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Feng YY, Du H, Huang KY, Ran JH, Wang XQ. Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce. Commun Biol 2024; 7:114. [PMID: 38242964 PMCID: PMC10799047 DOI: 10.1038/s42003-024-05786-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.
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Affiliation(s)
- Yuan-Yuan Feng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Kai-Yuan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Akhter S, Westrin KJ, Zivi N, Nordal V, Kretzschmar WW, Delhomme N, Street NR, Nilsson O, Emanuelsson O, Sundström JF. Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway. THE NEW PHYTOLOGIST 2022; 236:1951-1963. [PMID: 36076311 PMCID: PMC9825996 DOI: 10.1111/nph.18449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.
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Affiliation(s)
- Shirin Akhter
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
| | - Karl Johan Westrin
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Nathan Zivi
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
- Skogforsk, Uppsala Science ParkUppsalaSE‐751 83Sweden
| | - Veronika Nordal
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
| | - Warren W. Kretzschmar
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Nicolas Delhomme
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences (SLU)SE‐901 83UmeåSweden
| | - Nathaniel R. Street
- Department of Plant Physiology, Umeå Plant Science CentreUmeå UniversitySE‐901 87UmeåSweden
| | - Ove Nilsson
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural Sciences (SLU)SE‐901 83UmeåSweden
| | - Olof Emanuelsson
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologySE‐171 65SolnaSweden
| | - Jens F. Sundström
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentreSwedish University of Agricultural Sciences (SLU)SE‐750 07UppsalaSweden
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Fritsche S, Rippel Salgado L, Boron AK, Hanning KR, Donaldson LA, Thorlby G. Transcriptional Regulation of Pine Male and Female Cone Initiation and Development: Key Players Identified Through Comparative Transcriptomics. Front Genet 2022; 13:815093. [PMID: 35368695 PMCID: PMC8971679 DOI: 10.3389/fgene.2022.815093] [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: 11/15/2021] [Accepted: 02/24/2022] [Indexed: 11/24/2022] Open
Abstract
With long reproductive timescales, large complex genomes, and a lack of reliable reference genomes, understanding gene function in conifers is extremely challenging. Consequently, our understanding of which genetic factors influence the development of reproductive structures (cones) in monoecious conifers remains limited. Genes with inferred roles in conifer reproduction have mostly been identified through homology and phylogenetic reconstruction with their angiosperm counterparts. We used RNA-sequencing to generate transcriptomes of the early morphological stages of cone development in the conifer species Pinus densiflora and used these to gain a deeper insight into the transcriptional changes during male and female cone development. Paired-end Illumina sequencing was used to generate transcriptomes from non-reproductive tissue and male and female cones at four time points with a total of 382.82 Gbp of data generated. After assembly and stringent filtering, a total of 37,164 transcripts were retrieved, of which a third were functionally annotated using the Mercator plant pipeline. Differentially expressed gene (DEG) analysis resulted in the identification of 172,092 DEGs in the nine tissue types. This, alongside GO gene enrichment analyses, pinpointed transcripts putatively involved in conifer reproductive structure development, including co-orthologs of several angiosperm flowering genes and several that have not been previously reported in conifers. This study provides a comprehensive transcriptome resource for male and early female cone development in the gymnosperm species Pinus densiflora. Characterisation of this resource has allowed the identification of potential key players and thus provides valuable insights into the molecular regulation of reproductive structure development in monoecious conifers.
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Affiliation(s)
- Steffi Fritsche
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
| | - Leonardo Rippel Salgado
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
- Molecular and Digital Breeding, The New Zealand Institute for Plant and Food Research, Te Puke, New Zealand
| | | | | | | | - Glenn Thorlby
- Forest Genetics and Biotechnology, Scion, Rotorua, New Zealand
- *Correspondence: Glenn Thorlby,
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Ma JJ, Chen X, Song YT, Zhang GF, Zhou XQ, Que SP, Mao F, Pervaiz T, Lin JX, Li Y, Li W, Wu HX, Niu SH. MADS-box transcription factors MADS11 and DAL1 interact to mediate the vegetative-to-reproductive transition in pine. PLANT PHYSIOLOGY 2021; 187:247-262. [PMID: 34618133 PMCID: PMC8418398 DOI: 10.1093/plphys/kiab250] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/12/2021] [Indexed: 06/13/2023]
Abstract
The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.
