1
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Li S, Fan J, Xue C, Shan H, Kong H. Spur development and evolution: An update. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102573. [PMID: 38896925 DOI: 10.1016/j.pbi.2024.102573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
Floral spurs, widely recognized as a classic example of key morphological and functional innovation and thought to have promoted the origin and adaptive evolution of many flowering plant lineages, have attracted the attention of researchers for centuries. Despite this, the mechanisms underlying the development and evolution of these structures remain poorly understood. Recent studies have discovered the phytohormones and transcription factor genes that play key roles in regulating patterns of cell division and cell expansion during spur morphogenesis. Spur morphogenesis was also found to be tightly linked with the programs specifying floral zygomorphy, floral organ identity determination, and nectary development. Independent origins and losses of spurs in different flowering plant lineages, therefore, may be attributed to changes in the spur program and/or its upstream ones.
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Affiliation(s)
- Shuixian Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiannan Fan
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Xue
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Hongyan Shan
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongzhi Kong
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA. Current status of community resources and priorities for weed genomics research. Genome Biol 2024; 25:139. [PMID: 38802856 PMCID: PMC11129445 DOI: 10.1186/s13059-024-03274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.
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Affiliation(s)
- Jacob Montgomery
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Sarah Morran
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Dana R MacGregor
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - J Scott McElroy
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Paul Neve
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Célia Neto
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Martin M Vila-Aiub
- IFEVA-Conicet-Department of Ecology, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Analia I Menéndez
- Department of Ecology, Faculty of Agronomy, University of Buenos Aires, Buenos Aires, Argentina
| | - Julia M Kreiner
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Longjiang Fan
- Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Jagoda Mika
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Aldo Merotto
- Department of Crop Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Nithya K Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Luan Cutti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Robert Cicchillo
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Roger Gast
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Neeta Soni
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Terry R Wright
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | | | - Gregory May
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Jenna M Malone
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Deepmala Sehgal
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Shiv Shankhar Kaundun
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Richard P Dale
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Barend Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Bodo Peters
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Roland Beffa
- Senior Scientist Consultant, Herbicide Resistance Action Committee / CropLife International, Liederbach, Germany
| | | | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Kevin Fengler
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Victor Llaca
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Eric L Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA.
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3
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Cullen E, Wang Q, Glover BJ. How do you build a nectar spur? A transcriptomic comparison of nectar spur development in Linaria vulgaris and gibba development in Antirrhinum majus. FRONTIERS IN PLANT SCIENCE 2023; 14:1190373. [PMID: 37426957 PMCID: PMC10328749 DOI: 10.3389/fpls.2023.1190373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/23/2023] [Indexed: 07/11/2023]
Abstract
Nectar spurs (tubular outgrowths of floral organs) have long fascinated biologists. However, given that no model species possess nectar spurs, there is still much to learn about their development. In this study we combined morphological analysis with comparative transcriptomics to gain a global insight into the morphological and molecular basis of spur outgrowth in Linaria. Whole transcriptome sequencing was performed on two related species at three key developmental stages (identified by our morphological analysis), one with a spur (Linaria vulgaris), and one without a spur (Antirrhinum majus). A list of spur-specific genes was selected, on which we performed a gene enrichment analysis. Results from our RNA-seq analysis agreed with our morphological observations. We describe gene activity during spur development and provide a catalogue of spur-specific genes. Our list of spur-specific genes was enriched for genes connected to the plant hormones cytokinin, auxin and gibberellin. We present a global view of the genes involved in spur development in L. vulgaris, and define a suite of genes which are specific to spur development. This work provides candidate genes for spur outgrowth and development in L. vulgaris which can be investigated in future studies.
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Affiliation(s)
- Erin Cullen
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Qi Wang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Beverley J. Glover
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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4
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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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5
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van der Niet T, Egan PA, Schlüter PM. Evolutionarily inspired solutions to the crop pollination crisis. Trends Ecol Evol 2023; 38:435-445. [PMID: 36737302 DOI: 10.1016/j.tree.2022.12.010] [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: 05/31/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 02/04/2023]
Abstract
The global decline in insect diversity threatens pollination services, potentially impacting crop production and food security. Here, we argue that this looming pollination crisis is generally approached from an ecological standpoint, and that consideration of evolutionary principles offers a novel perspective. First, we outline that wild plant species have overcome 'pollination crises' throughout evolutionary history, and show how associated principles can be applied to crop pollination. We then highlight technological advances that can be used to adapt crop flowers for optimal pollination by local wild pollinators, especially by increasing generalization in pollination systems. Thus, synergies among fundamental evolutionary research, genetic engineering, and agro-ecological science provide a promising template for addressing a potential pollination crisis, complementing much-needed strategies focused on pollinator conservation.
