduced cytochrome c-dependent respiratory activity. Our findings demonstrate that archaeplastid HCCS homologs function as system III components in the absence of system I. These results elucidate the evolutionary trajectory and functional divergence of CCM pathways in Archaeplastida, providing insight into the causes, mechanisms, and consequences of repeated cooption of an entire biological pathway.
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Affiliation(s)
- Huang Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Soujanya Akella
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Carina Engstler
- Department Biologie I-Botanik, Ludwig-Maximilians-Universität München, D-82152, Planegg-Martinsried, Germany
| | - Joy J Omini
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Moira Rodriguez
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Toshihiro Obata
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Chris Carrie
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Heriberto Cerutti
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
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Peng Y, Wang Z, Li M, Wang T, Su Y. Characterization and analysis of multi-organ full-length transcriptomes in Sphaeropteris brunoniana and Alsophila latebrosa highlight secondary metabolism and chloroplast RNA editing pattern of tree ferns. BMC PLANT BIOLOGY 2024; 24:73. [PMID: 38273309 PMCID: PMC10811885 DOI: 10.1186/s12870-024-04746-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: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Sphaeropteris brunoniana and Alsophila latebrosa are both old relict and rare tree ferns, which have experienced the constant changes of climate and environment. However, little is known about their high-quality genetic information and related research on environmental adaptation mechanisms of them. In this study, combined with PacBio and Illumina platforms, transcriptomic analysis was conducted on the roots, rachis, and pinna of S. brunoniana and A. latebrosa to identify genes and pathways involved in environmental adaptation. Additionally, based on the transcriptomic data of tree ferns, chloroplast genes were mined to analyze their gene expression levels and RNA editing events. RESULTS In the study, we obtained 11,625, 14,391 and 10,099 unigenes of S. brunoniana root, rachis, and pinna, respectively. Similarly, a total of 13,028, 11,431 and 12,144 unigenes were obtained of A. latebrosa root, rachis, and pinna, respectively. According to the enrichment results of differentially expressed genes, a large number of differentially expressed genes were enriched in photosynthesis and secondary metabolic pathways of S. brunoniana and A. latebrosa. Based on gene annotation results and phenylpropanoid synthesis pathways, two lignin synthesis pathways (H-lignin and G-lignin) were characterized of S. brunoniana. Among secondary metabolic pathways of A. latebrosa, three types of WRKY transcription factors were identified. Additionally, based on transcriptome data obtained in this study, reported transcriptome data, and laboratory available transcriptome data, positive selection sites were identified from 18 chloroplast protein-coding genes of four tree ferns. Among them, RNA editing was found in positive selection sites of four tree ferns. RNA editing affected the protein secondary structure of the rbcL gene. Furthermore, the expression level of chloroplast genes indicated high expression of genes related to the chloroplast photosynthetic system in all four species. CONCLUSIONS Overall, this work provides a comprehensive transcriptome resource of S. brunoniana and A. latebrosa, laying the foundation for future tree fern research.
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Affiliation(s)
- Yang Peng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ting Wang
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
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7
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Yang C, Li X, Yang L, Chen S, Liao J, Li K, Zhou J, Shen W, Zhuang X, Bai M, Bassham DC, Gao C. A positive feedback regulation of SnRK1 signaling by autophagy in plants. MOLECULAR PLANT 2023; 16:1192-1211. [PMID: 37408307 DOI: 10.1016/j.molp.2023.07.001] [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: 12/11/2022] [Revised: 06/02/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
SnRK1, an evolutionarily conserved heterotrimeric kinase complex that acts as a key metabolic sensor in maintaining energy homeostasis in plants, is an important upstream activator of autophagy that serves as a cellular degradation mechanism for the healthy growth of plants. However, whether and how the autophagy pathway is involved in regulating SnRK1 activity remains unknown. In this study, we identified a clade of plant-specific and mitochondria-localized FCS-like zinc finger (FLZ) proteins as currently unknown ATG8-interacting partners that actively inhibit SnRK1 signaling by repressing the T-loop phosphorylation of the catalytic α subunits of SnRK1, thereby negatively modulating autophagy and plant tolerance to energy deprivation caused by long-term carbon starvation. Interestingly, these AtFLZs are transcriptionally repressed by low-energy stress, and AtFLZ proteins undergo a selective autophagy-dependent pathway to be delivered to the vacuole for degradation, thereby constituting a positive feedback regulation to relieve their repression of SnRK1 signaling. Bioinformatic analyses show that the ATG8-FLZ-SnRK1 regulatory axis first appears in gymnosperms and seems to be highly conserved during the evolution of seed plants. Consistent with this, depletion of ATG8-interacting ZmFLZ14 confers enhanced tolerance, whereas overexpression of ZmFLZ14 leads to reduced tolerance to energy deprivation in maize. Collectively, our study reveals a previously unknown mechanism by which autophagy contributes to the positive feedback regulation of SnRK1 signaling, thereby enabling plants to better adapt to stressful environments.
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Affiliation(s)
- Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China; Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xibao Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lianming Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shunquan Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jun Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Kailin Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jun Zhou
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Mingyi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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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: 4] [Impact Index Per Article: 4.0] [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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Phokas A, Meyberg R, Briones‐Moreno A, Hernandez‐Garcia J, Wadsworth PT, Vesty EF, Blazquez MA, Rensing SA, Coates JC. DELLA proteins regulate spore germination and reproductive development in Physcomitrium patens. THE NEW PHYTOLOGIST 2023; 238:654-672. [PMID: 36683399 PMCID: PMC10952515 DOI: 10.1111/nph.18756] [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: 09/12/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Proteins of the DELLA family integrate environmental signals to regulate growth and development throughout the plant kingdom. Plants expressing non-degradable DELLA proteins underpinned the development of high-yielding 'Green Revolution' dwarf crop varieties in the 1960s. In vascular plants, DELLAs are regulated by gibberellins, diterpenoid plant hormones. How DELLA protein function has changed during land plant evolution is not fully understood. We have examined the function and interactions of DELLA proteins in the moss Physcomitrium (Physcomitrella) patens, in the sister group of vascular plants (Bryophytes). PpDELLAs do not undergo the same regulation as flowering plant DELLAs. PpDELLAs are not degraded by diterpenes, do not interact with GID1 gibberellin receptor proteins and do not participate in responses to abiotic stress. PpDELLAs do share a function with vascular plant DELLAs during reproductive development. PpDELLAs also regulate spore germination. PpDELLAs interact with moss-specific photoreceptors although a function for PpDELLAs in light responses was not detected. PpDELLAs likely act as 'hubs' for transcriptional regulation similarly to their homologues across the plant kingdom. Taken together, these data demonstrate that PpDELLA proteins share some biological functions with DELLAs in flowering plants, but other DELLA functions and regulation evolved independently in both plant lineages.