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Affiliation(s)
- Jing-Jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Xi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yi-Tong Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Gui-Fang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Xian-Qing Zhou
- Qigou State-Owned Forest Farm, Pingquan, Hebei Province 067509, PR China
| | - Shu-Peng Que
- Beijing Ming Tombs Forest Farm, Beijing 102200, PR China, Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Fei Mao
- Beijing Ming Tombs Forest Farm, Beijing 102200, PR China, Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Tariq Pervaiz
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Jin-Xing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Harry X. Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
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Wang D, Hao Z, Long X, Wang Z, Zheng X, Ye D, Peng Y, Wu W, Hu X, Wang G, Zheng R, Shi J, Chen J. The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development. BMC PLANT BIOLOGY 2020; 20:508. [PMID: 33153428 PMCID: PMC7643283 DOI: 10.1186/s12870-020-02634-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/30/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Cunninghamia lanceolata (Chinese fir), a member of the conifer family Cupressaceae, is one of the most popular cultivated trees for wood production in China. Continuous research is being performed to improve C. lanceolata breeding values. Given the high rate of seed abortion (one of the reasons being the failure of ovule and pollen development) in C. lanceolata, the proper formation of female/male cones could theoretically increase the number of offspring in future generations. MIKC MADS-box genes are well-known for their roles in the flower/cone development and comprise the typical/atypical floral development model for both angiosperms and gymnosperms. RESULTS We performed a transcriptomic analysis to find genes differentially expressed between female and male cones at a single, carefully determined developmental stage, focusing on the MIKC MADS-box genes. We finally obtained 47 unique MIKC MADS-box genes from C. lanceolata and divided these genes into separate branches. 27 out of the 47 MIKC MADS-box genes showed differential expression between female and male cones, and most of them were not expressed in leaves. Out of these 27 genes, most B-class genes (AP3/PI) were up-regulated in the male cone, while TM8 genes were up-regulated in the female cone. Then, with no obvious overall preference for AG (class C + D) genes in female/male cones, it seems likely that these genes are involved in the development of both cones. Finally, a small number of genes such as GGM7, SVP, AGL15, that were specifically expressed in female/male cones, making them candidate genes for sex-specific cone development. CONCLUSIONS Our study identified a number of MIKC MADS-box genes showing differential expression between female and male cones in C. lanceolata, illustrating a potential link of these genes with C. lanceolata cone development. On the basis of this, we postulated a possible cone development model for C. lanceolata. The gene expression library showing differential expression between female and male cones shown here, can be used to discover unknown regulatory networks related to sex-specific cone development in the future.
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Affiliation(s)
- Dandan Wang
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhaodong Hao
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaofei Long
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Xueyan Zheng
- National Germplasm Bank of Chinese fir at Fujian Yangkou Forest Farm, Shunchang, 353211, China
| | - Daiquan Ye
- National Germplasm Bank of Chinese fir at Fujian Yangkou Forest Farm, Shunchang, 353211, China
| | - Ye Peng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Weihuang Wu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Renhua Zheng
- Fujian Academy of Forestry, Fuzhou, 350012, China
| | - Jisen Shi
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Fritsche S, Klocko AL, Boron A, Brunner AM, Thorlby G. Strategies for Engineering Reproductive Sterility in Plantation Forests. FRONTIERS IN PLANT SCIENCE 2018; 9:1671. [PMID: 30498505 PMCID: PMC6249417 DOI: 10.3389/fpls.2018.01671] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/26/2018] [Indexed: 05/03/2023]
Abstract
A considerable body of research exists concerning the development of technologies to engineer sterility in forest trees. The primary driver for this work has been to mitigate concerns arising from gene flow from commercial plantings of genetically engineered (GE) trees to non-GE plantations, or to wild or feral relatives. More recently, there has been interest in the use of sterility technologies as a means to mitigate the global environmental and socio-economic damage caused by the escape of non-native invasive tree species from planted forests. The current sophisticated understanding of the molecular processes underpinning sexual reproduction in angiosperms has facilitated the successful demonstration of a number of control strategies in hardwood tree species, particularly in the model hardwood tree Poplar. Despite gymnosperm softwood trees, such as pines, making up the majority of the global planted forest estate, only pollen sterility, via cell ablation, has been demonstrated in softwoods. Progress has been limited by the lack of an endogenous model system, long timescales required for testing, and key differences between softwood reproductive pathways and those of well characterized angiosperm model systems. The availability of comprehensive genome and transcriptome resources has allowed unprecedented insights into the reproductive processes of both hardwood and softwood tree species. This increased fundamental knowledge together with the implementation of new breeding technologies, such as gene editing, which potentially face a less oppressive regulatory regime, is making the implementation of engineered sterility into commercial forestry a realistic possibility.
