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Sharma B, Pandher MK, Alcaraz Echeveste AQ, Romo RK, Bravo M. Delphinium as a model for development and evolution of complex zygomorphic flowers. FRONTIERS IN PLANT SCIENCE 2024; 15:1453951. [PMID: 39224845 PMCID: PMC11366623 DOI: 10.3389/fpls.2024.1453951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The complex zygomorphic flowers of the early-diverging eudicot Delphinium provide an opportunity to explore intriguing evolutionary, developmental, and genetic questions. The dorsal perianth organs, consisting of a spurred sepal and the nectar-bearing spurred petal(s) in Delphinium, contribute to the dorso-ventralization and zygomorphic flower morphology. The seamless integration of the two or three dorsal petaloid spurred organs is considered a synorganization, and the resulting organ complex is referred to as a hyperorgan. The hyperorgan shows variability within the tribe due to variation in the number, size, and shape of the spurs. Research in recent decades within this tribe has enhanced our understanding of morphological evolution of flowers. More recently, functional studies using the RNAi approach of Virus-Induced Gene Silencing (VIGS) have unraveled interesting results highlighting the role of gene duplication in the functional diversification of organ identity and symmetry genes. Research in this early-diverging eudicot genus bridges the gaps in understanding the morphological innovations that are mostly studied in model grass and core eudicot clades. This first comprehensive review synthesizes eco-evo-devo research on Delphinium, developing a holistic understanding of recent advancements and establishing the genus as an exceptional model for addressing fundamental questions in developmental genetics, particularly in the evolution of complex flowers. This progress highlights Delphinium's significant potential for future studies in this field.
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Affiliation(s)
- Bharti Sharma
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, United States
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Lv X, Wang Y, Wang X, Zhang M, Zhang Y, Zhao L, Zhang X. Development and anatomy of petals with specialized nectar holder and pollen container in Fumarioideae (Papaveraceae). PLANTA 2024; 260:21. [PMID: 38847829 DOI: 10.1007/s00425-024-04453-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/28/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION Petal developmental characteristics in Fumarioideae were similar at early stages, and the specialized nectar holder/pollen container formed by the outer/inner petals. The micro-morphology of these two structures, however, shows diversity in seven species. Elaborate petals have been modified to form different types, including petal lobes, ridges, protuberances, and spurs, each with specialized functions. Nectar holder and pollen container presumably have a function in plant-pollinator interactions. In Fumarioideae, four elaborate petals of the disymmetric/zygomorphic flower present architecture forming the "nectar holder" and "pollen container" structure at the bottom and top separately. In the present study, the petals of seven species in Fumarioideae were investigated by scanning electron microscopy, light microscope, and transmission electron microscopes. The results show that petal development could divided into six stages: initiation, enlargement, adaxial/abaxial differentiation, elaborate specializations (sacs, spurs, and lobes formed), extension, and maturation, while the specialized "nectar holder" and "pollen container" structures mainly formed in stage 4. "Nectar holder" is developed from the shallow sac/spur differentiated at the base of the outer petal, eventually forming a multi-organized complex structure, together with staminal nectaries (1-2) with individual sizes. A semi-closed ellipsoidal "pollen container" is developed from the apical part of the 3-lobed inner petals fused by middle lobes and attain different sizes. The adaxial epidermis cells are specialized, with more distinct punctate/dense columnar protrusions or wavy cuticles presented on obviously thickening cell walls. In addition, a large and well-developed cavity appears between the inner and outer epidermis of the petals. As an exception, Hypecoum erectum middle lobes present stamen mimicry. Elaborate petal structure is crucial for comprehending the petal diversity in Fumarioideae and provides more evidence for further exploration of the reproductive study in Papaveraceae.
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Affiliation(s)
- Xuqian Lv
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Yaxi Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Xiaojia Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Mingyue Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China
| | - Yuqu Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, 712046, Xianyang, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Xiaohui Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China.
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, Shaanxi Normal University, Xi'an, 710119, Shaanxi, China.
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Xu L, Wang J, Zhang T, Xiao H, Wang H. Characterizing complete mitochondrial genome of Aquilegia amurensis and its evolutionary implications. BMC PLANT BIOLOGY 2024; 24:142. [PMID: 38413922 PMCID: PMC10900605 DOI: 10.1186/s12870-024-04844-9] [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: 11/10/2023] [Accepted: 02/21/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Aquilegia is a model system for studying the evolution of adaptive radiation. However, very few studies have been conducted on the Aquilegia mitochondrial genome. Since mitochondria play a key role in plant adaptation to abiotic stress, analyzing the mitochondrial genome may provide a new perspective for understanding adaptive evolution. RESULTS The Aquilegia amurensis mitochondrial genome was characterized by a circular chromosome and two linear chromosomes, with a total length of 538,736 bp; the genes included 33 protein-coding genes, 24 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. We subsequently conducted a phylogenetic analysis based on single nucleotide polymorphisms (SNPs) in the mitochondrial genomes of 18 Aquilegia species, which were roughly divided into two clades: the European-Asian clade and the North American clade. Moreover, the genes mttB and rpl5 were shown to be positively selected in European-Asian species, and they may help European and Asian species adapt to environmental changes. CONCLUSIONS In this study, we assembled and annotated the first mitochondrial genome of the adaptive evolution model plant Aquilegia. The subsequent analysis provided us with a basis for further molecular studies on Aquilegia mitochondrial genomes and valuable information on adaptive evolution in Aquilegia.
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Affiliation(s)
- Luyuan Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jinghan Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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Bao T, Kimani S, Li Y, Li H, Yang S, Zhang J, Wang Q, Wang Z, Ning G, Wang L, Gao X. Allelic variation of terpene synthases drives terpene diversity in the wild species of the Freesia genus. PLANT PHYSIOLOGY 2023; 192:2419-2435. [PMID: 36932696 PMCID: PMC10315281 DOI: 10.1093/plphys/kiad172] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Terpene synthases (TPSs) play pivotal roles in conferring the structural diversity of terpenoids, which are mainly emitted from flowers, whereas the genetic basis of the release of floral volatile terpenes remains largely elusive. Though quite similar in sequence, TPS allelic variants still function divergently, and how they drive floral terpene diversity in closely related species remains unknown. Here, TPSs responsible for the floral scent of wild Freesia species were characterized, and the functions of their natural allelic variants, as well as the causal amino acid residues, were investigated in depth. Besides the 8 TPSs previously reported in modern cultivars, 7 additional TPSs were functionally evaluated to contribute to the major volatiles emitted from wild Freesia species. Functional characterization of allelic natural variants demonstrated that allelic TPS2 and TPS10 variants changed the enzymatic capacity while allelic TPS6 variants drove the diversity of floral terpene products. Further residue substitution analysis revealed the minor residues determining the enzyme catalytic activity and product specificity. The clarification of TPSs in wild Freesia species reveals that allelic TPS variants evolved differently to determine the interspecific floral volatile terpenes in the genus and might be used for modern cultivar improvement.
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Affiliation(s)
- Tingting Bao
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Shadrack Kimani
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
- School of Pure and Applied Sciences, Karatina University, Karatina 10101, Kenya
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Hongjie Li
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Song Yang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Jia Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Qiuyue Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Zhaoxuan Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun 130024, China
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Cheng J, Yao X, Li X, Yue L, Duan X, Li B, Fu X, Li S, Shan H, Yin X, Whitewoods C, Coen E, Kong H. Diversification of ranunculaceous petals in shape supports a generalized model for plant lateral organ morphogenesis and evolution. SCIENCE ADVANCES 2023; 9:eadf8049. [PMID: 37083529 PMCID: PMC10121167 DOI: 10.1126/sciadv.adf8049] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Peltate organs, such as the prey-capturing traps of carnivorous plants and nectary-bearing petals of ranunculaceous species, are widespread in nature and have intrigued and perplexed scientists for centuries. Shifts in the expression domains of adaxial/abaxial genes have been shown to control leaf peltation in some carnivorous plants, yet the mechanisms underlying the generation of other peltate organs remain unclear. Here, we show that formation of various peltate ranunculaceous petals was also caused by shifts in the expression domains of adaxial/abaxial genes, followed by differentiated regional growth sculpting the margins and/or other parts of the organs. By inducing parameters to specify the time, position, and degree of the shifts and growth, we further propose a generalized modeling system, through which various unifacial, bifacial, and peltate organs can be simulated. These results demonstrate the existence of a hierarchical morphospace system and pave the way to understand the mechanisms underlying plant organ diversification.