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Affiliation(s)
- Alexandros Phokas
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of BiologyUniversity of MarburgKarl‐von‐Frisch‐Straße 8Marburg35043Germany
| | - Asier Briones‐Moreno
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | - Jorge Hernandez‐Garcia
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | | | - Eleanor F. Vesty
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
| | - Miguel A. Blazquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC‐Universitat Politècnica de València)C/Ingeniero Fausto Elio s/nValencia46022Spain
| | - Stefan A. Rensing
- Faculty of Chemistry and PharmacyUniversity of FreiburgStefan‐Meier‐Straße 19Freiburg79104Germany
| | - Juliet C. Coates
- School of BiosciencesUniversity of BirminghamEdgbastinBirminghamB15 2TTUK
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10
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Fujiwara T, Liu H, Meza-Torres EI, Morero RE, Vega AJ, Liang Z, Ebihara A, Leitch IJ, Schneider H. Evolution of genome space occupation in ferns: linking genome diversity and species richness. ANNALS OF BOTANY 2023; 131:59-70. [PMID: 34259813 PMCID: PMC9904345 DOI: 10.1093/aob/mcab094] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/10/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The dynamics of genome evolution caused by whole genome duplications and other processes are hypothesized to shape the diversification of plants and thus contribute to the astonishing variation in species richness among the main lineages of land plants. Ferns, the second most species-rich lineage of land plants, are highly suitable to test this hypothesis because of several unique features that distinguish fern genomes from those of seed plants. In this study, we tested the hypothesis that genome diversity and disparity shape fern species diversity by recording several parameters related to genome size and chromosome number. METHODS We conducted de novo measurement of DNA C-values across the fern phylogeny to reconstruct the phylogenetic history of the genome space occupation in ferns by integrating genomic parameters such as genome size, chromosome number and average DNA amount per chromosome into a time-scaled phylogenetic framework. Using phylogenetic generalized least square methods, we determined correlations between chromosome number and genome size, species diversity and evolutionary rates of their transformation. KEY RESULTS The measurements of DNA C-values for 233 species more than doubled the taxon coverage from ~2.2 % in previous studies to 5.3 % of extant diversity. The dataset not only documented substantial differences in the accumulation of genomic diversity and disparity among the major lineages of ferns but also supported the predicted correlation between species diversity and the dynamics of genome evolution. CONCLUSIONS Our results demonstrated substantial genome disparity among different groups of ferns and supported the prediction that alterations of reproductive modes alter trends of genome evolution. Finally, we recovered evidence for a close link between the dynamics of genome evolution and species diversity in ferns for the first time.
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Affiliation(s)
- Tao Fujiwara
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, Japan
| | - Hongmei Liu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Esteban I Meza-Torres
- Instituto de Botánica del Nordeste, Universidad Nacional del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Corrientes, Argentina
| | - Rita E Morero
- Instituto Multidiscipinario de Biologia Vegetal, Universidad Nacional de Cordoba, Consejo Nacional de Investigaciones Científicas y Tecnicas, Cordoba, Argentina
| | - Alvaro J Vega
- Instituto de Botánica del Nordeste, Universidad Nacional del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas, Corrientes, Argentina
| | - Zhenlong Liang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Sciences, Tsukuba, Japan
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11
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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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12
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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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13
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Wu X, Liu X, Zhang S, Zhou Y. Cell Division and Meristem Dynamics in Fern Gametophytes. PLANTS (BASEL, SWITZERLAND) 2023; 12:209. [PMID: 36616337 PMCID: PMC9823664 DOI: 10.3390/plants12010209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/31/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
One of the most important questions in all multicellular organisms is how to define and maintain different cell fates during continuous cell division and proliferation. Plant meristems provide a unique research system to address this fundamental question because meristems dynamically maintain themselves and sustain organogenesis through balancing cell division and cell differentiation. Different from the gametophytes of seed plants that depend on their sporophytes and lack meristems, the gametophytes of seed-free ferns develop different types of meristems (including apical cell-based meristems and multicellular apical and marginal meristems) to promote independent growth and proliferation during the sexual gametophyte phase. Recent studies combining confocal time-lapse imaging and computational image analysis reveal the cellular basis of the initiation and proliferation of different types of meristems in fern gametophytes, providing new insights into the evolution of meristems in land plants. In this review, we summarize the recent progress in understanding the cell growth dynamics in fern gametophytes and discuss both conserved and diversified mechanisms underlying meristem cell proliferation in seed-free vascular plants.
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Affiliation(s)
- Xiao Wu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Liu
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
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14
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Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, Rössner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Theißen G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, Chen ZH. Dynamic genome evolution in a model fern. NATURE PLANTS 2022; 8:1038-1051. [PMID: 36050461 PMCID: PMC9477723 DOI: 10.1038/s41477-022-01226-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/15/2022] [Indexed: 05/31/2023]
Abstract
The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.
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Affiliation(s)
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Shengguan Cai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Fei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | | | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Rijan R Dhakal
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Clemens Rössner
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Annette Becker
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuhuan Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Tao Tong
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yuanyuan Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shengchun Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Honglang Duan
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | | | | | | | | | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
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15
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Fang Y, Qin X, Liao Q, Du R, Luo X, Zhou Q, Li Z, Chen H, Jin W, Yuan Y, Sun P, Zhang R, Zhang J, Wang L, Cheng S, Yang X, Yan Y, Zhang X, Zhang Z, Bai S, Van de Peer Y, Lucas WJ, Huang S, Yan J. The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences. NATURE PLANTS 2022; 8:1024-1037. [PMID: 36050462 PMCID: PMC7613604 DOI: 10.1038/s41477-022-01222-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 07/13/2022] [Indexed: 05/06/2023]
Abstract
Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.
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Affiliation(s)
- Yuhan Fang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Xing Qin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qinggang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xizhi Luo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qian Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Peng Cheng Laboratory, Artificial Intelligence Research Center, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wanting Jin
- State Key Laboratory of Protein and Plant Gene Research, Quantitative Biology Center, College of Life Sciences, Peking University, Beijing, China
| | - Yaning Yuan
- State Key Laboratory of Protein and Plant Gene Research, Quantitative Biology Center, College of Life Sciences, Peking University, Beijing, China
| | - Pengbo Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Rui Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiao Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuehong Yan
- The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Shunong Bai
- State Key Laboratory of Protein and Plant Gene Research, Quantitative Biology Center, College of Life Sciences, Peking University, Beijing, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - William John Lucas
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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16
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Woudenberg S, Renema J, Tomescu AMF, De Rybel B, Weijers D. Deep origin and gradual evolution of transporting tissues: Perspectives from across the land plants. PLANT PHYSIOLOGY 2022; 190:85-99. [PMID: 35904762 PMCID: PMC9434249 DOI: 10.1093/plphys/kiac304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/08/2022] [Indexed: 05/31/2023]
Abstract
The evolution of transporting tissues was an important innovation in terrestrial plants that allowed them to adapt to almost all nonaquatic environments. These tissues consist of water-conducting cells and food-conducting cells and bridge plant-soil and plant-air interfaces over long distances. The largest group of land plants, representing about 95% of all known plant species, is associated with morphologically complex transporting tissue in plants with a range of additional traits. Therefore, this entire clade was named tracheophytes, or vascular plants. However, some nonvascular plants possess conductive tissues that closely resemble vascular tissue in their organization, structure, and function. Recent molecular studies also point to a highly conserved toolbox of molecular regulators for transporting tissues. Here, we reflect on the distinguishing features of conductive and vascular tissues and their evolutionary history. Rather than sudden emergence of complex, vascular tissues, plant transporting tissues likely evolved gradually, building on pre-existing developmental mechanisms and genetic components. Improved knowledge of the intimate structure and developmental regulation of transporting tissues across the entire taxonomic breadth of extant plant lineages, combined with more comprehensive documentation of the fossil record of transporting tissues, is required for a full understanding of the evolutionary trajectory of transporting tissues.