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Affiliation(s)
| | - Amy L. Klocko
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | | | - Amy M. Brunner
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, United States
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Pirone-Davies C, Prior N, von Aderkas P, Smith D, Hardie D, Friedman WE, Mathews S. Insights from the pollination drop proteome and the ovule transcriptome of Cephalotaxus at the time of pollination drop production. ANNALS OF BOTANY 2016; 117:973-84. [PMID: 27045089 PMCID: PMC4866313 DOI: 10.1093/aob/mcw026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 01/08/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Many gymnosperms produce an ovular secretion, the pollination drop, during reproduction. The drops serve as a landing site for pollen, but also contain a suite of ions and organic compounds, including proteins, that suggests diverse roles for the drop during pollination. Proteins in the drops of species of Chamaecyparis, Juniperus, Taxus, Pseudotsuga, Ephedra and Welwitschia are thought to function in the conversion of sugars, defence against pathogens, and pollen growth and development. To better understand gymnosperm pollination biology, the pollination drop proteomes of pollination drops from two species of Cephalotaxus have been characterized and an ovular transcriptome for C. sinensis has been assembled. METHODS Mass spectrometry was used to identify proteins in the pollination drops of Cephalotaxus sinensis and C. koreana RNA-sequencing (RNA-Seq) was employed to assemble a transcriptome and identify transcripts present in the ovules of C. sinensis at the time of pollination drop production. KEY RESULTS About 30 proteins were detected in the pollination drops of both species. Many of these have been detected in the drops of other gymnosperms and probably function in defence, polysaccharide metabolism and pollen tube growth. Other proteins appear to be unique to Cephalotaxus, and their putative functions include starch and callose degradation, among others. Together, the proteins appear either to have been secreted into the drop or to occur there due to breakdown of ovular cells during drop production. Ovular transcripts represent a wide range of gene ontology categories, and some may be involved in drop formation, ovule development and pollen-ovule interactions. CONCLUSIONS The proteome of Cephalotaxus pollination drops shares a number of components with those of other conifers and gnetophytes, including proteins for defence such as chitinases and for carbohydrate modification such as β-galactosidase. Proteins likely to be of intracellular origin, however, form a larger component of drops from Cephalotaxus than expected from studies of other conifers. This is consistent with the observation of nucellar breakdown during drop formation in Cephalotaxus The transcriptome data provide a framework for understanding multiple metabolic processes that occur within the ovule and the pollination drop just before fertilization. They reveal the deep conservation of WUSCHEL expression in ovules and raise questions about whether any of the S-locus transcripts in Cephalotaxus ovules might be involved in pollen-ovule recognition.
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Affiliation(s)
| | | | | | - Derek Smith
- UVic Genome BC Proteomics Centre, Victoria, BC, Canada
| | - Darryl Hardie
- UVic Genome BC Proteomics Centre, Victoria, BC, Canada
| | - William E Friedman
- The Arnold Arboretum of Harvard University, Boston, MA, USA, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Sarah Mathews
- CSIRO, Centre for Australian National Biodiversity Research, Canberra, Australia and
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Yu X, Duan X, Zhang R, Fu X, Ye L, Kong H, Xu G, Shan H. Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution. FRONTIERS IN PLANT SCIENCE 2016; 7:598. [PMID: 27200066 PMCID: PMC4852290 DOI: 10.3389/fpls.2016.00598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/18/2016] [Indexed: 05/19/2023]
Abstract
AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies.