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Affiliation(s)
- Timotheüs van der Niet
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, P. Bag X01, 3209, Scottsville, Pietermaritzburg, South Africa.
| | - Paul A Egan
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden
| | - Philipp M Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany
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6
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Li Y, Wei CM, Li XY, Meng DC, Gu ZJ, Qu SP, Huang MJ, Huang HQ. De novo transcriptome sequencing of Impatiens uliginosa and the analysis of candidate genes related to spur development. BMC PLANT BIOLOGY 2022; 22:553. [PMID: 36456926 PMCID: PMC9713998 DOI: 10.1186/s12870-022-03894-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Spur, a structure capable of producing and storing nectar, not only plays a vital role in the pollination process but also promotes the rapid diversification of some plant lineages, which is considered a key innovation in plants. Spur is the focus of many studies, such as evolution and ecological hypothesis, but the current understanding of spur development is limited. High-throughput sequencing of Impatiens uliginosa was carried out to study the molecular mechanism of its spur development, which is believed to provide some insights into the spur development of Impatiens. RESULTS Transcriptomic sequencing and analysis were performed on spurs and limbs of I. uliginosa at three developmental stages. A total of 47.83 Gb of clean data were obtained, and 49,716 unigene genes were assembled. After comparison with NR, Swiss-Prot, Pfam, COG, GO and KEGG databases, a total of 27,686 genes were annotated successfully. Through comparative analysis, 19,356 differentially expressed genes were found and enriched into 208 GO terms and 146 KEGG pathways, among which plant hormone signal transduction was the most significantly enriched pathway. One thousand thirty-two transcription factors were identified, which belonged to 33 TF families such as MYB, bHLH and TCP. Twenty candidate genes that may be involved in spur development were screened and verified by qPCR, such as SBP, IAA and ABP. CONCLUSIONS Transcriptome data of different developmental stages of spurs were obtained, and a series of candidate genes related to spur development were identified. The importance of genes related to cell cycle, cell division, cell elongation and hormones in spur development was clarified. This study provided valuable information and resources for understanding the molecular mechanism of spur development in Impatiens.
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Affiliation(s)
- Yang Li
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, 650224 Yunnan China
| | - Chun-Mei Wei
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, 650224 Yunnan China
| | - Xin-Yi Li
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, 650224 Yunnan China
| | - Dan-Chen Meng
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, 650224 Yunnan China
| | - Zhi-Jia Gu
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Su-Ping Qu
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 Yunnan China
| | - Mei-Juan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, 650224 Yunnan China
| | - Hai-Quan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, 650224 Yunnan China
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7
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Edwards MB, Ballerini ES, Kramer EM. Complex developmental and transcriptional dynamics underlie pollinator-driven evolutionary transitions in nectar spur morphology in Aquilegia (columbine). AMERICAN JOURNAL OF BOTANY 2022; 109:1360-1381. [PMID: 35971626 DOI: 10.1002/ajb2.16046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Determining the developmental programs underlying morphological variation is key to elucidating the evolutionary processes that generated the stunning biodiversity of the angiosperms. Here, we characterized the developmental and transcriptional dynamics of the elaborate petal nectar spur of Aquilegia (columbine) in species with contrasting pollination syndromes and spur morphologies. METHODS We collected petal epidermal cell number and length data across four Aquilegia species, two with short, curved nectar spurs of the bee-pollination syndrome and two with long, straight spurs of the hummingbird-pollination syndrome. We also performed RNA-seq on A. brevistyla (bee) and A. canadensis (hummingbird) distal and proximal spur compartments at multiple developmental stages. Finally, we intersected these data sets with a previous QTL mapping study on spur length and shape to identify new candidate loci. RESULTS The differential growth between the proximal and distal surfaces of curved spurs is primarily driven by differential cell division. However, independent transitions to straight spurs in the hummingbird syndrome have evolved by increasing differential cell elongation between spur surfaces. The RNA-seq data reveal these tissues to be transcriptionally distinct and point to auxin signaling as being involved with the differential cell elongation responsible for the evolution of straight spurs. We identify several promising candidate genes for future study. CONCLUSIONS Our study, taken together with previous work in Aquilegia, reveals the complexity of the developmental mechanisms underlying trait variation in this system. The framework we established here will lead to exciting future work examining candidate genes and processes involved in the rapid radiation of the genus.