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Affiliation(s)
| | | | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University–Humboldt, Arcata, California 95521, USA
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17
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Aragón-Raygoza A, Herrera-Estrella L, Cruz-Ramírez A. Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem. FRONTIERS IN PLANT SCIENCE 2022; 13:924660. [PMID: 36035690 PMCID: PMC9413220 DOI: 10.3389/fpls.2022.924660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Gene expression in roots has been assessed in different plant species in studies ranging from complete organs to specific cell layers, and more recently at the single cell level. While certain genes or functional categories are expressed in the root of all or most plant species, lineage-specific genes have also been discovered. An increasing amount of transcriptomic data is available for angiosperms, while a limited amount of data is available for ferns, and few studies have focused on fern roots. Here, we present a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte. Differential gene expression analysis of the root tip transcriptional program showed an enrichment of functional categories related to histogenesis and cell division, indicating an active apical meristem. Analysis of a diverse set of orthologous genes revealed conserved expression in the root meristem, suggesting a preserved role for different developmental roles in this tissue, including stem cell maintenance. The reconstruction of evolutionary trajectories for ground tissue specification genes suggests a high degree of conservation in vascular plants, but not for genes involved in root cap development, showing that certain genes are absent in Ceratopteris or have intricate evolutionary paths difficult to track. Overall, our results suggest different processes of conservation and divergence of genes involved in root development.
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Affiliation(s)
- Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
- Metabolic Engineering Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, United States
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
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18
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Zhong Y, Liu Y, Wu W, Chen J, Sun C, Liu H, Shu J, Ebihara A, Yan Y, Zhou R, Schneider H. Genomic insights into genetic diploidization in the homosporous fern Adiantum nelumboides. Genome Biol Evol 2022; 14:evac127. [PMID: 35946426 PMCID: PMC9387920 DOI: 10.1093/gbe/evac127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Whole genome duplication has been recognized as a major process in speciation of land plants, especially in ferns. Whereas genome downsizing contributes greatly to the post-genome shock responses of polyploid flowering plants, diploidization of polyploid ferns diverges by maintaining most of the duplicated DNA and is thus expected to be dominated by genic processes. As a consequence, fern genomes provide excellent opportunities to study ecological speciation enforced by expansion of protein families via polyploidy. To test the key predictions of this hypothesis, we reported the de novo genome sequence of Adiantum nelumboides, a tetraploid homosporous fern. The obtained draft genome had a size of 6.27 Gb assembled into 11,767 scaffolds with the contig N50 of 1.37 Mb. Repetitive DNA sequences contributed with about 81.7%, a remarkably high proportion of the genome. With 69,568 the number of predicted protein-coding genes exceeded those reported in most other land plant genomes. Intragenomic synteny analyses recovered 443 blocks with the average block size of 1.29 Mb and the average gene content of 16 genes. The results are consistent with the hypothesis of high ancestral chromosome number, lack of substantial genome downsizing, and dominance of genic diploidization. As expected in the calciphilous plants, a notable number of detected genes were involved in calcium uptake and transport. In summary, the genome sequence of a tetraploid homosporous fern not only provides access to a genomic resource of a derived fern, but also supports the hypothesis of maintenance of high chromosome numbers and duplicated DNA in young polyploid ferns.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - Wei Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jingfang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenyu Sun
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hongmei Liu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Jiangping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, and the Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, and the Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
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19
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Kitaoku Y, Taira T, Numata T, Ohnuma T, Fukamizo T. Structure, mechanism, and phylogeny of LysM-chitinase conjugates specifically found in fern plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111310. [PMID: 35696910 DOI: 10.1016/j.plantsci.2022.111310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/28/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
A unique GH18 chitinase containing two N-terminal lysin motifs (PrLysM1 and PrLysM2) was first found in fern, Pteris ryukyuensis (Onaga and Taira, Glycobiology, 18, 414-423, 2008). This type of LysM-chitinase conjugates is not usually found in plants but in fungi. Here, we produced a similar GH18 chitinase with one N-terminal LysM module (EaLysM) from the fern, Equisetum arvense (EaChiA, Inamine et al., Biosci. Biotechnol. Biochem., 79, 1296-1304, 2015), using an Escherichia coli expression system and characterized for its structure and mechanism of action. The crystal structure of EaLysM exhibited an almost identical fold (βααβ) to that of PrLysM2. From isothermal titration calorimetry and nuclear magnetic resonance, the binding mode and affinities of EaLysM for chitooligosaccharides (GlcNAc)n (3, 4, 5, and 6) were found to be comparable to those of PrLysM2. The LysM module in EaChiA is likely to bind (GlcNAc)n almost independently through CH-π stacking of a Tyr residue with the pyranose ring. The (GlcNAc)n-binding mode of LysMs in the LysM-chitinase conjugates from fern plants appears to differ from that of plant LysMs acting in chitin- or Nod-signal perception, in which multiple LysMs cooperatively act on (GlcNAc)n. Phylogenetic analysis suggested that LysM-GH18 conjugates of fern plants formed a monophyletic group and had been separated earlier than forming the clade of fungal chitinases with LysMs.
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Affiliation(s)
- Yoshihito Kitaoku
- Department of Advanced Bioscience, Kindai University, 3327-204, Nakamachi, Nara 631-8505, Japan
| | - Toki Taira
- Department of Bioscience and Biotechnology, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takayuki Ohnuma
- Department of Advanced Bioscience, Kindai University, 3327-204, Nakamachi, Nara 631-8505, Japan; Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, 3327-204, Nakamachi, Nara 631-8505, Japan.
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204, Nakamachi, Nara 631-8505, Japan.
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20
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Pelosi JA, Kim EH, Barbazuk WB, Sessa EB. Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:882441. [PMID: 35909764 PMCID: PMC9330400 DOI: 10.3389/fpls.2022.882441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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Affiliation(s)
- Jessie A. Pelosi
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Emily H. Kim
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
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21
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Geng Y, Yan A, Zhou Y. Positional cues and cell division dynamics drive meristem development and archegonium formation in Ceratopteris gametophytes. Commun Biol 2022; 5:650. [PMID: 35778477 PMCID: PMC9249879 DOI: 10.1038/s42003-022-03627-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Fern gametophytes are autotrophic and independent of sporophytes, and they develop pluripotent meristems that drive prothallus development and sexual reproduction. To reveal cellular dynamics during meristem development in fern gametophytes, we performed long-term time-lapse imaging and determined the real-time lineage, identity and division activity of each single cell from meristem initiation to establishment in gametophytes of the fern Ceratopteris richardii. Our results demonstrate that in Ceratopteris gametophytes, only a few cell lineages originated from the marginal layer contribute to meristem initiation and proliferation, and the meristem lacks a distinguishable central zone or apical cell with low division activity. Within the meristem, cell division is independent of cell lineages and cells at the marginal layer are more actively dividing than inner cells. Furthermore, the meristem triggers differentiation of adjacent cells into egg-producing archegonia in a position-dependent manner. These findings advance the understanding of diversified meristem and gametophyte development in land plants. Time-lapse imaging of the fern Ceratopteris richardii during meristem initiation and proliferation provides insights into the lineage, identity and division activity of each cell throughout the growth of gametophytes.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - An Yan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
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22
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Wu X, Yan A, Yang X, Banks JA, Zhang S, Zhou Y. Cell growth dynamics in two types of apical meristems in fern gametophytes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:149-163. [PMID: 35451138 PMCID: PMC9541313 DOI: 10.1111/tpj.15784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 05/02/2023]
Abstract
In contrast to seed plants, the gametophytes of seed-free plants develop pluripotent meristems, which promote and sustain their independent growth and development. To date, the cellular basis of meristem development in gametophytes of seed-free ferns remains largely unknown. In this study, we used Woodsia obtusa, the blunt-lobe cliff fern, to quantitatively determine cell growth dynamics in two different types of apical meristems - the apical initial centered meristem and the multicellular apical meristem in gametophytes. Through confocal time-lapse live imaging and computational image analysis and quantification, we determined unique patterns of cell division and growth that sustain or terminate apical initials, dictate the transition from apical initials to multicellular apical meristems, and drive proliferation of apical meristems in ferns. Quantitative results showed that small cells correlated to active cell division in fern gametophytes. The marginal cells of multicellular apical meristems in fern gametophytes undergo division in both anticlinal and periclinal orientations, not only increasing cell numbers but also playing a dominant role in increasing cell layers during gametophyte development. All these findings provide insights into the function and regulation of meristems in gametophytes of seed-free vascular plants, suggesting both conserved and diversified mechanisms underlying meristem cell proliferation across land plants.