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Affiliation(s)
- Xianxian Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Xiaoshan Duan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Xuehao Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Lingling Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Guixia Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- *Correspondence: Guixia Xu
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesBeijing, China
- Hongyan Shan
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9
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Uddenberg D, Akhter S, Ramachandran P, Sundström JF, Carlsbecker A. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology. FRONTIERS IN PLANT SCIENCE 2015; 6:970. [PMID: 26579190 PMCID: PMC4630563 DOI: 10.3389/fpls.2015.00970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/22/2015] [Indexed: 05/20/2023]
Abstract
Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.
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Affiliation(s)
- Daniel Uddenberg
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Shirin Akhter
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Prashanth Ramachandran
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Jens F. Sundström
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Annelie Carlsbecker
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
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Gramzow L, Weilandt L, Theißen G. MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants. ANNALS OF BOTANY 2014; 114:1407-29. [PMID: 24854168 PMCID: PMC4204780 DOI: 10.1093/aob/mcu066] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 03/10/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. METHODS The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. KEY RESULTS Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14-16 Type II MADS-box genes. CONCLUSIONS The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is the first that provides a comprehensive overview of MADS-box genes in conifers and thus will provide a framework for future work on MADS-box genes in seed plants.
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Affiliation(s)
- Lydia Gramzow
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Lisa Weilandt
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany
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11
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Carlsbecker A, Sundström JF, Englund M, Uddenberg D, Izquierdo L, Kvarnheden A, Vergara-Silva F, Engström P. Molecular control of normal and acrocona mutant seed cone development in Norway spruce (Picea abies) and the evolution of conifer ovule-bearing organs. THE NEW PHYTOLOGIST 2013; 200:261-275. [PMID: 0 DOI: 10.1111/nph.12360] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/03/2013] [Indexed: 05/03/2023]
Abstract
Reproductive organs in seed plants are morphologically divergent and their evolutionary history is often unclear. The mechanisms controlling their development have been extensively studied in angiosperms but are poorly understood in conifers and other gymnosperms. Here, we address the molecular control of seed cone development in Norway spruce, Picea abies. We present expression analyses of five novel MADS-box genes in comparison with previously identified MADS and LEAFY genes at distinct developmental stages. In addition, we have characterized the homeotic transformation from vegetative shoot to female cone and associated changes in regulatory gene expression patterns occurring in the acrocona mutant. The analyses identified genes active at the onset of ovuliferous and ovule development and identified expression patterns marking distinct domains of the ovuliferous scale. The reproductive transformation in acrocona involves the activation of all tested genes normally active in early cone development, except for an AGAMOUS-LIKE6/SEPALLATA (AGL6/SEP) homologue. This absence may be functionally associated with the nondeterminate development of the acrocona ovule-bearing scales. Our morphological and gene expression analyses give support to the hypothesis that the modern cone is a complex structure, and the ovuliferous scale the result of reductions and compactions of an ovule-bearing axillary short shoot in cones of Paleozoic conifers.
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Affiliation(s)
- Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
| | - Jens F Sundström
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and The Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Marie Englund
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
| | - Daniel Uddenberg
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and The Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Liz Izquierdo
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
| | - Anders Kvarnheden
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and The Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Francisco Vergara-Silva
- Laboratorio de Sistemática Molecular (Jardín Botánico), Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México DF, 04510, Mexico
| | - Peter Engström
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
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Uddenberg D, Reimegård J, Clapham D, Almqvist C, von Arnold S, Emanuelsson O, Sundström JF. Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor. PLANT PHYSIOLOGY 2013; 161:813-23. [PMID: 23221834 PMCID: PMC3561021 DOI: 10.1104/pp.112.207746] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 12/06/2012] [Indexed: 05/07/2023]
Abstract
Conifers normally go through a long juvenile period, for Norway spruce (Picea abies) around 20 to 25 years, before developing male and female cones. We have grown plants from inbred crosses of a naturally occurring spruce mutant (acrocona). One-fourth of the segregating acrocona plants initiate cones already in their second growth cycle, suggesting control by a single locus. The early cone-setting properties of the acrocona mutant were utilized to identify candidate genes involved in vegetative-to-reproductive phase change in Norway spruce. Poly(A(+)) RNA samples from apical and basal shoots of cone-setting and non-cone-setting plants were subjected to high-throughput sequencing (RNA-seq). We assembled and investigated 33,383 expressed putative protein-coding acrocona transcripts. Eight transcripts were differentially expressed between selected sample pairs. One of these (Acr42124_1) was significantly up-regulated in apical shoot samples from cone-setting acrocona plants, and the encoded protein belongs to the MADS box gene family of transcription factors. Using quantitative real-time polymerase chain reaction with independently derived plant material, we confirmed that the MADS box gene is up-regulated in both needles and buds of cone-inducing shoots when reproductive identity is determined. Our results constitute important steps for the development of a rapid cycling model system that can be used to study gene function in conifers. In addition, our data suggest the involvement of a MADS box transcription factor in the vegetative-to-reproductive phase change in Norway spruce.