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Affiliation(s)
- Jie Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xu Yao
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xukun Li
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, 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
| | - Liang Yue
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoshan Duan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Boka Li
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, 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
| | - Xuehao Fu
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Shuixian Li
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, 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
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xiaofeng Yin
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | | | - Enrico Coen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, 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
- Corresponding author.
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Characterization and expression analysis of bHLH transcription factors reveal their putative regulatory effects on nectar spur development in Aquilegia species. Gene 2023; 852:147057. [PMID: 36410606 DOI: 10.1016/j.gene.2022.147057] [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: 07/20/2022] [Revised: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
Nectar spur is a hollow extension of certain flower parts and shows strikingly diverse size and shape in Aquilegia. Nectar spur development is involved in cell division and expansion processes. The basic helix-loop-helix (bHLH) transcription factors (TFs) control a diversity of organ morphogenesis, including cell division and cell expansion processes. However, the role of bHLH genes in nectar spur development in Aquilegia is mainly unknown. We conducted a genome-wide identification of the bHLH gene family in Aquilegia to determine structural characteristics and phylogenetic relationships, and to analyze expression profiles of these genes during the development of nectar spur in spurless and spurred species. A total of 120 AqbHLH genes were identified from the Aquilegia coerulea genome. The phylogenetic tree showed that AqbHLH proteins were divided into 15 subfamilies, among which S7 and S8 subfamilies occurred marked expansion. The AqbHLH genes in the same clade had similar motif composition and gene structure characteristics. Conserved residue analysis indicated nineteen residues with conservation of more than 50% were found in the four conserved regions. In the upstream sequence of AqbHLH genes, the light-responsive element was the most abundant cis-acting element. Eighteen AqbHLH genes showed syntenic relationships, and eight genes from four syntenic pairs underwent tandem duplications. According to the expression profiling analysis by public RNA-Seq data and qRT-PCR results, five AqbHLH genes, including AqbHLH027, AqbHLH046, AqbHLH082, AqbHLH083 and AqbHLH092, were differentially expressed between different tissues in A. coerulea at early developmental stages, as well as between spurless and spurred Aquilegia species. Of them, AqbHLH046 was not only highly expressed in spur compared with blade, but also showed higher expression levels in spurred species than spurless specie, suggesting it plays an essential role in the development of spur by regulating cell division. This study lays a foundation to investigate the function of AqbHLH genes family in nectar spur development, and has potential implications for speciation and genetic breeding in the genus Aquilegia.
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Rushworth CA, Wagner MR, Mitchell-Olds T, Anderson JT. The Boechera model system for evolutionary ecology. AMERICAN JOURNAL OF BOTANY 2022; 109:1939-1961. [PMID: 36371714 DOI: 10.1002/ajb2.16090] [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: 01/17/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.
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Affiliation(s)
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
| | | | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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He J, Lyu R, Luo Y, Xiao J, Xie L, Wen J, Li W, Pei L, Cheng J. A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae. Mol Phylogenet Evol 2022; 174:107545. [PMID: 35690374 DOI: 10.1016/j.ympev.2022.107545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022]
Abstract
The utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using these data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms.
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Affiliation(s)
- Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | - Wenhe Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Linying Pei
- Beijing Engineering Technology Research Center for Garden Plants, Beijing Forestry University Forest Science Co. Ltd., Beijing 100083, PR China
| | - Jin Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
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Fu X, Shan H, Yao X, Cheng J, Jiang Y, Yin X, Kong H. Petal development and elaboration. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3308-3318. [PMID: 35275176 DOI: 10.1093/jxb/erac092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/07/2022] [Indexed: 05/12/2023]
Abstract
Petals can be simple or elaborate, depending on whether they have complex basic structures and/or highly specialized epidermal modifications. It has been proposed that the independent origin and diversification of elaborate petals have promoted plant-animal interactions and, therefore, the evolutionary radiation of corresponding plant groups. Recent advances in floral development and evolution have greatly improved our understanding of the processes, patterns, and mechanisms underlying petal elaboration. In this review, we compare the developmental processes of simple and elaborate petals, concluding that elaborate petals can be achieved through four main paths of modifications (i.e. marginal elaboration, ventral elaboration, dorsal elaboration, and surface elaboration). Although different types of elaborate petals were formed through different types of modifications, they are all results of changes in the expression patterns of genes involved in organ polarity establishment and/or the proliferation, expansion, and differentiation of cells. The deployment of existing genetic materials to perform a new function was also shown to be a key to making elaborate petals during evolution.
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Affiliation(s)
- Xuehao Fu
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xu Yao
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jie Cheng
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongchao Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaofeng Yin
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Genetic and Epigenetic Signatures Associated with the Divergence of Aquilegia Species. Genes (Basel) 2022; 13:genes13050793. [PMID: 35627179 PMCID: PMC9141525 DOI: 10.3390/genes13050793] [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: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Widely grown in the Northern Hemisphere, the genus Aquilegia (columbine) is a model system in adaptive radiation research. While morphological variations between species have been associated with environmental factors, such as pollinators, how genetic and epigenetic factors are involved in the rapid divergence in this genus remains under investigated. In this study, we surveyed the genomes and DNA methylomes of ten Aquilegia species, representative of the Asian, European and North American lineages. Our analyses of the phylogeny and population structure revealed high genetic and DNA methylomic divergence across these three lineages. By multi-level genome-wide scanning, we identified candidate genes exhibiting lineage-specific genetic or epigenetic variation patterns that were signatures of inter-specific divergence. We demonstrated that these species-specific genetic variations and epigenetic variabilities are partially independent and are both functionally related to various biological processes vital to adaptation, including stress tolerance, cell reproduction and DNA repair. Our study provides an exploratory overview of how genetic and epigenetic signatures are associated with the diversification of the Aquilegia species.
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Huang L, Geng FD, Fan JJ, Zhai W, Xue C, Zhang XH, Ren Y, Kang JQ. Evidence for two types of Aquilegia ecalcarata and its implications for adaptation to new environments. PLANT DIVERSITY 2022; 44:153-162. [PMID: 35505982 PMCID: PMC9043306 DOI: 10.1016/j.pld.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 06/14/2023]
Abstract
Spurs have played an important role in the radiation of the genus Aquilegia, but little is known about how the spurless state arose in A. ecalcarata. Here we aim to characterize the genetic divergence within A. ecalcarata and gain insights into the origin of this species. A total of 19 populations from A. ecalcarata and 23 populations from three of its closest relatives (Aquilegia kansuensis, Aquilegia rockii and Aquilegia yabeana) were sampled in this study. We sequenced fifteen nuclear gene fragments across the genome and three chloroplast loci to conduct phylogenetic, PCoA and STRUCTURE analyses. Our analyses indicate that A. ecalcarata may not be monophyletic and can be divided into two distinct lineages (A. ecalcarata I and A. ecalcarata II). A. ecalcarata I is genetically close to A. kansuensis, whereas A. ecalcarata II is close to A. rockii. Isolation-with-migration analysis suggested that historical gene flow was low between A. ecalcarata I and A. rockii, as well as between A. ecalcarata II and A. kansuensis. The two distinct lineages of A. ecalcarata show significant divergence in 13 floral traits and also have distinct distributions. In addition, both A. ecalcarata I and II are adapted to a stony environment that differs from that of their closest relatives, indicating a habitat shift may have driven new adaptations. Our findings enrich the understanding of how floral evolution contributes to species diversification.
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Affiliation(s)
| | | | | | | | | | | | - Yi Ren
- Corresponding author. Fax: +86 29 85310270.