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Affiliation(s)
- Xiao Wu
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIndiana47907USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIndiana47907USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Center of Pear Engineering Technology ResearchNanjing Agricultural UniversityNanjingJiangsu210095China
| | - An Yan
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCalifornia91125USA
- Howard Hughes Medical InstituteCalifornia Institute of TechnologyPasadenaCalifornia91125USA
| | - Xi Yang
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIndiana47907USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIndiana47907USA
| | - Jo Ann Banks
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIndiana47907USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIndiana47907USA
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Center of Pear Engineering Technology ResearchNanjing Agricultural UniversityNanjingJiangsu210095China
| | - Yun Zhou
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIndiana47907USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIndiana47907USA
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23
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Qiao X, Zhang S, Paterson AH. Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions. Comput Struct Biotechnol J 2022; 20:3248-3256. [PMID: 35782740 PMCID: PMC9237934 DOI: 10.1016/j.csbj.2022.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 01/09/2023] Open
Abstract
Whole-genome duplication (WGD) has occurred repeatedly during plant evolution and diversification, providing genetic layers for evolving new functions and phenotypes. Advances in long-read sequencing technologies have enabled sequencing and assembly of over 1000 plant genomes spanning nearly 800 species, in which a large set of ancient WGDs has been uncovered. Here, we review the recently reported WGDs that occurred in major plant lineages and key evolutionary positions, and highlight their contributions to morphological innovation and adaptive evolution. Current gaps and challenges in integrating enormous volumes of sequenced plant genomes, accurately inferring WGDs, and developing web-based analysis tools are emphasized. Looking to the future, ambitious genome sequencing projects and global efforts may substantially recapitulate the plant tree of life based on broader sampling of phylogenetic diversity, reveal much of the timetable of ancient WGDs, and address the biological significance of WGDs in plant adaptation and radiation.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA,Corresponding author.
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24
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Huang X, Wang W, Gong T, Wickell D, Kuo LY, Zhang X, Wen J, Kim H, Lu F, Zhao H, Chen S, Li H, Wu W, Yu C, Chen S, Fan W, Chen S, Bao X, Li L, Zhang D, Jiang L, Khadka D, Yan X, Liao Z, Zhou G, Guo Y, Ralph J, Sederoff RR, Wei H, Zhu P, Li FW, Ming R, Li Q. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. NATURE PLANTS 2022; 8:500-512. [PMID: 35534720 PMCID: PMC9122828 DOI: 10.1038/s41477-022-01146-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/30/2022] [Indexed: 05/03/2023]
Abstract
To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.
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Affiliation(s)
- Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Wenling Wang
- Shenzhen Branch, Guangdong 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, China
| | - Ting Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - David Wickell
- Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong 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, China
| | - Jialong Wen
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, China
| | - Hoon Kim
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Fachuang Lu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Changjiang Yu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wei Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Shuai Chen
- Shenzhen Branch, Guangdong 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, China
| | - Xiuqi Bao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Longyu Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dipak Khadka
- GoldenGate International College, Tribhuvan University, Battisputali, Kathmandu, Nepal
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Zhenyang Liao
- Shenzhen Branch, Guangdong 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, China
| | - Gongke Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Fay-Wei Li
- Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
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25
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Kinosian SP, Wolf PG. The biology of C. richardii as a tool to understand plant evolution. eLife 2022; 11:75019. [PMID: 35311640 PMCID: PMC8979586 DOI: 10.7554/elife.75019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/18/2022] [Indexed: 12/12/2022] Open
Abstract
The fern Ceratopteris richardii has been studied as a model organism for over 50 years because it is easy to grow and has a short life cycle. In particular, as the first homosporous vascular plant for which genomic resources were developed, C. richardii has been an important system for studying plant evolution. However, we know relatively little about the natural history of C. richardii. In this article, we summarize what is known about this aspect of C. richardii, and discuss how learning more about its natural history could greatly increase our understanding of the evolution of land plants.
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Affiliation(s)
- Sylvia P Kinosian
- Negaunee Institute for Plant Conservation Science, Chicago Botanic Garden, Chicago, United States
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama, Huntsville, United States
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26
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Cai Z, Xie Z, Huang L, Wang Z, Pan M, Yu X, Xu S, Luo J. Full-length transcriptome analysis of Adiantum flabellulatum gametophyte. PeerJ 2022; 10:e13079. [PMID: 35287343 PMCID: PMC8917799 DOI: 10.7717/peerj.13079] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Ferns are important components of plant communities on earth, but their genomes are generally very large, with many redundant genes, making whole genome sequencing of ferns prohibitively expensive and time-consuming. This means there is a significant lack of fern reference genomes, making molecular biology research difficult. The gametophytes of ferns can survive independently, are responsible for sexual reproduction and the feeding of young sporophytes, and play an important role in the alternation of generations. For this study, we selected Adiantum flabellulatum as it has both ornamental and medicinal value and is also an indicator plant of acidic soil. The full-length transcriptome sequencing of its gametophytes was carried out using PacBio three-generation sequencing technology. A total of 354,228 transcripts were obtained, and 231,705 coding sequences (CDSs) were predicted, including 5,749 transcription factors (TFs), 2,214 transcription regulators (TRs) and 4,950 protein kinases (PKs). The transcripts annotated by non-redundant protein sequence database (NR), Kyoto encyclopedia of genes and genomes (KEGG), eukaryotic ortholog groups (KOG), Swissprot, protein family (Pfma), nucleotide sequence database (NT) and gene ontology (GO) were 251,501, 197,474, 193,630, 194,639, 195,956, 113,069 and 197,883, respectively. In addition, 138,995 simple sequence repeats (SSRs) and 111,793 long non-coding RNAs (lncRNAs) were obtained. We selected nine chlorophyll synthase genes for qRT-PCR, and the results showed that the full-length transcript sequences and the annotation information were reliable. This study can provide a reference gene set for subsequent gene expression quantification.
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Affiliation(s)
- Zeping Cai
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Zhenyu Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Luyao Huang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Zixuan Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Min Pan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Xudong Yu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Shitao Xu
- College of Horticulture, Hainan University, Haikou, Hainan, China
| | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Kinosian SP, Rowe CA, Wolf PG. Why Do Heterosporous Plants Have So Few Chromosomes? FRONTIERS IN PLANT SCIENCE 2022; 13:807302. [PMID: 35251082 PMCID: PMC8888854 DOI: 10.3389/fpls.2022.807302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The mechanisms controlling chromosome number, size, and shape, and the relationship of these traits to genome size, remain some of the least understood aspects of genome evolution. Across vascular plants, there is a striking disparity in chromosome number between homosporous and heterosporous lineages. Homosporous plants (comprising most ferns and some lycophytes) have high chromosome numbers compared to heterosporous lineages (some ferns and lycophytes and all seed plants). Many studies have investigated why homosporous plants have so many chromosomes. However, homospory is the ancestral condition from which heterospory has been derived several times. Following this phylogenetic perspective, a more appropriate question to ask is why heterosporous plants have so few chromosomes. Here, we review life history differences between heterosporous and homosporous plants, previous work on chromosome number and genome size in each lineage, known mechanisms of genome downsizing and chromosomal rearrangements, and conclude with future prospects for comparative research.