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Affiliation(s)
| | | | - David Clapham
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE–750 07 Uppsala, Sweden (D.U., D.C., S.v.A., J.F.S.)
- KTH-Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, SE–171 65 Solna, Sweden (J.R., O.E.)
- Forestry Research Institute of Sweden, Uppsala Science Park, SE–751 83 Uppsala, Sweden (C.A.)
| | - Curt Almqvist
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE–750 07 Uppsala, Sweden (D.U., D.C., S.v.A., J.F.S.)
- KTH-Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, SE–171 65 Solna, Sweden (J.R., O.E.)
- Forestry Research Institute of Sweden, Uppsala Science Park, SE–751 83 Uppsala, Sweden (C.A.)
| | - Sara von Arnold
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE–750 07 Uppsala, Sweden (D.U., D.C., S.v.A., J.F.S.)
- KTH-Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, SE–171 65 Solna, Sweden (J.R., O.E.)
- Forestry Research Institute of Sweden, Uppsala Science Park, SE–751 83 Uppsala, Sweden (C.A.)
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Groth E, Tandre K, Engström P, Vergara-Silva F. AGAMOUS subfamily MADS-box genes and the evolution of seed cone morphology in Cupressaceae and Taxodiaceae. Evol Dev 2011; 13:159-70. [DOI: 10.1111/j.1525-142x.2011.00466.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Viaene T, Vekemans D, Becker A, Melzer S, Geuten K. Expression divergence of the AGL6 MADS domain transcription factor lineage after a core eudicot duplication suggests functional diversification. BMC PLANT BIOLOGY 2010; 10:148. [PMID: 20633275 PMCID: PMC3095293 DOI: 10.1186/1471-2229-10-148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 07/15/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND Because of their known role as transcriptional regulators of key plant developmental processes, the diversification of MADS-box gene function is thought to be a major driving force in the developmental evolution of plants. Yet the function of some MADS-box gene subfamilies has remained elusive thus far. One such lineage, AGL6, has now been functionally characterized in three angiosperm species, but a phylogenetic framework for comparison of AGL6 gene function is currently missing. RESULTS Based on phylogenetic analyses of newly isolated and EST-based sequences, we describe the duplication history of the AGL6 subfamily in angiosperms. Our analyses provide support for four ancient duplications in the evolution of the AGL6 lineage: one at the base of core eudicots resulting in euAGL6 and AGL6-like gene clades, one during basal angiosperm diversification and two in monocot evolution. To investigate whether the spatial domains in which AGL6 genes function have diverged after duplication, we use quantitative Real Time PCR. We show that the core eudicot AGL6-like clade acquired expression in vegetative tissues, while its paralog euAGL6 remains predominantly confined to reproductive tissues. CONCLUSIONS These and previous data lead us to propose that the AGL6 lineage in core eudicots, in addition to functions related to the expression in reproductive structures, may have acquired a function in developmental transitions of vegetative shoots.