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12
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Yang S, Wang N, Kimani S, Li Y, Bao T, Ning G, Li L, Liu B, Wang L, Gao X. Characterization of Terpene synthase variation in flowers of wild aquilegia species from Northeastern Asia. HORTICULTURE RESEARCH 2022; 9:uhab020. [PMID: 35039842 PMCID: PMC8771452 DOI: 10.1093/hr/uhab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 08/25/2021] [Accepted: 10/02/2021] [Indexed: 05/13/2023]
Abstract
There are several causes for the great diversity in floral terpenes. The terpene products are determined by the catalytic fidelity, efficiency and plasticity of the active sites of terpene synthases (TPSs). However, the molecular mechanism of TPS in catalyzing terpene biosynthesis and its evolutionary fate in wild plant species remain largely unknown. In this study, the functionality of terpene synthases and their natural variants were assessed in two Northeastern Asia endemic columbine species and their natural hybrid. Synoptically, TPS7, TPS8, and TPS9 were highly expressed in these Aquilegia species from the Zuojia population. The in vitro and in vivo enzymatic assays revealed that TPS7 and TPS8 mainly produced (+)-limonene and β-sesquiphellandrene, respectively, whereas TPS9 produced pinene, similar to the major components released from Aquilegia flowers. Multiple sequence alignment of Aquilegia TPS7 and TPS8 in the Zuojia population revealed amino acid polymorphisms. Domain swapping and amino acid substitution assays demonstrated that 413A, 503I and 529D had impacts on TPS7 catalytic activity, whereas 420G, 538F and 545 L affected the ratio of β-sesquiphellandrene to β-bisabolene in TPS8. Moreover, these key polymorphic amino acid residues were found in Aquilegia species from the Changbai Mountain population. Interestingly, amino acid polymorphisms in TPSs were present in individuals with low expression levels, and nonsynonymous mutations could impact the catalytic activity or product specificity of these genes. The results of this study will shed new light on the function and evolution of TPS genes in wild plant species and are beneficial to the modification of plant fragrances.
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Affiliation(s)
- Song Yang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Ning Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Shadrack Kimani
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
- School of Pure and Applied Sciences, Karatina University, Karatina, Kenya
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Tingting Bao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Guogui Ning
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
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13
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Klepikova AV, Shnayder ED, Kasianov AS, Remizowa MV, Sokoloff DD, Penin AA. lepidium-like, a Naturally Occurring Mutant of Capsella bursa-pastoris, and Its Implications on the Evolution of Petal Loss in Cruciferae. FRONTIERS IN PLANT SCIENCE 2021; 12:714711. [PMID: 34899769 PMCID: PMC8656458 DOI: 10.3389/fpls.2021.714711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/20/2021] [Indexed: 05/06/2023]
Abstract
Naturally occurring mutants whose phenotype recapitulates the changes that distinguish closely related species are of special interest from the evolutionary point of view. They can give a key about the genetic control of the changes that led to speciation. In this study, we described lepidium-like (lel), a naturally occurring variety of an allotetraploid species Capsella bursa-pastoris that is characterized by the typical loss of all four petals. In some cases, one or two basal flowers in the raceme had one or two small petals. The number and structure of other floral organs are not affected. Our study of flower development in the mutant showed that once initiated, petals either cease further development and cannot be traced in anthetic flowers or sometimes develop to various degrees. lel plants showed an earlier beginning of floral organ initiation and delayed petal initiation compared to the wild-type plants. lel phenotype has a wide geographical distribution, being found at the northern extremity of the species range as well as in the central part. The genetic analysis of inheritance demonstrated that lel phenotype is controlled by two independent loci. While the flower in the family Cruciferae generally has a very stable structure (i.e., four sepals, four petals, six stamens, and two carpels), several deviations from this ground plan are known, in particular in the genus Lepidium, C. bursa-pastoris is an emerging model for the study of polyploidy (which is also very widespread in Cruciferae); the identification and characterization of the apetalous mutant lays a foundation for further research of morphological evolution in polyploids.
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Affiliation(s)
- Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Elina D. Shnayder
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | | | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Aleksey A. Penin,
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14
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Zhang R, Min Y, Holappa LD, Walcher-Chevillet CL, Duan X, Donaldson E, Kong H, Kramer EM. A role for the Auxin Response Factors ARF6 and ARF8 homologs in petal spur elongation and nectary maturation in Aquilegia. THE NEW PHYTOLOGIST 2020; 227:1392-1405. [PMID: 32356309 DOI: 10.1111/nph.16633] [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: 01/22/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
The petal spur of the basal eudicot Aquilegia is a key innovation associated with the adaptive radiation of the genus. Previous studies have shown that diversification of Aquilegia spur length can be predominantly attributed to variation in cell elongation. However, the genetic pathways that control the development of petal spurs are still being investigated. Here, we focus on a pair of closely related homologs of the AUXIN RESPONSE FACTOR family, AqARF6 and AqARF8, to explore their roles in Aquileiga coerulea petal spur development. Expression analyses of the two genes show that they are broadly expressed in vegetative and floral organs, but have relatively higher expression in petal spurs, particularly at later stages. Knockdown of the two AqARF6 and AqARF8 transcripts using virus-induced gene silencing resulted in largely petal-specific defects, including a significant reduction in spur length due to a decrease in cell elongation. These spurs also exhibited an absence of nectar production, which was correlated with downregulation of STYLISH homologs that have previously been shown to control nectary development. This study provides the first evidence of ARF6/8 homolog-mediated petal development outside the core eudicots. The genes appear to be specifically required for cell elongation and nectary maturation in the Aquilegia petal spur.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ya Min
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA
| | - Lynn D Holappa
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA
| | - Cristina L Walcher-Chevillet
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA
- 10x Genomics, 6230 Stoneridge Mall Road, Pleasanton, CA, 94588-3260, USA
| | - Xiaoshan Duan
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Harvard University Herbaria, Harvard University, 22 Divinity Ave, Cambridge, MA, 02138, USA
| | - Emily Donaldson
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138, USA
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15
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Xie J, Zhao H, Li K, Zhang R, Jiang Y, Wang M, Guo X, Yu B, Kong H, Jiao Y, Xu G. A chromosome-scale reference genome of Aquilegia oxysepala var. kansuensis. HORTICULTURE RESEARCH 2020; 7:113. [PMID: 32637141 PMCID: PMC7326910 DOI: 10.1038/s41438-020-0328-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 05/21/2023]
Abstract
The genus Aquilegia (Ranunculaceae) has been cultivated as ornamental and medicinal plants for centuries. With petal spurs of strikingly diverse size and shape, Aquilegia has also been recognized as an excellent system for evolutionary studies. Pollinator-mediated selection for longer spurs is believed to have shaped the evolution of this genus, especially the North American taxa. Recently, however, an opposite evolutionary trend was reported in an Asian lineage, where multiple origins of mini- or even nonspurred morphs have occurred. Interesting as it is, the lack of genomic resources has limited our ability to decipher the molecular and evolutionary mechanisms underlying spur reduction in this special lineage. Using long-read sequencing (PacBio Sequel), in combination with optical maps (BioNano DLS) and Hi-C, we assembled a high-quality reference genome of A. oxysepala var. kansuensis, a sister species to the nonspurred taxon. The final assembly is approximately 293.2 Mb, 94.6% (277.4 Mb) of which has been anchored to 7 pseudochromosomes. A total of 25,571 protein-coding genes were predicted, with 97.2% being functionally annotated. When comparing this genome with that of A. coerulea, we detected a large rearrangement between Chr1 and Chr4, which might have caused the Chr4 of A. oxysepala var. kansuensis to partly deviate from the "decaying" path that was taken before the split of Aquilegia and Semiaquilegia. This high-quality reference genome is fundamental to further investigations on the development and evolution of petal spurs and provides a strong foundation for the breeding of new horticultural Aquilegia cultivars.
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Affiliation(s)
- Jinghe Xie
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Haifeng Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kunpeng Li
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Yongchao Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Meimei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xuelian Guo
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Ben Yu
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guixia Xu
- State Key Laboratory of Systematic and Evolutionary Botany, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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16
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Huang H. The complete chloroplast genome of Aquilegia barnebyi, a basal eudicot species. Mitochondrial DNA B Resour 2020; 5:1060-1061. [PMID: 33366874 PMCID: PMC7748838 DOI: 10.1080/23802359.2020.1719919] [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] [Indexed: 11/09/2022] Open
Abstract
Aquilegia barnebyi, belonging to the genus Aquilegia (Ranunculaceae), is a member of basal eudicot species. In this study, we obtained the complete chloroplast (cp) genome of A. barnebyi. The genome size is 161,954 bp with a GC content of 38.98%. A total of 113 unique genes including 79 protein-coding genes, 30 tRNA genes, four rRNA genes were annotated. The large single-copy region and small single-copy region contains 91,250 bp and 17,359 bp, respectively. The inverted repeat regions are 26,671 bp in length. The phyologenetic analysis indicated that A. barnebyi had a close relationship with A. coerulea. And four species in genus Aquilegia formed a monophyletic group with high support value. The availability of A. barnebyi cp genomic resources will greatly helpful for taxonomy, phylogeny and conservation genetic studies of basal eudicot specie.