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Affiliation(s)
- Sylvia P. Kinosian
- Negaunee Institute for Plant Conservation Science, Chicago Botanic Garden, Glencoe, IL, United States
| | - Carol A. Rowe
- Earth System Science Center, The University of Alabama in Huntsville, Huntsville, AL, United States
| | - Paul G. Wolf
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, United States
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28
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Hong Y, Wang Z, Li M, Su Y, Wang T. First Multi-Organ Full-Length Transcriptome of Tree Fern Alsophila spinulosa Highlights the Stress-Resistant and Light-Adapted Genes. Front Genet 2022; 12:784546. [PMID: 35186007 PMCID: PMC8854977 DOI: 10.3389/fgene.2021.784546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alsophila spinulosa, a relict tree fern, is a valuable plant for investigating environmental adaptations. Its genetic resources, however, are scarce. We used the PacBio and Illumina platforms to sequence the polyadenylated RNA of A. spinulosa root, rachis, and pinna, yielding 125,758, 89,107, and 89,332 unigenes, respectively. Combining the unigenes from three organs yielded a non-redundant reference transcriptome with 278,357 unigenes and N50 of 4141 bp, which were further reconstructed into 38,470 UniTransModels. According to functional annotation, pentatricopeptide repeat genes and retrotransposon-encoded polyprotein genes are the most abundant unigenes. Clean reads mapping to the full-length transcriptome is used to assess the expression of unigenes. The stress-induced ASR genes are highly expressed in all three organs, which is validated by qRT-PCR. The organ-specific upregulated genes are enriched for pathways involved in stress response, secondary metabolites, and photosynthesis. Genes for five types of photoreceptors, CRY signaling pathway, ABA biosynthesis and transduction pathway, and stomatal movement-related ion channel/transporter are profiled using the high-quality unigenes. The gene expression pattern coincides with the previously identified stomatal characteristics of fern. This study is the first multi-organ full-length transcriptome report of a tree fern species, the abundant genetic resources and comprehensive analysis of A. spinulosa, which provides the groundwork for future tree fern research.
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Affiliation(s)
- Yongfeng Hong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
| | - Ting Wang
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
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29
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Kress WJ, Soltis DE, Kersey PJ, Wegrzyn JL, Leebens-Mack JH, Gostel MR, Liu X, Soltis PS. Green plant genomes: What we know in an era of rapidly expanding opportunities. Proc Natl Acad Sci U S A 2022; 119:e2115640118. [PMID: 35042803 PMCID: PMC8795535 DOI: 10.1073/pnas.2115640118] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.
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Affiliation(s)
- W John Kress
- National Museum of Natural History, Smithsonian Institution, Department of Botany, Washington, DC 20013-7012;
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
- Arnold Arboretum, Harvard University, Boston, MA 02130
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
- Department of Biology, University of Florida, Gainesville, FL 32611
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, Institute for Systems Genomics: Computational Biology Core, University of Connecticut, Storrs, CT 06269-3214
| | - James H Leebens-Mack
- Department of Plant Biology, 2101 Miller Plant Sciences, University of Georgia, Athens, GA 30602-7271
| | - Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, TX 76107-3400
| | - Xin Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
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30
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Pucker B, Irisarri I, de Vries J, Xu B. Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. QUANTITATIVE PLANT BIOLOGY 2022; 3:e5. [PMID: 37077982 PMCID: PMC10095996 DOI: 10.1017/qpb.2021.18] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/24/2021] [Accepted: 12/21/2021] [Indexed: 05/03/2023]
Abstract
Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller plant genomes can be completed within days. This also resulted in an increased investigation of genomes from multiple species in large scale to address fundamental questions associated with the origin and evolution of land plants. Increased accessibility of sequencing devices and user-friendly software allows more researchers to get involved in genomics. Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.
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Affiliation(s)
- Boas Pucker
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
- Author for correspondence: Boas Pucker E-mail:
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Göttingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Göttingen, Germany
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB), University of Goettingen, Göttingen, Germany
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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31
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Wu X, Yan A, Liu X, Zhang S, Zhou Y. Quantitative live-imaging reveals the dynamics of apical cells during gametophyte development in ferns. QUANTITATIVE PLANT BIOLOGY 2022; 3:e25. [PMID: 37077984 PMCID: PMC10095955 DOI: 10.1017/qpb.2022.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/19/2022] [Accepted: 10/08/2022] [Indexed: 05/02/2023]
Abstract
Meristems in land plants share conserved functions but develop highly variable structures. Meristems in seed-free plants, including ferns, usually contain one or a few pyramid-/wedge-shaped apical cells (ACs) as initials, which are lacking in seed plants. It remained unclear how ACs promote cell proliferation in fern gametophytes and whether any persistent AC exists to sustain fern gametophyte development continuously. Here, we uncovered previously undefined ACs maintained even at late developmental stages in fern gametophytes. Through quantitative live-imaging, we determined division patterns and growth dynamics that maintain the persistent AC in Sphenomeris chinensis, a representative fern. The AC and its immediate progenies form a conserved cell packet, driving cell proliferation and prothallus expansion. At the apical centre of gametophytes, the AC and its adjacent progenies display small dimensions resulting from active cell division instead of reduced cell expansion. These findings provide insight into diversified meristem development in land plants.
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Affiliation(s)
- Xiao Wu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana47907, USA
- Purdue Centre for Plant Biology, Purdue University, West Lafayette, Indiana47907, USA
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - An Yan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California91125, USA
| | - Xing Liu
- Purdue Centre for Plant Biology, Purdue University, West Lafayette, Indiana47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, Indiana47907, USA
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Authors for correspondence: S. Zhang, Y. Zhou, E-mail: ;
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana47907, USA
- Purdue Centre for Plant Biology, Purdue University, West Lafayette, Indiana47907, USA
- Authors for correspondence: S. Zhang, Y. Zhou, E-mail: ;
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32
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Montgomery SA, Berger F. The evolution of imprinting in plants: beyond the seed. PLANT REPRODUCTION 2021; 34:373-383. [PMID: 33914165 PMCID: PMC8566399 DOI: 10.1007/s00497-021-00410-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/12/2021] [Indexed: 05/14/2023]
Abstract
Genomic imprinting results in the biased expression of alleles depending on if the allele was inherited from the mother or the father. Despite the prevalence of sexual reproduction across eukaryotes, imprinting is only found in placental mammals, flowering plants, and some insects, suggesting independent evolutionary origins. Numerous hypotheses have been proposed to explain the selective pressures that favour the innovation of imprinted gene expression and each differs in their experimental support and predictions. Due to the lack of investigation of imprinting in land plants, other than angiosperms with triploid endosperm, we do not know whether imprinting occurs in species lacking endosperm and with embryos developing on maternal plants. Here, we discuss the potential for uncovering additional examples of imprinting in land plants and how these observations may provide additional support for one or more existing imprinting hypotheses.
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Affiliation(s)
- Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria.