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Affiliation(s)
- Tom Viaene
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, Kasteelpark Arenberg 31, PO Box 2437, B-3001 Leuven, Belgium
| | - Dries Vekemans
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, Kasteelpark Arenberg 31, PO Box 2437, B-3001 Leuven, Belgium
| | - Annette Becker
- Evolutionary Developmental Genetics Group, University of Bremen, Leobener Str., UFT, 28359 Bremen, Germany
| | - Siegbert Melzer
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, Kasteelpark Arenberg 31, PO Box 2437, B-3001 Leuven, Belgium
| | - Koen Geuten
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, Kasteelpark Arenberg 31, PO Box 2437, B-3001 Leuven, Belgium
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Futamura N, Totoki Y, Toyoda A, Igasaki T, Nanjo T, Seki M, Sakaki Y, Mari A, Shinozaki K, Shinohara K. Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili. BMC Genomics 2008; 9:383. [PMID: 18691438 PMCID: PMC2568000 DOI: 10.1186/1471-2164-9-383] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 08/11/2008] [Indexed: 12/05/2022] Open
Abstract
Background Cryptomeria japonica D. Don is one of the most commercially important conifers in Japan. However, the allergic disease caused by its pollen is a severe public health problem in Japan. Since large-scale analysis of expressed sequence tags (ESTs) in the male strobili of C. japonica should help us to clarify the overall expression of genes during the process of pollen development, we constructed a full-length enriched cDNA library that was derived from male strobili at various developmental stages. Results We obtained 36,011 expressed sequence tags (ESTs) from either one or both ends of 19,437 clones derived from the cDNA library of C. japonica male strobili at various developmental stages. The 19,437 cDNA clones corresponded to 10,463 transcripts. Approximately 80% of the transcripts resembled ESTs from Pinus and Picea, while approximately 75% had homologs in Arabidopsis. An analysis of homologies between ESTs from C. japonica male strobili and known pollen allergens in the Allergome Database revealed that products of 180 transcripts exhibited significant homology. Approximately 2% of the transcripts appeared to encode transcription factors. We identified twelve genes for MADS-box proteins among these transcription factors. The twelve MADS-box genes were classified as DEF/GLO/GGM13-, AG-, AGL6-, TM3- and TM8-like MIKCC genes and type I MADS-box genes. Conclusion Our full-length enriched cDNA library derived from C. japonica male strobili provides information on expression of genes during the development of male reproductive organs. We provided potential allergens in C. japonica. We also provided new information about transcription factors including MADS-box genes expressed in male strobili of C. japonica. Large-scale gene discovery using full-length cDNAs is a valuable tool for studies of gymnosperm species.
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Affiliation(s)
- Norihiro Futamura
- Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan.
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16
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Vázquez-Lobo A, Carlsbecker A, Vergara-Silva F, Alvarez-Buylla ER, Piñero D, Engström P. Characterization of the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in female and male cones of the conifer genera Picea, Podocarpus, and Taxus: implications for current evo-devo hypotheses for gymnosperms. Evol Dev 2007; 9:446-59. [PMID: 17845516 DOI: 10.1111/j.1525-142x.2007.00182.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identity of genes causally implicated in the development and evolutionary origin of reproductive characters in gymnosperms is largely unknown. Working within the framework of plant evolutionary developmental biology, here we have cloned, sequenced, performed phylogenetic analyses upon and tested the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in reproductive structures from selected species of the conifer genera Picea, Podocarpus, and Taxus. Contrary to expectations based on previous assessments, expression of LFY/FLO and NLY in cones of these taxa was found to occur simultaneously in a single reproductive axis, initially overlapping but later in mutually exclusive primordia and/or groups of developing cells in both female and male structures. These observations directly affect the status of the "mostly male theory" for the origin of the angiosperm flower. On the other hand, comparative spatiotemporal patterns of the expression of these genes suggest a complex genetic regulatory network of cone development, as well as a scheme of functional divergence for LFY/FLO with respect to NLY homologs in gymnosperms, both with clear heterochronic aspects. Results presented in this study contribute to the understanding of the molecular-genetic basis of morphological evolution in conifer cones, and may aid in establishing a foundation for gymnosperm-specific, testable evo-devo hypotheses.
