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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Menger FM, Rizvi SAA. Preassembly Theory Invoking Prehistoric DNA Alterations. WORLD FUTURES 2023; 79:635-646. [DOI: 10.1080/02604027.2023.2226594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2023]
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Gobo WV, Kunzmann L, Iannuzzi R, Dos Santos TB, da Conceição DM, Rodrigues do Nascimento D, da Silva Filho WF, Bachelier JB, Coiffard C. A new remarkable Early Cretaceous nelumbonaceous fossil bridges the gap between herbaceous aquatic and woody protealeans. Sci Rep 2023; 13:8978. [PMID: 37268714 DOI: 10.1038/s41598-023-33356-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/12/2023] [Indexed: 06/04/2023] Open
Abstract
Dating back to the late Early Cretaceous, the macrofossil record of the iconic lotus family (Nelumbonaceae) is one of the oldest of flowering plants and suggests that their unmistakable leaves and nutlets embedded in large pitted receptacular fruits evolved relatively little in the 100 million years since their first known appearance. Here we describe a new fossil from the late Barremian/Aptian Crato Formation flora (NE Brazil) with both vegetative and reproductive structures, Notocyamus hydrophobus gen. nov. et sp. nov., which is now the oldest and most complete fossil record of Nelumbonaceae. In addition, it displays a unique mosaic of ancestral and derived macro- and micromorphological traits that has never been documented before in this family. This new Brazilian fossil-species also provides a rare illustration of the potential morphological and anatomical transitions experienced by Nelumbonaceae prior to a long period of relative stasis. Its potential plesiomorphic and apomorphic features shared with Proteaceae and Platanaceae not only fill a major morphological gap within Proteales but also provide new support for their unexpected relationships first suggested by molecular phylogenies.
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Affiliation(s)
- William Vieira Gobo
- Departamento de Paleontologia e Estratigrafia, Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Ave. Bento Gonçalves 9500, Porto Alegre, 91501-970, Brazil.
| | - Lutz Kunzmann
- Abteilung Museum für Mineralogie und Geologie, Senckenberg Naturhistorische Sammlungen Dresden, Königsbrücker Landstrasse. 159, D-01109, Dresden, Germany.
| | - Roberto Iannuzzi
- Departamento de Paleontologia e Estratigrafia, Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Ave. Bento Gonçalves 9500, Porto Alegre, 91501-970, Brazil
| | - Thamiris Barbosa Dos Santos
- Departamento de Paleontologia e Estratigrafia, Universidade Federal do Rio Grande do Sul (UFRGS), Rio Grande do Sul, Ave. Bento Gonçalves 9500, Porto Alegre, 91501-970, Brazil
| | - Domingas Maria da Conceição
- Universidade Regional do Cariri (URCA), St. Cel. Antônio Luíz 1161, Museu de Paleontologia Plácido Cidade Nuvens, Crato, Ceará, 63105-010, Brazil
| | - Daniel Rodrigues do Nascimento
- Departamento de Geologia, Universidade Federal do Ceará (UFC), Campus do Pici - 912, Fortaleza, Ceará, 60440-554, Brazil
| | | | - Julien B Bachelier
- Structural and Functional Plant Diversity Group, Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Altensteinstrasse 6, 14195, Berlin, Germany
| | - Clément Coiffard
- Structural and Functional Plant Diversity Group, Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Altensteinstrasse 6, 14195, Berlin, Germany
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Zhang C, Jiao C, Sun X, Li X. A MYB Transcription Factor Atlas Provides Insights into the Evolution of Environmental Adaptations in Plants. Int J Mol Sci 2023; 24:ijms24032566. [PMID: 36768888 PMCID: PMC9916579 DOI: 10.3390/ijms24032566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
The MYB transcription factor superfamily includes key regulators of plant development and responses to environmental changes. The diversity of lifestyles and morphological characteristics exhibited by plants are potentially associated with the genomic dynamics of the MYB superfamily. With the release of the plant genomes, a comprehensive phylogenomic analysis of the MYB superfamily across Viridiplantae is allowed. The present study performed phylogenetic, phylogenomic, syntenic, horizontal gene transfer, and neo/sub-functionalization analysis of the MYB superfamily to explore the evolutionary contributions of MYB members to species diversification, trait formation, and environmental adaptation in 437 different plant species. We identified major changes in copy number variation and genomic context within subclades across lineages. Multiple MYB subclades showed highly conserved copy number patterns and synteny across flowering plants, whereas others were more dynamic and showed lineage-specific patterns. As examples of lineage-specific morphological divergence, we hypothesize that the gain of a MYB orthogroup associated with flower development and environmental responses and an orthogroup associated with auxin and wax biosynthesis in angiosperms were correlated with the emergence of flowering plants, unbiased neo-/sub-functionalization of gene duplicates contributed to environmental adaptation, and species-specific neo-/sub-functionalization contributed to phenotype divergence between species. Transposable element insertion in promoter regions may have facilitated the sub-/neo-functionalization of MYB genes and likely played a tissue-specific role contributing to sub-/neo-functionalization in plant root tissues. This study provides new insights into the evolutionary divergence of the MYB superfamily across major flowering and non-flowering lineages and emphasizes the need for lineage-/tissue-specific characterization to further understand trait variability and environmental adaptation.
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Affiliation(s)
- Chaofan Zhang
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A & F University, Hangzhou 311300, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou 311300, China
| | - Chen Jiao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xuepeng Sun
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A & F University, Hangzhou 311300, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou 311300, China
- Correspondence: (X.S.); (X.L.)
| | - Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A & F University, Hangzhou 311300, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou 311300, China
- Correspondence: (X.S.); (X.L.)