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33
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Wu X, Yan A, McAdam SAM, Banks JA, Zhang S, Zhou Y. Timing of meristem initiation and maintenance determines the morphology of fern gametophytes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6990-7001. [PMID: 34181730 DOI: 10.1093/jxb/erab307] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
The alternation of generations in land plants occurs between the sporophyte phase and the gametophyte phase. The sporophytes of seed plants develop self-maintained, multicellular meristems, and these meristems determine plant architecture. The gametophytes of seed plants lack meristems and are heterotrophic. In contrast, the gametophytes of seed-free vascular plants, including ferns, are autotrophic and free-living, developing meristems to sustain their independent growth and proliferation. Compared with meristems in the sporophytes of seed plants, the cellular mechanisms underlying meristem development in fern gametophytes remain largely unknown. Here, using confocal time-lapse live imaging and computational segmentation and quantification, we determined different patterns of cell divisions associated with the initiation and proliferation of two distinct types of meristems in gametophytes of two closely related Pteridaceae ferns, Pteris vittata and Ceratopteris richardii. Our results reveal how the simple timing of a switch between two meristems has considerable consequences for the divergent gametophyte morphologies of the two ferns. They further provide evolutionary insight into the function and regulation of gametophyte meristems in seed-free vascular plants.
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Affiliation(s)
- Xiao Wu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - An Yan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Scott A M McAdam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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34
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Plackett ARG, Emms DM, Kelly S, Hetherington AM, Langdale JA. Conditional stomatal closure in a fern shares molecular features with flowering plant active stomatal responses. Curr Biol 2021; 31:4560-4570.e5. [PMID: 34450089 DOI: 10.1016/j.cub.2021.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/23/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Stomata evolved as plants transitioned from water to land, enabling carbon dioxide uptake and water loss to be controlled. In flowering plants, the most recently divergent land plant lineage, stomatal pores actively close in response to drought. In this response, the phytohormone abscisic acid (ABA) triggers signaling cascades that lead to ion and water loss in the guard cells of the stomatal complex, causing a reduction in turgor and pore closure. Whether this stimulus-response coupling pathway acts in other major land plant lineages is unclear, with some investigations reporting that stomatal closure involves ABA but others concluding that closure is passive. Here, we show that in the model fern Ceratopteris richardii active stomatal closure is conditional on sensitization by pre-exposure to either low humidity or exogenous ABA and is promoted by ABA. RNA-seq analysis and de novo transcriptome assembly reconstructed the protein-coding complement of the C. richardii genome, with coverage comparable to other plant models, enabling transcriptional signatures of stomatal sensitization and closure to be inferred. In both cases, changes in abundance of homologs of ABA, Ca2+, and ROS-related signaling components were observed, suggesting that the closure-response pathway is conserved in ferns and flowering plants. These signatures further suggested that sensitization is achieved by lowering the threshold required for a subsequent closure-inducing signal to trigger a response. We conclude that the canonical signaling network for active stomatal closure functioned in at least a rudimentary form in the stomata of the last common ancestor of ferns and flowering plants.
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Affiliation(s)
- Andrew R G Plackett
- University of Oxford, Department of Plant Sciences, South Parks Road, Oxford OX1 3RB, UK.
| | - David M Emms
- University of Oxford, Department of Plant Sciences, South Parks Road, Oxford OX1 3RB, UK
| | - Steven Kelly
- University of Oxford, Department of Plant Sciences, South Parks Road, Oxford OX1 3RB, UK
| | - Alistair M Hetherington
- University of Bristol, School of Biological Sciences, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jane A Langdale
- University of Oxford, Department of Plant Sciences, South Parks Road, Oxford OX1 3RB, UK
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35
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Ruiz-Ruano FJ, Navarro-Domínguez B, Camacho JPM, Garrido-Ramos MA. Transposable element landscapes illuminate past evolutionary events in the endangered fern Vandenboschia speciosa. Genome 2021; 65:95-103. [PMID: 34555288 DOI: 10.1139/gen-2021-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vandenboschia speciosa is an endangered tetraploid fern species with a large genome (10.5 Gb). Its geographical distribution is characterized by disjoined tertiary flora refuges, with relict populations that survived past climate crises. Here, we analyzed the transposable elements (TEs) and found that they comprise approximately 76% of the V. speciosa genome, thus being the most abundant type of DNA sequence in this gigantic genome. The V. speciosa genome is composed of 51% and 5.6% of Class I and Class II elements, respectively. LTR retrotransposons were the most abundant TEs in this species (at least 42% of the genome), followed by non-LTR retrotransposons, which constituted at least 8.7% of the genome of this species. We introduce an additional analysis to identify the nature of non-annotated elements (19% of the genome). A BLAST search of the non-annotated contigs against the V. speciosa TE database allowed for the identification of almost half of them, which were most likely diverged sequence variants of the annotated TEs. In general, the TE composition in V. speciosa resembles the TE composition in seed plants. In addition, repeat landscapes revealed three episodes of amplification for all TEs, most likely due to demographic changes associated with past climate crises.
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Affiliation(s)
- Francisco J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain.,Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Beatriz Navarro-Domínguez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain.,Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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36
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De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel. Genes (Basel) 2021; 12:genes12071017. [PMID: 34208974 PMCID: PMC8304985 DOI: 10.3390/genes12071017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.
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37
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Adeola HA, Bano A, Vats R, Vashishtha A, Verma D, Kaushik D, Mittal V, Rahman MH, Najda A, Albadrani GM, Sayed AA, Farouk SM, Hassanein EHM, Akhtar MF, Saleem A, Abdel-Daim MM, Bhardwaj R. Bioactive compounds and their libraries: An insight into prospective phytotherapeutics approach for oral mucocutaneous cancers. Biomed Pharmacother 2021; 141:111809. [PMID: 34144454 DOI: 10.1016/j.biopha.2021.111809] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/25/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Oral mucocutaneous cancers (OMCs) are cancers that affect both the oral mucosa and perioral cutaneous structures. Common OMCs are squamous cell carcinoma (SCC), basal cell carcinoma (BCC) and malignant melanoma (MM). Anatomical similarities and conventions which categorizes these lesions blur the magnitude of OMCs in diverse populations. The burden of OMC is high in the sub-Saharan Africa and Indian subcontinents, and the cost of management is prohibitive in the resource-limited, developing world. Hence, there is a pressing demand for the use of cost-effective in silico approaches to identify diagnostic tools and treatment targets for diseases with high burdens in these regions. Due to their ubiquitousness and accessibility, the use of therapeutic efficacy of plant bioactive compounds in the management of OMC is both appropriate and plausible. Furthermore, screening known mechanistic disease targets with well annotated plant bioactive compound libraries is poised to improve the routine management of OMCs provided that the requisite access to database resources are available and accessible. Using natural products minimizes the side effects and morbidities associated with conventional therapies. The development of innovative treatments approaches would tremendously benefit the African and Indian populace and reduce the mortalities associated with OMCs in the developing world. Hence, we discuss herein, the potential benefits, opportunities and challenges of using bioactive compound libraries in the management of OMCs.
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Affiliation(s)
- Henry A Adeola
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape and Tygerberg Hospital, Cape Town, South Africa; Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.
| | - Afsareen Bano
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India.
| | - Ravina Vats
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India.
| | - Amit Vashishtha
- Deptartment Of Botany, Sri Venkateswara college, University of Delhi, India.
| | | | - Deepak Kaushik
- Department of Pharmaceutical sciences, Maharshi Dayanand University Rohtak, 124001, India.
| | - Vineet Mittal
- Department of Pharmaceutical sciences, Maharshi Dayanand University Rohtak, 124001, India.
| | - Md Habibur Rahman
- Department of Pharmacy, Southeast University, Banani, Dhaka 1213, Bangladesh.
| | - Agnieszka Najda
- Department of Vegetable Crops and Medicinal Plants University of Life Sciences in Lublin 50A Doświadczalna Street, 20-280 Lublin, Poland.
| | - Ghadeer M Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11474, Saudi Arabia.
| | - Amany A Sayed
- Zoology Department, Faculty of Science, Cairo University, Giza 12613, Egypt.
| | - Sameh M Farouk
- Cytology and Histology Department, Faculty of Veterinary Medicine, Suez Canal University, 41522 Ismailia, Egypt.
| | - Emad H M Hassanein
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt.
| | - Muhammad Furqan Akhtar
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore Campus, Pakistan.
| | - Ammara Saleem
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan.