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Affiliation(s)
- Alejandra Vázquez-Lobo
- Departamento de Ecología Evolutiva, Instituto de Ecología, UNAM AP 70-275 México DF 04510, Mexico
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Brunner AM, Li J, DiFazio SP, Shevchenko O, Montgomery BE, Mohamed R, Wei H, Ma C, Elias AA, VanWormer K, Strauss SH. Genetic containment of forest plantations. TREE GENETICS & GENOMES 2007; 3:75-100. [PMID: 0 DOI: 10.1007/s11295-006-0067-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
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18
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Nilsson L, Carlsbecker A, Sundås-Larsson A, Vahala T. APETALA2 like genes from Picea abies show functional similarities to their Arabidopsis homologues. PLANTA 2007; 225:589-602. [PMID: 16953432 DOI: 10.1007/s00425-006-0374-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2006] [Accepted: 08/03/2006] [Indexed: 05/07/2023]
Abstract
In angiosperm flower development the identity of the floral organs is determined by the A, B and C factors. Here we present the characterisation of three homologues of the A class gene APETALA2 (AP2) from the conifer Picea abies (Norway spruce), Picea abies APETALA2 LIKE1 (PaAP2L1), PaAP2L2 and PaAP2L3. Similar to AP2 these genes contain sequence motifs complementary to miRNA172 that has been shown to regulate AP2 in Arabidopsis. The genes display distinct expression patterns during plant development; in the female-cone bud PaAP2L1 and PaAP2L3 are expressed in the seed-bearing ovuliferous scale in a pattern complementary to each other, and overlapping with the expression of the C class-related gene DAL2. To study the function of PaAP2L1 and PaAP2L2 the genes were expressed in Arabidopsis. The transgenic PaAP2L2 plants were stunted and flowered later than control plants. Flowers were indeterminate and produced an excess of floral organs most severely in the two inner whorls, associated with an ectopic expression of the meristem-regulating gene WUSCHEL. No homeotic changes in floral-organ identities occurred, but in the ap2-1 mutant background PaAP2L2 was able to promote petal identity, indicating that the spruce AP2 gene has the capacity to substitute for an A class gene in Arabidopsis. In spite of the long evolutionary distance between angiosperms and gymnosperms and the fact that gymnosperms lack structures homologous to sepals and petals our data supports a functional conservation of AP2 genes among the seed plants.
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Affiliation(s)
- Lars Nilsson
- Department of Physiological Botany, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
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Kaufmann K, Anfang N, Saedler H, Theissen G. Mutant analysis, protein-protein interactions and subcellular localization of the Arabidopsis B sister (ABS) protein. Mol Genet Genomics 2005; 274:103-18. [PMID: 16080001 DOI: 10.1007/s00438-005-0010-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Accepted: 05/10/2005] [Indexed: 11/29/2022]
Abstract
Recently, close relatives of class B floral homeotic genes, termed B(sister) genes, have been identified in both angiosperms and gymnosperms. In contrast to the B genes themselves, B(sister) genes are exclusively expressed in female reproductive organs, especially in the envelopes or integuments surrounding the ovules. This suggests an important ancient function in ovule or seed development for B(sister) genes, which has been conserved for about 300 million years. However, investigation of the first loss-of-function mutant for a B(sister) gene (ABS/TT16 from Arabidopsis) revealed only a weak phenotype affecting endothelium formation. Here, we present an analysis of two additional mutant alleles, which corroborates this weak phenotype. Transgenic plants that ectopically express ABS show changes in the growth and identity of floral organs, suggesting that ABS can interact with floral homeotic proteins. Yeast-two-hybrid and three-hybrid analyses indicated that ABS can form dimers with SEPALLATA (SEP) floral homeotic proteins and multimeric complexes that also include the AGAMOUS-like proteins SEEDSTICK (STK) or SHATTERPROOF1/2 (SHP1, SHP2). These data suggest that the formation of multimeric transcription factor complexes might be a general phenomenon among MIKC-type MADS-domain proteins in angiosperms. Heterodimerization of ABS with SEP3 was confirmed by gel retardation assays. Fusion proteins tagged with CFP (Cyan Fluorescent Protein) and YFP (Yellow Fluorescent Protein) in Arabidopsis protoplasts showed that ABS is localized in the nucleus. Phylogenetic analysis revealed the presence of a structurally deviant, but closely related, paralogue of ABS in the Arabidopsis genome. Thus the evolutionary developmental genetics of B(sister) genes can probably only be understood as part of a complex and redundant gene network that may govern ovule formation in a conserved manner, which has yet to be fully explored.