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Affiliation(s)
- Molly B Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
| | - Evangeline S Ballerini
- Department of Biological Sciences, California State University Sacramento, 6000 J St., Sacramento, CA, 95819, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
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Delpeuch P, Jabbour F, Damerval C, Schönenberger J, Pamperl S, Rome M, Nadot S. A flat petal as ancestral state for Ranunculaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:961906. [PMID: 36212342 PMCID: PMC9532948 DOI: 10.3389/fpls.2022.961906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/23/2022] [Indexed: 05/19/2023]
Abstract
Ranunculaceae comprise ca. 2,500 species (ca. 55 genera) that display a broad range of floral diversity, particularly at the level of the perianth. Petals, when present, are often referred to as "elaborate" because they have a complex morphology. In addition, the petals usually produce and store nectar, which gives them a crucial functional role in the interaction with pollinators. Its morphological diversity and species richness make this family a particularly suitable model group for studying the evolution of complex morphologies. Our aims are (1) to reconstruct the ancestral form of the petal and evolutionary stages at the scale of Ranunculaceae, (2) to test the hypothesis that there are morphogenetic regions on the petal that are common to all species and that interspecific morphological diversity may be due to differences in the relative proportions of these regions during development. We scored and analyzed traits (descriptors) that characterize in detail the complexity of mature petal morphology in 32 genera. Furthermore, we described petal development using high resolution X-Ray computed tomography (HRX-CT) in six species with contrasting petal forms (Ficaria verna, Helleborus orientalis, Staphisagria picta, Aconitum napellus, Nigella damascena, Aquilegia vulgaris). Ancestral state reconstruction was performed using a robust and dated phylogeny of the family, allowing us to produce new hypotheses for petal evolution in Ranunculaceae. Our results suggest a flat ancestral petal with a short claw for the entire family and for the ancestors of all tribes except Adonideae. The elaborate petals that are present in different lineages have evolved independently, and similar morphologies are the result of convergent evolution.
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Affiliation(s)
- Pauline Delpeuch
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, Orsay, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- *Correspondence: Pauline Delpeuch,
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Susanne Pamperl
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Maxime Rome
- Jardin du Lautaret, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, Orsay, France
- Sophie Nadot,
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9
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Martínez-Salazar S, González F, Alzate JF, Pabón-Mora N. Molecular framework underlying floral bilateral symmetry and nectar spur development in Tropaeolum, an atypical member of the Brassicales. AMERICAN JOURNAL OF BOTANY 2021; 108:1315-1330. [PMID: 34458983 DOI: 10.1002/ajb2.1719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Floral spurs are key innovations associated with elaborate pollination mechanisms that have evolved independently several times across angiosperms. Spur formation can shift the floral symmetry from radial to bilateral, as it is the case in Tropaeolum, the only member of the Brassicales with floral nectar spurs. The genetic mechanisms underlying both spur and bilateral symmetry in the family have not yet been investigated. METHODS We studied flower development and morphoanatomy of Tropaeolum longifolium. We also generated a reference transcriptome and isolated all candidate genes involved in adaxial-abaxial differential growth during spur formation. Finally, we evaluated the evolution of the targeted genes across Brassicales and examined their expression in dissected floral parts. RESULTS Five sepals initiate spirally, followed by five petals alternate to the sepals, five antesepalous stamens, three antepetalous stamens, and three carpels. Intercalary growth at the common base of sepals and petals forms a floral tube. The spur is an outgrowth from the adaxial region of the tube, lined up with the medial sepal. We identified Tropaeolum specific duplications in the TCP3/4L and STM gene lineages, which are critical for spur formation in other taxa. In addition, we found that TM6 (MADS-box), RL2 (RAD-like7), and KN2/6L2 and OSH6L (KNOX1 genes), have been lost in core Brassicales but retained in Tropaeolum. CONCLUSIONS Three genes are pivotal during the extreme adaxial-abaxial asymmetry of the floral tube, namely, TlTCP4L2 restricted to the adaxial side where the spur is formed, and TlTCP12 and TlSTM1 to the abaxial side, lacking a spur.
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Affiliation(s)
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, AA 7495, Bogotá, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, AA 1226, Medellín, Colombia
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10
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Preston JC. Insights into the evo-devo of plant reproduction using next-generation sequencing approaches. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1536-1545. [PMID: 33367867 DOI: 10.1093/jxb/eraa543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
The development of plant model organisms has traditionally been analyzed using resource-heavy, tailored applications that are not easily transferable to distantly related non-model taxa. Thus, our understanding of plant development has been limited to a subset of traits, and evolutionary studies conducted most effectively either across very wide [e.g. Arabidopsis thaliana and Oryza sativa (rice)] or narrow (i.e. population level) phylogenetic distances. As plant biologists seek to capitalize on natural diversity for crop improvement, enhance ecosystem functioning, and better understand plant responses to climate change, high-throughput and broadly applicable forms of existing molecular biology assays are becoming an invaluable resource. Next-generation sequencing (NGS) is increasingly becoming a powerful tool in evolutionary developmental biology (evo-devo) studies, particularly through its application to understanding trait evolution at different levels of gene regulation. Here, I review some of the most common and emerging NGS-based methods, using exemplar studies in reproductive plant evo-devo to illustrate their potential.