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt.
| | - Rashmi Bhardwaj
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India.
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38
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Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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Szövényi P, Gunadi A, Li FW. Charting the genomic landscape of seed-free plants. NATURE PLANTS 2021; 7:554-565. [PMID: 33820965 DOI: 10.1038/s41477-021-00888-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 05/02/2023]
Abstract
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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40
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Rothfels CJ. Polyploid phylogenetics. THE NEW PHYTOLOGIST 2021; 230:66-72. [PMID: 33491778 DOI: 10.1111/nph.17105] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/27/2020] [Indexed: 05/23/2023]
Abstract
Polyploidy is a dominant feature of extant plant diversity. However, major research questions, including whether polyploidy is important to long-term evolution or is just 'evolutionary noise', remain unresolved due to difficulties associated with the generation and analysis of data from polyploid lineages. Many of these difficulties have been recently overcome, such that it is now often relatively straightforward to infer the full and often reticulate phylogenetic history of groups with recently formed polyploids. This nascent field of 'polyploid phylogenetics' allows researchers to tackle long-standing questions of polyploid macroevolution, supplies the foundation for mechanistic models of ploidy change, and provides the opportunity to include a more complete and representative sample of plant taxa in our analyses in general.
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Affiliation(s)
- Carl J Rothfels
- Department of Integrative Biology, University Herbarium, University of California, Berkeley, CA, 94702, USA
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41
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Delaux PM, Schornack S. Plant evolution driven by interactions with symbiotic and pathogenic microbes. Science 2021; 371:371/6531/eaba6605. [PMID: 33602828 DOI: 10.1126/science.aba6605] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today's continuum of associations, ranging from parasitism to mutualism. Through phylogenetics, cell biology, and reverse genetics extending beyond flowering plants into bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms used in nonflowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen-resilient crops.
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Affiliation(s)
- Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Castanet Tolosan, France.
| | - Sebastian Schornack
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge CB2 1LR, UK.
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42
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Geng Y, Cai C, McAdam SAM, Banks JA, Wisecaver JH, Zhou Y. A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants. Genome Biol Evol 2021; 13:6157829. [PMID: 33681974 PMCID: PMC7975763 DOI: 10.1093/gbe/evab042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 01/26/2023] Open
Abstract
As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Chao Cai
- Purdue University Libraries and School of Information Studies, Purdue University, West Lafayette, Indiana, USA
| | - Scott A M McAdam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer H Wisecaver
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.,Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
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43
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Chaudhary K, Geeta R, Panjabi P. Origin and diversification of ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3) genes in land plants and phylogenetic evidence that the ancestral CER1/3 gene resulted from the fusion of pre-existing domains. Mol Phylogenet Evol 2021; 159:107101. [PMID: 33592235 DOI: 10.1016/j.ympev.2021.107101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 12/28/2022]
Abstract
ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3) are key genes in synthesis of alkanes, a major component of cuticular waxes in land plants. The genes share extensive similarity, including the N-terminal (ERG3/FAH) and C-terminal (WAX2) domains. This study, traces the origin, evolutionary history, phylogenetic relationships and variation in copy number of the two genes within and beyond the Viridiplantae (green plants). Protein homologs of both CER1 and CER3 were identified across most Embryophyta (land plants), a single homolog (CER1/3) in charophytes and prasinophytes, and none in the other green, red or brown algae. Ancestral state reconstructions in 100 sequenced Archaeplastida using presence/absence of CER1/3 family genes revealed that the CER1/3 gene probably originated in the common ancestor of Viridiplantae. Phylogenetic analysis of CER1 and CER3 protein sequences from 146 plant species strongly suggests that the two genes originated by duplication of CER1/3 in the ancestral embryophyte. The evolution of CER1 and CER3 genes involved differential divergence of the two domains. Outside Embryophyta, CER1/3 similar sequences identified in diatoms and a cryptophyte, were the closest relatives of the CER1/3 family proteins. Proteins harbouring WAX2-wxAR (WAX2 associated region) similar regions were identified in proteins of bacteria, Archaea, cryptophytes, dinoflagellates and Stramenopiles. The independent existence of both ERG3/FAH and WAX2-wxAR domains in diverse lineages strongly points to the origin of CER1/3 gene in green plants by the fusion of pre-existing domains.
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Affiliation(s)
- Komal Chaudhary
- Department of Botany, University of Delhi, Delhi 110007, India
| | - R Geeta
- Department of Botany, University of Delhi, Delhi 110007, India.
| | - Priya Panjabi
- Department of Botany, University of Delhi, Delhi 110007, India.
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44
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Geng Y, Zhou Y. HAM Gene Family and Shoot Meristem Development. FRONTIERS IN PLANT SCIENCE 2021; 12:800332. [PMID: 34987539 PMCID: PMC8720772 DOI: 10.3389/fpls.2021.800332] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/19/2021] [Indexed: 05/18/2023]
Abstract
Land plants develop highly diversified shoot architectures, all of which are derived from the pluripotent stem cells in shoot apical meristems (SAMs). As sustainable resources for continuous organ formation in the aboveground tissues, SAMs play an important role in determining plant yield and biomass production. In this review, we summarize recent advances in understanding one group of key regulators - the HAIRY MERISTEM (HAM) family GRAS domain proteins - in shoot meristems. We highlight the functions of HAM family members in dictating shoot stem cell initiation and proliferation, the signaling cascade that shapes HAM expression domains in shoot meristems, and the conservation and diversification of HAM family members in land plants. We also discuss future directions that potentially lead to a more comprehensive view of the HAM gene family and stem cell homeostasis in land plants.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- *Correspondence: Yun Zhou,
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45
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Aragón-Raygoza A, Vasco A, Blilou I, Herrera-Estrella L, Cruz-Ramírez A. Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii. Genes (Basel) 2020; 11:E1455. [PMID: 33291610 PMCID: PMC7761924 DOI: 10.3390/genes11121455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.
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Affiliation(s)
- Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group at Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
- Metabolic Engineering Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
| | - Alejandra Vasco
- Botanical Research Institute of Texas (BRIT), Fort Worth, TX 76107-3400, USA;
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group at Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
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46
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Biswal DP, Panigrahi KCS. Light- and hormone-mediated development in non-flowering plants: An overview. PLANTA 2020; 253:1. [PMID: 33245411 DOI: 10.1007/s00425-020-03501-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Light, hormones and their interaction regulate different aspects of development in non-flowering plants. They might have played a role in the evolution of different plant groups by conferring specific adaptive evolutionary changes. Plants are sessile organisms. Unlike animals, they lack the opportunity to abandon their habitat in unfavorable conditions. They respond to different environmental cues and adapt accordingly to control their growth and developmental pattern. While phytohormones are known to be internal regulators of plant development, light is a major environmental signal that shapes plant processes. It is plausible that light-hormone crosstalk might have played an important role in plant evolution. But how the crosstalk between light and phytohormone signaling pathways might have shaped the plant evolution is unclear. One of the possible reasons is that flowering plants have been studied extensively in context of plant development, which cannot serve the purpose of evolutionary comparisons. In order to elucidate the role of light, hormone and their crosstalk in the evolutionary adaptation in plant kingdom, one needs to understand various light- and hormone-mediated processes in diverse non-flowering plants. This review is an attempt to outline major light- and phytohormone-mediated responses in non-flowering plant groups such as algae, bryophytes, pteridophytes and gymnosperms.