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Affiliation(s)
- Kerstin Kaufmann
- Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, 07743 Jena, Germany
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20
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Kaufmann K, Melzer R, Theissen G. MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene 2005; 347:183-98. [PMID: 15777618 DOI: 10.1016/j.gene.2004.12.014] [Citation(s) in RCA: 325] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2004] [Revised: 12/11/2004] [Accepted: 12/16/2004] [Indexed: 11/19/2022]
Abstract
MIKC-type proteins represent a class of MADS-domain transcription factors and are defined by a unique domain structure: in addition to the highly conserved DNA-binding MADS-domain, they have three other domains ('I', 'K' and 'C'), with the keratin-like K-domain being the most highly conserved and characteristic one. The number and functional diversity of MIKC-type proteins increased considerably during land plant evolution, culminating in higher flowering plants, where they dominate the control of reproductive development from early to late stages. We wonder how one special class of proteins became important in the control of essentially all stages of a morphogenetic process. All MADS-domain proteins appear to bind to DNA as homo- or heterodimers and may function as part of ternary transcription factor complexes involving non-MADS-domain proteins. Only MIKC-type proteins, however, generate complex intrafamily interaction networks. These are based on the special potential of MIKC-type proteins to form complexes involving more than two homologous proteins constituting transcriptional regulators. We speculate that the potential to form heteromultimers of homologous proteins was achieved by the acquisition of the K-domain during evolution. There is emerging evidence that organismal complexity arises from progressively more elaborate regulation of gene expression. We hypothesize that combinatorial multimer formation of MIKC-type MADS-domain proteins facilitated an unusually efficient and rapid functional diversification based on gene duplication, sequence divergence and fixation. This 'networking' may have enabled a more sophisticated transcriptional control of target genes which was recruited for controlling increasingly complex and diverse developmental pathways during the rapid origin and diversification of plant reproductive structures. Therefore, MIKC-type proteins may owe their evolutionary 'success' and present-day developmental importance in part to their modular domain structure. Investigating the evolution of MIKC-type genes may thus help to better understand origin and diversification of gene regulatory networks.
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Affiliation(s)
- Kerstin Kaufmann
- Friedrich-Schiller-Universität Jena, Lehrstuhl für Genetik, Philosophenweg 12, D-07743 Jena, Germany
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Carlsbecker A, Tandre K, Johanson U, Englund M, Engström P. The MADS-box gene DAL1 is a potential mediator of the juvenile-to-adult transition in Norway spruce (Picea abies). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 40:546-57. [PMID: 15500470 DOI: 10.1111/j.1365-313x.2004.02226.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Progression through the plant life cycle involves change in many essential features, most notably in the capacity to reproduce. The transition from a juvenile vegetative and non-reproductive to an adult reproductive phase is gradual and can take many years; in the conifer Norway spruce, Picea abies, typically 20-25 years. We present a detailed analysis of the activities of three regulatory genes with potential roles in this transition in Norway spruce: DAL1, a MADS-box gene related to the AGL6 group of genes from angiosperms, and the two LEAFY-related genes PaLFY and PaNLY. DAL1 activity is initiated in the shoots of juvenile trees at an age of 3-5 years, and then increases with age, whereas both LFY genes are active throughout the juvenile phase. The activity of DAL1 further shows a spatial pattern along the stem of the tree that parallels a similar gradient in physiological and morphological features associated with maturation to the adult phase. Constitutive expression of DAL1 in transgenic Arabidopsis plants caused a dramatic attenuation of both juvenile and adult growth phases; flowers forming immediately after the embryonic phase of development in severely affected plants. Taken together, our results support the notion that DAL1 may have a regulatory role in the juvenile-to-adult transition in Norway spruce.
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Affiliation(s)
- Annelie Carlsbecker
- Department of Physiological Botany, Evolutionary Biology Center, Uppsala University, Villavägen 6, SE-752 36 Uppsala, Sweden
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