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Affiliation(s)
- Hui Huang
- Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
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17
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Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James). Genes (Basel) 2019; 10:genes10100734. [PMID: 31546687 PMCID: PMC6826667 DOI: 10.3390/genes10100734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/05/2019] [Accepted: 09/18/2019] [Indexed: 01/20/2023] Open
Abstract
Reproductive success in plants is dependent on many factors but the precise timing of flowering is certainly among the most crucial. Perennial plants often have a vernalization or over-wintering requirement in order to successfully flower in the spring. The shoot apical meristem undergoes drastic developmental and molecular changes as it transitions into inflorescence meristem (IM) identity, which then gives rise to floral meristems (FMs). In this study, we have examined the developmental and gene expression changes underlying the transition from the vegetative to reproductive phases in the basal eudicot Aquilegia coerulea, which has evolved a vernalization response independently relative to other established model systems. Results from both our histology and scanning electron studies demonstrate that developmental changes in the meristem occur gradually during the third and fourth weeks of vernalization. Based on RNAseq data and cluster analysis, several known flowering time loci, including AqFT and AqFL1, exhibit dramatic changes in expression during the fourth week. Further consideration of candidate gene homologs as well as unexpected loci of interest creates a framework in which we can begin to explore the genetic basis of the flowering time transition in Aquilegia.
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18
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Li MR, Wang HY, Ding N, Lu T, Huang YC, Xiao HX, Liu B, Li LF. Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala. Genome Biol Evol 2019; 11:919-930. [PMID: 30793209 PMCID: PMC6433176 DOI: 10.1093/gbe/evz038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
Elucidating the mechanisms underlying the genetic divergence between closely related species is crucial to understanding the origin and evolution of biodiversity. The genus Aquilegia L. has undergone rapid adaptive radiation, generating about 70 well-recognized species that are specialized to distinct habitats and pollinators. In this study, to address the underlying evolutionary mechanisms that drive the genetic divergence, we analyzed the whole genomes of two ecologically isolated Aquilegia species, A. oxysepala and A. japonica as well as their putative hybrid. Our comparative genomic analyses reveal that while the two species diverged only recently and experienced recurrent gene flow, a high level of genetic divergence is observed in their nuclear genomes. In particular, candidate genomic regions that show signature of selection differ dramatically between the two species. Given that the splitting time of the two species is broadly matched with the decrease in effective population sizes, we propose that allopatric isolation together with natural selection have preceded the interspecific gene flow in the process of speciation. The observed high genetic divergence is likely an outcome of combined effects of natural selection, genetic drift and divergent sorting of ancestral polymorphisms. Our study provides a genome-wide view of how genetic divergence has evolved between closely related species.
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Affiliation(s)
- Ming-Rui Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hua-Ying Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ning Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Tianyuan Lu
- McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Ye-Chao Huang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong-Xing Xiao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
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19
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Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae. Mol Phylogenet Evol 2019; 135:12-21. [DOI: 10.1016/j.ympev.2019.02.024] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 11/23/2022]
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20
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Bosch M, Herrando-Moraira S, Hoyo AD, López-Pujol J, Massó S, Rosselló JA, Simon J, Blanché C. New conservation viewpoints when plants are viewed at one level higher. Integration of phylogeographic structure, niche modeling and genetic diversity in conservation planning of W Mediterranean larkspurs. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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21
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Filiault DL, Ballerini ES, Mandáková T, Aköz G, Derieg NJ, Schmutz J, Jenkins J, Grimwood J, Shu S, Hayes RD, Hellsten U, Barry K, Yan J, Mihaltcheva S, Karafiátová M, Nizhynska V, Kramer EM, Lysak MA, Hodges SA, Nordborg M. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. eLife 2018; 7:e36426. [PMID: 30325307 PMCID: PMC6255393 DOI: 10.7554/elife.36426] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/17/2018] [Indexed: 12/21/2022] Open
Abstract
The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome - a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.
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Affiliation(s)
- Danièle L Filiault
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| | - Evangeline S Ballerini
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Terezie Mandáková
- Central-European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Gökçe Aköz
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Nathan J Derieg
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Jeremy Schmutz
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Jerry Jenkins
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Jane Grimwood
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Shengqiang Shu
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Richard D Hayes
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Uffe Hellsten
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Kerrie Barry
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Juying Yan
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | | | - Miroslava Karafiátová
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| | - Elena M Kramer
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
| | - Martin A Lysak
- Central-European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Scott A Hodges
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
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22
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Lin Z, Damaris RN, Shi T, Li J, Yang P. Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera). BMC Genomics 2018; 19:554. [PMID: 30053802 PMCID: PMC6062958 DOI: 10.1186/s12864-018-4950-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/19/2018] [Indexed: 12/26/2022] Open
Abstract
Background Flower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying this phenomenon is still obscure. Results Here, the comparative transcriptomic analysis was performed among petal, stamen petaloid and stamen through RNA-seq. Using pairwise comparison analysis, a large number of genes involved in hormonal signal transduction pathways and transcription factors, especially the MADS-box genes, were identified as candidate genes for stamen petaloid in lotus. Conclusions Taken together, these results provide an insight into the molecular networks underlying lotus floral organ development and stamen petaloid. Electronic supplementary material The online version of this article (10.1186/s12864-018-4950-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhongyuan Lin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rebecca Njeri Damaris
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Tao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Juanjuan Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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23
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Yang ML, Wang LL, Zhang GP, Meng LH, Yang YP, Duan YW. Equipped for Migrations Across High Latitude Regions? Reduced Spur Length and Outcrossing Rate in a Biennial Halenia elliptica (Gentianaceae) With Mixed Mating System Along a Latitude Gradient. Front Genet 2018; 9:223. [PMID: 29988524 PMCID: PMC6026625 DOI: 10.3389/fgene.2018.00223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/04/2018] [Indexed: 11/30/2022] Open
Abstract
Halenia (Gentianaceae) originated from the mountain regions of East Asia, and diversified in America following long migrations via Beringia. While Halenia elliptica, one species of the genus in China, migrated toward high latitudes in China. Spur length of H. elliptica is highly variable. We examined the relationship between spur length and mating pattern along a latitude gradient. Field experiments were performed in two populations of H. elliptica, and we found that this species could produce seeds via both autonomous selfing and the aid of pollinators, suggesting a mixed mating system. In seven populations of H. elliptica along a latitudinal gradient, we found a trend of decrease in spur length with the increase of latitude. Based on molecular data from 11 microsatellite loci, we found that multilocus outcrossing rate decreased with the increase of latitude while the estimated inbreeding depression increased significantly, indicating that a high degree of inbreeding depression might have prevented evolution toward complete selfing in the high latitude populations with short spur length, and thus maintained mixed mating system of H. elliptica. Our results suggest that the mixed mating system of this species might be helpful in overcoming pollinator scarcity in newly colonized populations toward high latitudes after its origination in the mountain regions of China, and the decrease of spur length in the high latitude populations could result from reduced resource allocation to pollinator associated traits.
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Affiliation(s)
- Ming-Liu Yang
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Lin-Lin Wang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guo-Peng Zhang
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Li-Hua Meng
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of University in Yunnan Province, School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Yong-Ping Yang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, China
| | - Yuan-Wen Duan
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, China
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Min Y, Kramer EM. The Aquilegia JAGGED homolog promotes proliferation of adaxial cell types in both leaves and stems. THE NEW PHYTOLOGIST 2017; 216:536-548. [PMID: 27864962 DOI: 10.1111/nph.14282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
In order to explore the functional conservation of JAGGED, a key gene involved in the sculpting of lateral organs in several model species, we identified its ortholog AqJAG in the lower eudicot species Aquilegia coerulea. We analyzed the expression patterns of AqJAG in various tissues and developmental stages, and used RNAi-based methods to generate knockdown phenotypes of AqJAG. AqJAG was strongly expressed in shoot apices, floral meristems, lateral root primordia and all lateral organ primordia. Silencing of AqJAG revealed a wide range of defects in the developing stems, leaves and flowers; strongest phenotypes include severe reduction of leaflet laminae due to a decrease in cell size and number, change of adaxial cell identity, outgrowth of laminar-like tissue on the inflorescence stem, and early arrest of floral meristems and floral organ primordia. Our results indicate that AqJAG plays a critical role in controlling primordia initiation and distal growth of floral organs, and laminar development of leaflets. Most strikingly, we demonstrated that AqJAG disproportionally controls the behavior of cells with adaxial identity in vegetative tissues, providing evidence of how cell proliferation is controlled in an identity-specific manner.