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Affiliation(s)
- Jill C Preston
- The University of Vermont, Department of Plant Biology, 63 Carrigan Drive, Burlington, VT, USA
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11
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Min Y, Kramer EM. Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea. Sci Rep 2020; 10:19637. [PMID: 33184405 PMCID: PMC7665038 DOI: 10.1038/s41598-020-76750-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
The earliest phases of floral development include a number of crucial processes that lay the foundation for the subsequent morphogenesis of floral organs and success in reproduction. Currently, key transcriptional changes during this developmental window have been characterized in the model species Arabidopsis thaliana, but little is known about how transcriptional dynamics change over the course of these developmental processes in other plant systems. Here, we have conducted the first in-depth transcriptome profiling of early floral development in Aquilegia at four finely dissected developmental stages, with eight biological replicates per stage. Using differential gene expression analysis and weighted gene co-expression network analysis, we identified both crucial genes whose expression changes mark the transitions between developmental stages and hub genes in co-expression modules. Our results support the potential functional conservation of key genes in early floral development that have been identified in other systems, but also reveal a number of previously unknown or overlooked loci that are worthy of further investigation. In addition, our results highlight not only the dynamics of transcriptional regulation during early floral development, but also the potential involvement of the complex, essential networks of small RNA and post-translational regulation to these developmental stages.
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Affiliation(s)
- Ya Min
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, USA
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, USA.
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Wessinger CA, Hileman LC. Parallelism in Flower Evolution and Development. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-124511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Flower evolution is characterized by widespread repetition, with adaptations to pollinator environment evolving in parallel. Recent studies have expanded our understanding of the developmental basis of adaptive floral novelties—petal fusion, bilateral symmetry, heterostyly, and floral dimensions. In this article, we describe patterns of trait evolution and review developmental genetic mechanisms underlying floral novelties. We discuss the diversity of mechanisms for parallel adaptation, the evidence for constraints on these mechanisms, and how constraints help explain observed macroevolutionary patterns. We describe parallel evolution resulting from similarities at multiple hierarchical levels—genetic, developmental, morphological, functional—which indicate general principles in floral evolution, including the central role of hormone signaling. An emerging pattern is mutational bias that may contribute to rapid patterns of parallel evolution, especially if the derived trait can result from simple degenerative mutations. We argue that such mutational bias may be less likely to govern the evolution of novelties patterned by complex developmental pathways.
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Affiliation(s)
- Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Lena C. Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
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Ballerini ES, Min Y, Edwards MB, Kramer EM, Hodges SA. POPOVICH, encoding a C2H2 zinc-finger transcription factor, plays a central role in the development of a key innovation, floral nectar spurs, in Aquilegia. Proc Natl Acad Sci U S A 2020; 117:22552-22560. [PMID: 32848061 PMCID: PMC7486772 DOI: 10.1073/pnas.2006912117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The evolution of novel features, such as eyes or wings, that allow organisms to exploit their environment in new ways can lead to increased diversification rates. Therefore, understanding the genetic and developmental mechanisms involved in the origin of these key innovations has long been of interest to evolutionary biologists. In flowering plants, floral nectar spurs are a prime example of a key innovation, with the independent evolution of spurs associated with increased diversification rates in multiple angiosperm lineages due to their ability to promote reproductive isolation via pollinator specialization. As none of the traditional plant model taxa have nectar spurs, little is known about the genetic and developmental basis of this trait. Nectar spurs are a defining feature of the columbine genus Aquilegia (Ranunculaceae), a lineage that has experienced a relatively recent and rapid radiation. We use a combination of genetic mapping, gene expression analyses, and functional assays to identify a gene crucial for nectar spur development, POPOVICH (POP), which encodes a C2H2 zinc-finger transcription factor. POP plays a central role in regulating cell proliferation in the Aquilegia petal during the early phase (phase I) of spur development and also appears to be necessary for the subsequent development of nectaries. The identification of POP opens up numerous avenues for continued scientific exploration, including further elucidating of the genetic pathway of which it is a part, determining its role in the initial evolution of the Aquilegia nectar spur, and examining its potential role in the subsequent evolution of diverse spur morphologies across the genus.
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Affiliation(s)
- Evangeline S Ballerini
- Ecology, Evolution and Marine Biology Department, University of California, Santa Barbara, CA 93106;
| | - Ya Min
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02318
| | - Molly B Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02318
| | - Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02318
| | - Scott A Hodges
- Ecology, Evolution and Marine Biology Department, University of California, Santa Barbara, CA 93106;
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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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