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Affiliation(s)
- Durga Prasad Biswal
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha, India
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kishore Chandra Sekhar Panigrahi
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha, India.
- Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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47
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Sun J, Li GS. Leaf dorsoventrality candidate gene CpARF4 has conserved expression pattern but divergent tasiR-ARF regulation in the water fern Ceratopteris pteridoides. AMERICAN JOURNAL OF BOTANY 2020; 107:1470-1480. [PMID: 33216953 DOI: 10.1002/ajb2.1570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Leaves are traditionally classified into microphylls and megaphylls, and recently have been regarded as independently originating in lycophytes, ferns, and seed plants. The developmental genetics of leaf dorsoventrality, a synapomorphy in vascular plants, has been extensively studied in flowering plants. AUXIN RESPONSE FACTOR4 (ARF4) genes are key to leaf abaxial identity in flowering plants, but whether they exist in ferns is still an open question. METHODS ARF4 genes from Ceratopteris pteridoides, Cyrtomium guizhouense, and Parathelypteris nipponica were mined from transcriptomes and investigated in terms of evolutionary phylogeny and sequence motifs, with a focus on the tasiR-ARF binding site. In situ hybridization was used to localize expression of CpARF4 in Ceratopteris pteridoides. 5'RNA ligase-mediated-RACE was employed to verify whether CpARF4 transcripts were sliced by tasiR-ARF. RESULTS ARF4 genes exist in ferns, and this lineage originates from a gene duplication in the common ancestor of ferns and seed plants. ARF4 genes are of a single copy in the ferns studied here, and they contain divergent and, at most, one tasiR-ARF binding site. CpARF4 is expressed in the abaxial but not the adaxial domain of leaf primordia at various developmental stages. Transcript slicing guided by tasiR-ARF is active in C. pteridoides, but CpARF4 probably has not been affected by it. CONCLUSIONS Fern ARF4 genes differ in copy number and tasiR-ARF regulation relative to flowering plants, though they can be similarly expressed in the abaxial domain of leaves, revealing a key role for ARF4 genes in the evolution of leaf dorsoventrality of vascular plants.
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Affiliation(s)
- Jun Sun
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou, 416000, China
| | - Gui-Sheng Li
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou, 416000, China
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48
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Ferreira-Guerra M, Marquès-Bueno M, Mora-García S, Caño-Delgado AI. Delving into the evolutionary origin of steroid sensing in plants. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:87-95. [PMID: 32861054 DOI: 10.1016/j.pbi.2020.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/16/2020] [Accepted: 06/24/2020] [Indexed: 05/05/2023]
Abstract
Brassinosteroids (BRs) are steroid hormones that play crucial roles in plant growth, development and adaptation to shifting environmental conditions. Our current understanding of the origin, evolution and functional significance of BRs is influenced by a double-edged bias: most we know stems from studies on a single species and, on the flip side, dearth of information from a phylogenetically broad and significant array of land plants precludes well-grounded comparisons. Here, we provide an update on BR presence and sensing along land plant evolution. Furthermore, a comprehensive search in all major plant lineages reveals the widespread presence of BR-receptor related sequences, suggesting that steroid-related signals may have been functional early in the evolution of land plants.
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Affiliation(s)
- Mar Ferreira-Guerra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Mar Marquès-Bueno
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Santiago Mora-García
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, C1405BWE Buenos Aires, Argentina.
| | - Ana I Caño-Delgado
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
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49
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Spencer V, Nemec Venza Z, Harrison CJ. What can lycophytes teach us about plant evolution and development? Modern perspectives on an ancient lineage. Evol Dev 2020; 23:174-196. [PMID: 32906211 DOI: 10.1111/ede.12350] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
All Evo-Devo studies rely on representative sampling across the tree of interest to elucidate evolutionary trajectories through time. In land plants, genetic resources are well established in model species representing lineages including bryophytes (mosses, liverworts, and hornworts), monilophytes (ferns and allies), and seed plants (gymnosperms and flowering plants), but few resources are available for lycophytes (club mosses, spike mosses, and quillworts). Living lycophytes are a sister group to the euphyllophytes (the fern and seed plant clade), and have retained several ancestral morphological traits despite divergence from a common ancestor of vascular plants around 420 million years ago. This sister relationship offers a unique opportunity to study the conservation of traits such as sporophyte branching, vasculature, and indeterminacy, as well as the convergent evolution of traits such as leaves and roots which have evolved independently in each vascular plant lineage. To elucidate the evolution of vascular development and leaf formation, molecular studies using RNA Seq, quantitative reverse transcription polymerase chain reaction, in situ hybridisation and phylogenetics have revealed the diversification and expression patterns of KNOX, ARP, HD-ZIP, KANADI, and WOX gene families in lycophytes. However, the molecular basis of further trait evolution is not known. Here we describe morphological traits of living lycophytes and their extinct relatives, consider the molecular underpinnings of trait evolution and discuss future research required in lycophytes to understand the key evolutionary innovations enabling the growth and development of all vascular plants.
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Affiliation(s)
- Victoria Spencer
- School of Biological Sciences, The University of Bristol, Bristol, UK
| | - Zoe Nemec Venza
- School of Biological Sciences, The University of Bristol, Bristol, UK
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50
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Kinosian SP, Pearse WD, Wolf PG. Cryptic diversity in the model fern genus Ceratopteris (Pteridaceae). Mol Phylogenet Evol 2020; 152:106938. [PMID: 32791300 DOI: 10.1016/j.ympev.2020.106938] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 07/23/2020] [Accepted: 08/06/2020] [Indexed: 11/28/2022]
Abstract
Cryptic species are present throughout the tree of life. They are especially prevalent in ferns, because of processes such hybridization, polyploidy, and reticulate evolution. In addition, the simple morphology of ferns limits phenotypic variation and makes it difficult to detect cryptic species. The model fern genus Ceratopteris has long been suspected to harbor cryptic diversity, in particular within the highly polymorphic C. thalictroides. Yet no studies have included samples from throughout its pan-tropical range or utilized genomic sequencing, making it difficult to assess the full extent of cryptic variation within this genus. Here, we present the first multilocus phylogeny of the genus using reduced representation genomic sequencing (RADseq) and examine population structure, phylogenetic relationships, and ploidy level variation. We recover similar species relationships found in previous studies, find support for the cryptic species C. gaudichaudii as genetically distinct, and identify novel genomic variation within two of the mostly broadly distributed species in the genus, C. thalictroides and C. cornuta. Finally, we detail the utility of our approach for working on cryptic, reticulate groups of ferns. Specifically, it does not require a reference genome, of which there are very few available for ferns. RADseq is a cost-effective way to work with study groups lacking genomic resources, and to obtain the thousands of nuclear markers needed to untangle species complexes.
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Affiliation(s)
- Sylvia P Kinosian
- Ecology Center and Department of Biology, Utah State University, Logan, UT 84322, USA.
| | - William D Pearse
- Ecology Center and Department of Biology, Utah State University, Logan, UT 84322, USA; Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, UK
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama in Huntsville, Hunstville, AL 35899, USA
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