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Affiliation(s)
- Ya Min
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
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Katsuhara KR, Kitamura S, Ushimaru A. Functional significance of petals as landing sites in fungus‐gnat pollinated flowers of
Mitella pauciflora
(Saxifragaceae). Funct Ecol 2017. [DOI: 10.1111/1365-2435.12842] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Koki R. Katsuhara
- Graduate School of Human Development and Environment Kobe University 3‐11, Tsurukabuto Kobe657‐8501 Japan
| | - Shumpei Kitamura
- Department of Environmental Science Faculty of Bioresources and Environmental Sciences Ishikawa Prefectural University 1‐308, Suematsu Nonoichi Ishikawa921‐8836 Japan
| | - Atushi Ushimaru
- Graduate School of Human Development and Environment Kobe University 3‐11, Tsurukabuto Kobe657‐8501 Japan
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Abstract
The origin of the flower was a key innovation in the history of complex organisms, dramatically altering Earth's biota. Advances in phylogenetics, developmental genetics, and genomics during the past 25 years have substantially advanced our understanding of the evolution of flowers, yet crucial aspects of floral evolution remain, such as the series of genetic and morphological changes that gave rise to the first flowers; the factors enabling the origin of the pentamerous eudicot flower, which characterizes ∼70% of all extant angiosperm species; and the role of gene and genome duplications in facilitating floral innovations. A key early concept was the ABC model of floral organ specification, developed by Elliott Meyerowitz and Enrico Coen and based on two model systems,Arabidopsis thalianaandAntirrhinum majus Yet it is now clear that these model systems are highly derived species, whose molecular genetic-developmental organization must be very different from that of ancestral, as well as early, angiosperms. In this article, we will discuss how new research approaches are illuminating the early events in floral evolution and the prospects for further progress. In particular, advancing the next generation of research in floral evolution will require the development of one or more functional model systems from among the basal angiosperms and basal eudicots. More broadly, we urge the development of "model clades" for genomic and evolutionary-developmental analyses, instead of the primary use of single "model organisms." We predict that new evolutionary models will soon emerge as genetic/genomic models, providing unprecedented new insights into floral evolution.
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Field Guide to Plant Model Systems. Cell 2017; 167:325-339. [PMID: 27716506 DOI: 10.1016/j.cell.2016.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/28/2016] [Accepted: 08/15/2016] [Indexed: 12/20/2022]
Abstract
For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
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Antoń S, Kamińska M. Comparative floral spur anatomy and nectar secretion in four representatives of Ranunculaceae. PROTOPLASMA 2015; 252:1587-601. [PMID: 25772682 PMCID: PMC4628095 DOI: 10.1007/s00709-015-0794-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 03/02/2015] [Indexed: 05/11/2023]
Abstract
Nectaries are common in Ranunculaceae. These secretory structures, however, have not been studied in detail despite their importance in plant-animal interactions, and data relating to the structure of nectary spurs, which are so characteristic of several genera of this family, remain scarce. In order to redress this imbalance, we sought, in the present paper, to analyze the anatomical and ultrastructural organization of the nectary spurs of four representatives of Ranunculaceae, i.e., Aconitum lycoctonum L., Aquilegia vulgaris L., Consolida regalis Gray, and Delphinium elatum L. Nectary spurs were examined using light, fluorescence, scanning electron, and transmission electron microscopy. The floral nectaries of A. lycoctonum and A. vulgaris are situated at the apices of the spurs, whereas in C. regalis and D. elatum, the nectary is located along the floor surface of the spurs. Nectar in C. regalis and D. elatum is exuded through micro-channels in the cuticle, whereas in A. lycoctonum and A. vulgaris, it is released by means of cell wall disruption, indicating that the method of nectar secretion here is holocrine. Structurally, the nectary of all four investigated species is quite similar, and its cells are typical of nectar-producing cells described in the literature. It is proposed that in A. lycoctonum and A. vulgaris, disruption of the cell wall and the release of the entire cell contents into the spur cavity contribute to the composition of the nectar that the latter contains, enriching it with cytoplasmic components. We conclude that the manner of nectar exudation may vary considerably between closely related plant species, regardless of their geographical origin and phylogeny.
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Affiliation(s)
- Sebastian Antoń
- Department of Botany, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland.
| | - Magdalena Kamińska
- Department of Botany, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
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Li LF, Wang HY, Pang D, Liu Y, Liu B, Xiao HX. Phenotypic and genetic evidence for ecological speciation of Aquilegia japonica and A. oxysepala. THE NEW PHYTOLOGIST 2014; 204:1028-1040. [PMID: 25117915 DOI: 10.1111/nph.12967] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
Natural selection is thought to be a driving force that can cause the evolution of reproductive isolation. The genus Aquilegia is a model system to address how natural selection promotes the process of speciation. Morphological differences between A. oxysepala, A. japonica and their hybrids were quantified for two vegetative (plant height and leaf area) and three floral morphological (sepal area, corolla length and diameter) traits. We also evaluated the genetic variability of the two species and their hybrids based on two chloroplast (1225 bp), four nuclear (5811 bp) genes and 15 microsatellites. Our results revealed that differentiation of A. japonica and A. oxysepala at the ecological and morphological levels also involved divergence at the genetic level. In addition, the analysis of nucleotide variation patterns showed that the two species possessed numerous fixation sites at nuclear genes gAA4, gA7 and gAA12. Furthermore, we found that all of the phenotypic hybrids also showed a genetically admixed ancestry. These findings suggest that natural selection has indeed facilitated the formation of distinct genetic variation patterns in the two Aquilegia species and habitat adaptation has been driving the ecologically based evolution of reproductive isolation.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
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Noutsos C, Borevitz JO, Hodges SA. Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and betweenAquilegia formosaandA. pubescens. Mol Ecol 2014; 23:5589-98. [DOI: 10.1111/mec.12962] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 09/30/2014] [Accepted: 10/03/2014] [Indexed: 11/30/2022]
Affiliation(s)
- C. Noutsos
- Department of Ecology and Evolution; University of Chicago; 1101E 57th Street Chicago IL 60637 USA
- Cold Spring Harbor Lab; Cold Spring Harbor NY 11724 USA
| | - J. O. Borevitz
- Department of Ecology and Evolution; University of Chicago; 1101E 57th Street Chicago IL 60637 USA
- Research School of Biology; The Australian National University; Canberra ACT 0200 Australia
| | - S. A. Hodges
- Department of Ecology; Evolution & Marine Biology; University of California; Santa Barbara CA 93106-9620 USA
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Fourquin C, Ferrándiz C. The essential role of NGATHA genes in style and stigma specification is widely conserved across eudicots. THE NEW PHYTOLOGIST 2014; 202:1001-1013. [PMID: 24483275 DOI: 10.1111/nph.12703] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/25/2013] [Indexed: 05/07/2023]
Abstract
Carpel development and evolution are central issues for plant biology. The conservation of genetic functions conferring carpel identity has been widely studied in higher plants. However, although genetic networks directing the development of characteristic features of angiosperm carpels such as stigma and style are increasingly known in Arabidopsis thaliana, little information is available on the conservation and diversification of these networks in other species. Here, we have studied the functional conservation of NGATHA transcription factors in widely divergent species within the eudicots. We determined by in situ hybridization the expression patterns of NGATHA orthologs in Eschscholzia californica and Nicotiana benthamiana. Virus-induced gene silencing (VIGS)-mediated inactivation of NGATHA genes in both species was performed and different microscopy techniques were used for phenotypic characterization. We found the expression patterns of EcNGA and NbNGA genes during flower development to be highly similar to each other, as well as to those reported for Arabidopsis NGATHA genes. Inactivation of EcNGA and NbNGA also caused severe defects in style and stigma development in both species. These results demonstrate the widely conserved essential role of NGATHA genes in style and stigma specification and suggest that the angiosperm-specific NGATHA genes were likely recruited to direct a carpel-specific developmental program.