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Sauquet H, Ramírez-Barahona S, Magallón S. What is the age of flowering plants? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3840-3853. [PMID: 35438718 DOI: 10.1093/jxb/erac130] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ~140 million years (Ma; Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both macroevolutionary analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age); the age(s) of emergence of their unique, distinctive features including flowers (morphological age); and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior distribution (typically a calibration density set by the user in Bayesian analyses). Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as largely unknown (140-270 Ma) and that contrasting age estimates in the literature mostly reflect conflicting prior distributions. We also suggest that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | | | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Qiao X, Zhang S, Paterson AH. Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions. Comput Struct Biotechnol J 2022; 20:3248-3256. [PMID: 35782740 PMCID: PMC9237934 DOI: 10.1016/j.csbj.2022.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 01/09/2023] Open
Abstract
Whole-genome duplication (WGD) has occurred repeatedly during plant evolution and diversification, providing genetic layers for evolving new functions and phenotypes. Advances in long-read sequencing technologies have enabled sequencing and assembly of over 1000 plant genomes spanning nearly 800 species, in which a large set of ancient WGDs has been uncovered. Here, we review the recently reported WGDs that occurred in major plant lineages and key evolutionary positions, and highlight their contributions to morphological innovation and adaptive evolution. Current gaps and challenges in integrating enormous volumes of sequenced plant genomes, accurately inferring WGDs, and developing web-based analysis tools are emphasized. Looking to the future, ambitious genome sequencing projects and global efforts may substantially recapitulate the plant tree of life based on broader sampling of phylogenetic diversity, reveal much of the timetable of ancient WGDs, and address the biological significance of WGDs in plant adaptation and radiation.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA,Corresponding author.
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Klymiuk AA, Rothwell GW, Stockey RA. A novel cupulate seed plant, Xadzigacalix quatsinoensis gen. et sp. nov., provides new insight into the Mesozoic radiation of gymnosperms. AMERICAN JOURNAL OF BOTANY 2022; 109:966-985. [PMID: 35435244 PMCID: PMC9328379 DOI: 10.1002/ajb2.1853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Anatomically preserved evidence for a novel clade of gymnosperms emphasizes diversity of seed plants immediately prior to the appearance of angiosperm fossils in the paleontological record. METHODS Cupulate seeds from the Early Cretaceous Apple Bay locality (Vancouver Island) are described from serial cellulose acetate peels and three-dimensional reconstruction. Phylogenetic context is assessed through the comparative analysis of gymnosperm seed producing fructifications and maximum parsimony analysis of a revised morphological data set for seed plant phylogeny. RESULTS Xadzigacalix quatsinoensis gen. et sp. nov. is characterized by an orthotropous ovule with an elongated micropyle and complex integument, enclosed within a radial cupule. The micropylar canal is elongated; and the nucellus extends into the micropyle to seal the post pollination ovule. Except at the apex of the micropyle, the seed is completely enclosed by a parenchymatous cupule with ca. 20 axially elongated secretory ducts. The cupulate seed is produced upon a triangular woody stele, consisting of a parenchymatous pith surrounded by radially aligned tracheids. The stele produces three short terete traces that terminate within the base of the cupule as transfusion tissue at the seed chalaza. CONCLUSIONS Organography, vascularization, nature of the integument and nucellus, and configuration of the micropylar canal distinguish Xadzigacalix quatsinoensis from all other gymnosperm clades. Cladistic analyses suggest the new plant may have affinities with gnetophytes or angiosperms. These results are complemented with a critical re-evaluation of ovulate structures for Mesozoic gymnosperms, providing new insight into plant diversity immediately antecedent to the explosive diversification of flowering plants.
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Affiliation(s)
- Ashley A. Klymiuk
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaR3T 2N2Canada
- Gantz Family Collections Center, Field Museum, 1400 S Lake Shore DriveChicagoIL60605USA
| | - Gar W. Rothwell
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331−2902USA
- Department of Environmental and Plant Biology317 Porter Hall, Ohio UniversityAthensOH45701USA
| | - Ruth A. Stockey
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331−2902USA
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Menger FM, Rizvi SAA. Evolution of Complexity. Molecular Aspects of Preassembly. Molecules 2021; 26:6618. [PMID: 34771027 PMCID: PMC8587518 DOI: 10.3390/molecules26216618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
An extension of neo-Darwinism, termed preassembly, states that genetic material required for many complex traits, such as echolocation, was present long before emergence of the traits. Assembly of genes and gene segments had occurred over protracted time-periods within large libraries of non-coding genes. Epigenetic factors ultimately promoted transfers from noncoding to coding genes, leading to abrupt formation of the trait via de novo genes. This preassembly model explains many observations that to this present day still puzzle biologists: formation of super-complexity in the absence of multiple fossil precursors, as with bat echolocation and flowering plants; major genetic and physical alterations occurring in just a few thousand years, as with housecat evolution; lack of precursors preceding lush periods of species expansion, as in the Cambrian explosion; and evolution of costly traits that exceed their need during evolutionary times, as with human intelligence. What follows in this paper is a mechanism that is not meant to supplant neo-Darwinism; instead, preassembly aims to supplement current ideas when complexity issues leave them struggling.
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Affiliation(s)
| | - Syed A. A. Rizvi
- School of Pharmacy, Hampton University, Hampton, VA 23669, USA; or
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