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Affiliation(s)
- Chloé Fourquin
- Instituto de Biología Molecular y Celular de Plantas, UPV-CSIC, 46022, Valencia, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, UPV-CSIC, 46022, Valencia, Spain
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33
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Erst AS, Vaulin OV. Phylogenetic relationships among North Asian species of the genus Aquilegia based on molecular markers. ACTA ACUST UNITED AC 2014. [DOI: 10.1134/s2079059714010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sharma B, Yant L, Hodges SA, Kramer EM. Understanding the development and evolution of novel floral form in Aquilegia. CURRENT OPINION IN PLANT BIOLOGY 2014; 17:22-27. [PMID: 24507490 DOI: 10.1016/j.pbi.2013.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 05/29/2023]
Abstract
Flowers of the lower eudicot Aquilegia (columbine) possess morphological innovations, namely elaborate petal spurs and a fifth distinct organ identity, the staminodium, that are well suited to the investigation of key questions in developmental evolution. The recent evolution of these characteristics combined with a growing set of genetic and genomic resources has provided insight into how the traits arose and diversified. The petal spur appears to represent a key innovation that diversified largely via modification of specific aspects of cell expansion. In the case of the staminodium, gene duplication has played a role in allowing a novel organ identity to be carved out of the traditional ABC program.
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Affiliation(s)
- Bharti Sharma
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Levi Yant
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Scott A Hodges
- Department of Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9610, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
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Gleason EJ, Kramer EM. Conserved roles for Polycomb Repressive Complex 2 in the regulation of lateral organ development in Aquilegia x coerulea 'Origami'. BMC PLANT BIOLOGY 2013; 13:185. [PMID: 24256402 PMCID: PMC3840678 DOI: 10.1186/1471-2229-13-185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 11/06/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Epigenetic regulation is necessary for maintaining gene expression patterns in multicellular organisms. The Polycomb Group (PcG) proteins form several complexes with important and deeply conserved epigenetic functions in both the plant and animal kingdoms. One such complex, the Polycomb Repressive Complex 2 (PRC2), is critical to many developmental processes in plants including the regulation of major developmental transitions. In addition, PRC2 restricts the expression domain of various transcription factor families in Arabidopsis, including the class I KNOX genes and several of the ABCE class MADS box genes. While the functions of these transcription factors are known to be deeply conserved, whether or not their regulation by PRC2 is similarly conserved remains an open question. RESULTS Here we use virus-induced gene silencing (VIGS) to characterize the function of the PRC2 complex in lateral organ development of Aquilegia x coerulea 'Origami', a member of the lower eudicot order Ranunculales. Leaves with PRC2 down-regulation displayed a range of phenotypes including ruffled or curled laminae, additional lobing, and an increased frequency of higher order branching. Sepals and petals were also affected, being narrowed, distorted, or, in the case of the sepals, exhibiting partial homeotic transformation. Many of the petal limbs also had a particularly intense yellow coloration due to an accumulation of carotenoid pigments. We show that the A. x coerulea floral MADS box genes AGAMOUS1 (AqAG1), APETALA3-3 (AqAP3-3) and SEPALLATA3 (AqSEP3) are up-regulated in many tissues, while expression of the class I KNOX genes and several candidate genes involved in carotenoid production or degradation are largely unaffected. CONCLUSIONS PRC2 targeting of several floral MADS box genes may be conserved in dicots, but other known targets do not appear to be. In the case of the type I KNOX genes, this may reflect a regulatory shift associated with the evolution of compound leaves.
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Affiliation(s)
- Emily J Gleason
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138, USA
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Hsieh MH, Pan ZJ, Lai PH, Lu HC, Yeh HH, Hsu CC, Wu WL, Chung MC, Wang SS, Chen WH, Chen HH. Virus-induced gene silencing unravels multiple transcription factors involved in floral growth and development in Phalaenopsis orchids. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3869-84. [PMID: 23956416 PMCID: PMC3745740 DOI: 10.1093/jxb/ert218] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Orchidaceae, one of the largest angiosperm families, has significant commercial value. Isolation of genes involved in orchid floral development and morphogenesis, scent production, and colouration will advance knowledge of orchid flower formation and facilitate breeding new varieties to increase the commercial value. With high-throughput virus-induced gene silencing (VIGS), this study identified five transcription factors involved in various aspects of flower morphogenesis in the orchid Phalaenopsis equestris. These genes are PeMADS1, PeMADS7, PeHB, PebHLH, and PeZIP. Silencing PeMADS1 and PebHLH resulted in reduced flower size together with a pelaloid column containing petal-like epidermal cells and alterations of epidermal cell arrangement in lip lateral lobes, respectively. Silencing PeMADS7, PeHB, and PeZIP alone resulted in abortion of the first three fully developed flower buds of an inflorescence, which indicates the roles of the genes in late flower development. Furthermore, double silencing PeMADS1 and PeMADS6, C- and B-class MADS-box genes, respectively, produced a combinatorial phenotype with two genes cloned in separate vectors. Both PeMADS1 and PeMADS6 are required to ensure the normal development of the lip and column as well as the cuticle formation on the floral epidermal cell surface. Thus, VIGS allows for unravelling the interaction between two classes of MADS transcription factors for dictating orchid floral morphogenesis.
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Affiliation(s)
- Ming-Hsien Hsieh
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Tainan District Agricultural Research and Extension Station, Council of Agriculture, Tainan 712Taiwan
| | - Zhao-Jun Pan
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Pei-Han Lai
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsiang-Chia Lu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Hung Yeh
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 106, Taiwan
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Mei-Chu Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Shyh-Shyan Wang
- Tainan District Agricultural Research and Extension Station, Council of Agriculture, Tainan 712Taiwan
| | - Wen-Huei Chen
- Orchid Research Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Orchid Research Center, National Cheng Kung University, Tainan 701, Taiwan
- * To whom correspondence should be addressed. E-mail:
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Fior S, Li M, Oxelman B, Viola R, Hodges SA, Ometto L, Varotto C. Spatiotemporal reconstruction of the Aquilegia rapid radiation through next-generation sequencing of rapidly evolving cpDNA regions. THE NEW PHYTOLOGIST 2013; 198:579-592. [PMID: 23379348 DOI: 10.1111/nph.12163] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/20/2012] [Indexed: 05/02/2023]
Abstract
Aquilegia is a well-known model system in the field of evolutionary biology, but obtaining a resolved and well-supported phylogenetic reconstruction for the genus has been hindered by its recent and rapid diversification. Here, we applied 454 next-generation sequencing to PCR amplicons of 21 of the most rapidly evolving regions of the plastome to generate c. 24 kb of sequences from each of 84 individuals from throughout the genus. The resulting phylogeny has well-supported resolution of the main lineages of the genus, although recent diversification such as in the European taxa remains unresolved. By producing a chronogram of the whole Ranunculaceae family based on published data, we inferred calibration points for dating the Aquilegia radiation. The genus originated in the upper Miocene c. 6.9 million yr ago (Ma) in Eastern Asia, and diversification occurred c. 4.8 Ma with the split of two main clades, one colonizing North America, and the other Western Eurasia through the mountains of Central Asia. This was followed by a back-to-Asia migration, originating from the European stock using a North Asian route. These results provide the first backbone phylogeny and spatiotemporal reconstruction of the Aquilegia radiation, and constitute a robust framework to address the adaptative nature of speciation within the group.
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Affiliation(s)
- Simone Fior
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Mingai Li
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Bengt Oxelman
- Department of Biology and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30, Gothenburg, Sweden
| | - Roberto Viola
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Scott A Hodges
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Lino Ometto
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Claudio Varotto
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
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Sharma B, Kramer EM. Virus-induced gene silencing in the rapid cycling columbine Aquilegia coerulea "Origami". Methods Mol Biol 2013; 975:71-81. [PMID: 23386296 DOI: 10.1007/978-1-62703-278-0_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Aquilegia Origami is an emerging model system for ecology and evolution, which has numerous genetic and genomic tools. Virus-induced gene silencing (VIGS) has been established as an effective approach to study gene function in Aquilegia. In the current protocol, we demonstrate VIGS using Agrobacterium strain GV3101 carrying tobacco rattle virus (TRV)-based constructs to infect Aquilegia coerulea "Origami" plants via vacuum infiltration.
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Affiliation(s)
- Bharti Sharma
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Feng CM, Liu X, Yu Y, Xie D, Franks RG, Xiang QYJ. Evolution of bract development and B-class MADS box gene expression in petaloid bracts of Cornus s. l. (Cornaceae). THE NEW PHYTOLOGIST 2012; 196:631-643. [PMID: 22897242 DOI: 10.1111/j.1469-8137.2012.04255.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Despite increasing interest in the molecular mechanisms of floral diversity, few studies have investigated the developmental and genetic bases of petaloid bracts. This study examined morphological patterns of bract initiation and expression patterns of B-class MADS-box genes in bracts of several Cornus species. We suggest that petaloid bracts in this genus may not share a single evolutionary origin. Developmental pathways of bracts and spatiotemporal expression of B-class genes in bracts and flowers were examined for four closely related dogwood species. Divergent morphological progressions and gene expression patterns were found in the two sister lineages with petaloid bracts, represented by Cornus florida and Cornus canadensis. Phylogeny-based analysis identified developmental and gene expression changes that are correlated with the evolution of petaloid bracts in C. florida and C. canadensis. Our data support the existence of independent evolutionary origins of petaloid bracts in C. canadensis and C. florida. Additionally, we suggest that functional transference within B-class gene families may have contributed to the origin of bract petaloidy in C. florida. However, the underlying mechanisms of petaloid bract development likely differ between C. florida and C. canadensis. In the future this hypothesis can be tested by functional analyses of Cornus B-class genes.
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Affiliation(s)
- Chun-Miao Feng
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USADepartment of Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiang Liu
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USADepartment of Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - Yi Yu
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USADepartment of Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - Deyu Xie
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USADepartment of Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert G Franks
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USADepartment of Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - Qiu-Yun Jenny Xiang
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USADepartment of Genetics, North Carolina State University, Raleigh, NC 27695, USA
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Characterization of Aquilegia Polycomb Repressive Complex 2 homologs reveals absence of imprinting. Gene 2012; 507:54-60. [PMID: 22796128 DOI: 10.1016/j.gene.2012.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 06/11/2012] [Accepted: 07/03/2012] [Indexed: 01/08/2023]
Abstract
Epigenetic regulation is important for maintaining gene expression patterns in multicellular organisms. The Polycomb Group (PcG) proteins form several complexes with important and deeply conserved epigenetic functions in both the plant and animal kingdoms. The plant Polycomb Repressive Complex 2 (PRC2) contains four core proteins, Enhancer of Zeste (E(z)), Suppressor of Zeste 12 (Su(z)12), Extra Sex Combs (ESC), and Multicopy Suppressor of IRA 1 (MSI1), and functions in many developmental transitions. In some plant species, including rice and Arabidopsis, duplications in the core PRC2 proteins allow the formation of PRC2s with distinct developmental functions. In addition, members of the plant specific VEL PHD family have been shown to associate with the PRC2 complex in Arabidopsis and may play a role in targeting the PRC2 to specific loci. Here we examine the evolution and expression of the PRC2 and VEL PHD families in Aquilegia, a member of the lower eudicot order Ranunculales and an emerging model for the investigation of plant ecology, evolution and developmental genetics. We find that Aquilegia has a relatively simple PRC2 with only one homolog of Su(z)12, ESC and MSI1 and two ancient copies of E(z), AqSWN and AqCLF. Aquilegia has four members of the VEL PHD family, three of which appear to be closely related to Arabidopsis proteins known to associate with the PRC2. The PRC2 and VEL PHD family proteins are expressed at a relatively constant level throughout Aquilegia vulgaris development, with the VEL PHD family and MSI1 expressed at higher levels during and after vernalization and in the inflorescence. Both AqSWN and AqCLF are expressed in Aquilegia endosperm but neither copy is imprinted.
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Hu J, Zhang J, Shan H, Chen Z. Expression of floral MADS-box genes in Sinofranchetia chinensis (Lardizabalaceae): implications for the nature of the nectar leaves. ANNALS OF BOTANY 2012; 110:57-69. [PMID: 22652421 PMCID: PMC3380600 DOI: 10.1093/aob/mcs104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS The perianths of the Lardizabalaceae are diverse. The second-whorl floral organs of Sinofranchetia chinensis (Lardizabalaceae) are nectar leaves. The aim of this study was to explore the nature of this type of floral organ, and to determine its relationship to nectar leaves in other Ranunculales species, and to other floral organs in Sinofranchetia chinensis. METHODS Approaches of evolutionary developmental biology were used, including 3' RACE (rapid amplification of cDNA ends) for isolating floral MADS-box genes, phylogenetic analysis for reconstructing gene evolutionary history, in situ hybridization and tissue-specific RT-PCR for identifying gene expression patterns and SEM (scanning electron microscopy) for observing the epidermal cell morphology of floral organs. KEY RESULTS Fourteen new floral MADS-box genes were isolated from Sinofranchetia chinensis and from two other species of Lardizabalaceae, Holboellia grandiflora and Decaisnea insignis. The phylogenetic analysis of AP3-like genes in Ranunculales showed that three AP3 paralogues from Sinofranchetia chinensis belong to the AP3-I, -II and -III lineages. In situ hybridization results showed that SIchAP3-3 is significantly expressed only in nectar leaves at the late stages of floral development, and SIchAG, a C-class MADS-box gene, is expressed not only in stamens and carpels, but also in nectar leaves. SEM observation revealed that the adaxial surface of nectar leaves is covered with conical epidermal cells, a hallmark of petaloidy. CONCLUSIONS The gene expression data imply that the nectar leaves in S. chinensis might share a similar genetic regulatory code with other nectar leaves in Ranunculales species. Based on gene expression and morphological evidence, it is considered that the nectar leaves in S. chinensis could be referred to as petals. Furthermore, the study supports the hypothesis that the nectar leaves in some Ranunculales species might be derived from stamens.
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Affiliation(s)
- Jin Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- For correspondence. E-mail
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Box MS, Dodsworth S, Rudall PJ, Bateman RM, Glover BJ. Characterization of Linaria KNOX genes suggests a role in petal-spur development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:703-14. [PMID: 21790812 DOI: 10.1111/j.1365-313x.2011.04721.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Spurs are tubular outgrowths of perianth organs that have evolved iteratively among angiosperms. They typically contain nectar and often strongly influence pollinator specificity, potentially mediating reproductive isolation. The identification of Antirrhinum majus mutants with ectopic petal spurs suggested that petal-spur development is dependent on the expression of KNOTTED 1-like homeobox (KNOX) genes, which are better known for their role in maintaining the shoot apical meristem. Here, we tested the role of KNOX genes in petal-spur development by isolating orthologs of the A. majus KNOX genes Hirzina (AmHirz) and Invaginata (AmIna) from Linaria vulgaris, a related species that differs from A. majus in possessing long, narrow petal spurs. We name these genes LvHirz and LvIna, respectively. Using quantitative reverse-transcription PCR, we show that LvHirz is expressed at high levels in the developing petals and demonstrate that the expression of petal-associated KNOX genes is sufficient to induce sac-like outgrowths on petals in a heterologous host. We propose a model in which KNOX gene expression during early petal-spur development promotes and maintains further morphogenetic potential of the petal, as previously described for KNOX gene function in compound leaf development. These data indicate that petal spurs could have evolved by changes in regulatory gene expression that cause rapid and potentially saltational phenotypic modifications. Given the morphological similarity of spur ontogeny in distantly related taxa, changes in KNOX gene expression patterns could be a shared feature of spur development in angiosperms.
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Affiliation(s)
- Mathew S Box
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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Brachi B, Morris GP, Borevitz JO. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 2011; 12:232. [PMID: 22035733 PMCID: PMC3333769 DOI: 10.1186/gb-2011-12-10-232] [Citation(s) in RCA: 304] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context.
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Affiliation(s)
- Benjamin Brachi
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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Saski CA, Feltus FA, Staton ME, Blackmon BP, Ficklin SP, Kuhn DN, Schnell RJ, Shapiro H, Motamayor JC. A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6. BMC Genomics 2011; 12:413. [PMID: 21846342 PMCID: PMC3173454 DOI: 10.1186/1471-2164-12-413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 08/16/2011] [Indexed: 12/16/2022] Open
Abstract
Background The fermented dried seeds of Theobroma cacao (cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust T. cacao cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected. Results Here, we describe the construction of a BAC-based integrated genetic-physical map of the T. cacao cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size of T. cacao is 374.6 Mbp. A comparative analysis with A. thaliana, V. vinifera, and P. trichocarpa suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the two T. cacao cultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed. Conclusions The results presented in this study are a stand-alone resource for functional exploitation and enhancement of Theobroma cacao but are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of the T. cacao genome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.
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Affiliation(s)
- Christopher A Saski
- Subtropical Horticulture Research Station, USDA-ARS, 13601 Old Culter Road, Miami, FL 33158, USA
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Stpiczyńska M, Davies KL, Kamińska M. Comparative anatomy of the nectary spur in selected species of Aeridinae (Orchidaceae). ANNALS OF BOTANY 2011; 107:327-45. [PMID: 21183455 PMCID: PMC3043926 DOI: 10.1093/aob/mcq246] [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] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS To date, the structure of the nectary spur of Aeridinae has not been studied in detail, and data relating to the nectaries of ornithophilous orchids remain scarce. The present paper compares the structural organization of the floral nectary in a range of Aeridinae species, including both entomophilous and ornithophilous taxa. METHODS Nectary spurs of Ascocentrum ampullaceum (Roxb.) Schltr. var. aurantiacum Pradhan, A. curvifolium (Lindl.) Schltr., A. garayi Christenson, Papilionanthe vandarum (Rchb.f.) Garay, Schoenorchis gemmata (Lindl.) J.J. Sm., Sedirea japonica (Rchb.f.) Garay & H.R. Sweet and Stereochilus dalatensis (Guillaumin) Garay were examined by means of light microscopy, scanning electron microscopy and transmission electron microscopy. KEY RESULTS AND CONCLUSIONS The diverse anatomy of the nectary is described for a range of Aeridinae species. All species of Ascocentrum investigated displayed features characteristic of ornithophilous taxa. They have weakly zygomorphic, scentless, red or orange flowers, display diurnal anthesis, possess cryptic anther caps and produce nectar that is secluded in a relatively massive nectary spur. Unicellular, secretory hairs line the lumen at the middle part of the spur. Generally, however, with the exception of Papilionanthe vandarum, the nectary spurs of all entomophilous species studied here (Schoenorchis gemmata, Sedirea japonica, Stereochilus dalatensis) lack secretory trichomes. Moreover, collenchymatous secretory tissue, present only in the nectary spur of Asiatic Ascocentrum species, closely resembles that found in nectaries of certain Neotropical species that are hummingbird-pollinated and assigned to subtribes Maxillariinae Benth., Laeliinae Benth. and Oncidiinae Benth. This similarity in anatomical organization of the nectary, regardless of geographical distribution and phylogeny, indicates convergence.
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Affiliation(s)
- Małgorzata Stpiczyńska
- University of Life Sciences, ul. Akademicka 15, 20-950 Lublin, Poland
- University of Warsaw, Botanic Garden, Al. Ujazdowskie 4, 00-478 Warszawa, Poland
| | - Kevin L. Davies
- School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
- For correspondence. E-mail
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Ballerini ES, Kramer EM. Environmental and molecular analysis of the floral transition in the lower eudicot Aquilegia formosa. EvoDevo 2011; 2:4. [PMID: 21329499 PMCID: PMC3049749 DOI: 10.1186/2041-9139-2-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 02/17/2011] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Flowering is a critical transition in plant development, the timing of which can have considerable fitness consequences. Until recently, research into the genetic control of flowering time and its associated developmental changes was focused on core eudicots (for example, Arabidopsis) or monocots (for example, Oryza). Here we examine the flowering response of Aquilegia formosa, a member of the eudicot order Ranunculales that is emerging as an important model for the investigation of plant ecology and evolution. RESULTS We have determined that A. formosa has a strong vernalization requirement but little or no photoperiod response, making it a day neutral (DN) plant. Consistent with this, the Aquilegia homolog of FLOWERING LOCUS T (AqFT) is expressed in both long and short days but surprisingly, the locus is expressed before the transition to flowering. In situ hybridizations with homologs of several Arabidopsis Floral Pathway Integrators (FPIs) do not suggest conserved functions relative to Arabidopsis, the potential exceptions being AqLFY and AqAGL24.2. CONCLUSIONS In Aquilegia, vernalization is critical to flowering but this signal is not strictly required for the transcriptional activation of AqFT. The expression patterns of AqLFY and AqAGL24.2 suggest a hypothesis for the development of Aquilegia's determinate inflorescence whereby their differential expression controls the progression of each meristem from inflorescence to floral identity. Interestingly, none of the Aquilegia expression patterns are consistent with a function in floral repression which, combined with the lack of a FLC homolog, means that new candidate genes must be identified for the control of vernalization response in Aquilegia.
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Affiliation(s)
- Evangeline S Ballerini
- Dept, of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave,, Cambridge, MA, 02138, USA.
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Fang GC, Blackmon BP, Henry DC, Staton ME, Saski CA, Hodges SA, Tomkins JP, Luo H. Genomic tools development for Aquilegia: construction of a BAC-based physical map. BMC Genomics 2010; 11:621. [PMID: 21059242 PMCID: PMC3091760 DOI: 10.1186/1471-2164-11-621] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 11/08/2010] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance. RESULTS BAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from A. formosa. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome) suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5%) across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs) from the minimal tiling path (MTP) allowed a preview of the Aquilegia genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in Aquilegia suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes indicated a higher similarity to grapevine (Vitis vinifera) than to rice and Arabidopsis in the transcriptomes. CONCLUSIONS The A. formosa BAC-based genomic resources provide valuable tools to study Aquilegia genome. Further integration of other existing genomics resources, such as ESTs, into the physical map should enable better understanding of the molecular mechanisms underlying adaptive radiation and elaboration of floral morphology.
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Affiliation(s)
- Guang-Chen Fang
- Department of Genetics and Biochemistry, Clemson University, SC 29634, USA
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RYMER PAULD, MANNING JOHNC, GOLDBLATT PETER, POWELL MARTYNP, SAVOLAINEN VINCENT. Evidence of recent and continuous speciation in a biodiversity hotspot: a population genetic approach in southern African gladioli (
Gladiolus
; Iridaceae). Mol Ecol 2010; 19:4765-82. [PMID: 20735739 DOI: 10.1111/j.1365-294x.2010.04794.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- PAUL D. RYMER
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey TW9 3DS, UK
| | - JOHN C. MANNING
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7, Cape Town, South Africa
| | - PETER GOLDBLATT
- Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166‐0299, USA
| | - MARTYN P. POWELL
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - VINCENT SAVOLAINEN
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey TW9 3DS, UK
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Voelckel C, Borevitz JO, Kramer EM, Hodges SA. Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis. PLoS One 2010; 5:e9735. [PMID: 20352114 PMCID: PMC2843724 DOI: 10.1371/journal.pone.0009735] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 02/13/2010] [Indexed: 01/17/2023] Open
Abstract
Background The genus Aquilegia is an emerging model system in plant evolutionary biology predominantly because of its wide variation in floral traits and associated floral ecology. The anatomy of the Aquilegia flower is also very distinct. There are two whorls of petaloid organs, the outer whorl of sepals and the second whorl of petals that form nectar spurs, as well as a recently evolved fifth whorl of staminodia inserted between stamens and carpels. Methodology/Principal Findings We designed an oligonucleotide microarray based on EST sequences from a mixed tissue, normalized cDNA library of an A. formosa x A. pubescens F2 population representing 17,246 unigenes. We then used this array to analyze floral gene expression in late pre-anthesis stage floral organs from a natural A. formosa population. In particular, we tested for gene expression patterns specific to each floral whorl and to combinations of whorls that correspond to traditional and modified ABC model groupings. Similar analyses were performed on gene expression data of Arabidopsis thaliana whorls previously obtained using the Ath1 gene chips (data available through The Arabidopsis Information Resource). Conclusions/Significance Our comparative gene expression analyses suggest that 1) petaloid sepals and petals of A. formosa share gene expression patterns more than either have organ-specific patterns, 2) petals of A. formosa and A. thaliana may be independently derived, 3) staminodia express B and C genes similar to stamens but the staminodium genetic program has also converged on aspects of the carpel program and 4) staminodia have unique up-regulation of regulatory genes and genes that have been implicated with defense against microbial infection and herbivory. Our study also highlights the value of comparative gene expression profiling and the Aquilegia microarray in particular for the study of floral evolution and ecology.
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Affiliation(s)
- Claudia Voelckel
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.
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