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Ping J, Hao J, Li J, Yang Y, Su Y, Wang T. Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein-coding genes. Ecol Evol 2022; 12:e8499. [PMID: 35136556 PMCID: PMC8809450 DOI: 10.1002/ece3.8499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein-coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non-conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non-conifers. It is more obvious that in non-conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6- to 3.1-fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2- to 3.6-fold of non-conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein-coding genes due to gene function, plant habitat, or newly acquired IRs.
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Affiliation(s)
- Jingyao Ping
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jing Hao
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jinye Li
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yiqing Yang
- College of Life Science and TechnologyCentral South University of Forestry and TechnologyChangshaChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen UniversityShenzhenChina
| | - Ting Wang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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2
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Asaf S, Khan AL, Jan R, Khan A, Khan A, Kim KM, Lee IJ. The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence. THE PLANT GENOME 2021; 14:e20130. [PMID: 34505399 DOI: 10.1002/tpg2.20130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 05/25/2023]
Abstract
Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present-day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales-other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time-calibrated plastid-based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, Univ. of Nizwa, Nizwa, 616, Oman
| | - Abdul Latif Khan
- Dep. of Biotechnology, College of Technology, Univ. of Houston, Houston, TX, 77204, USA
| | - Rahmatullah Jan
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord Univ., Bodø, 8049, Norway
| | - Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, 79409, USA
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - In-Jung Lee
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
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Di Stilio VS, Ickert-Bond SM. Ephedra as a gymnosperm evo-devo model lineage. Evol Dev 2021; 23:256-266. [PMID: 33503333 DOI: 10.1111/ede.12370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/29/2020] [Accepted: 01/02/2021] [Indexed: 11/28/2022]
Abstract
Established model systems in the flowering plants have greatly advanced our understanding of plant developmental biology, facilitating in turn its investigation across diverse land plants. The reliance on a limited number of model organisms, however, constitutes a barrier for future progress in evolutionary developmental biology (evo-devo). In particular, a more thorough understanding of seed plant character evolution and of its genetic and developmental basis has been hampered in part by a lack of gymnosperm model systems, since most are trees with decades-long generation times. Guided by the premise that future model organisms should be selected based on their character diversity, rather than simply phylogenetic "position," we highlight biological questions of potential interest that can be addressed via comparative studies in Ephedra (Gnetales). In addition to having relatively small genomes and shorter generation times in comparison to most other gymnosperms, Ephedra are amenable to investigations on the evolution of the key reproductive seed plant innovations of pollination and seed dispersal, as well as on polyploidy, and adaptation to extreme environments.
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Affiliation(s)
- Alicia Toon
- School of Biological Sciences; The University of Queensland; Brisbane Queensland 4072 Australia
| | - L. Irene Terry
- School of Biological Sciences; University of Utah; Salt Lake City Utah USA
| | | | - Gimme H. Walter
- School of Biological Sciences; The University of Queensland; Brisbane Queensland 4072 Australia
| | - Lyn G. Cook
- School of Biological Sciences; The University of Queensland; Brisbane Queensland 4072 Australia
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5
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Tiny Plants with Enormous Potential: Phylogeny and Evolution of Duckweeds. THE DUCKWEED GENOMES 2020. [DOI: 10.1007/978-3-030-11045-1_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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6
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Deng N, Hou C, Ma F, Liu C, Tian Y. Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves of Gnetum (Gnetales). Int J Mol Sci 2019; 20:ijms20246350. [PMID: 31861078 PMCID: PMC6941099 DOI: 10.3390/ijms20246350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 01/09/2023] Open
Abstract
The limitations of RNA sequencing make it difficult to accurately predict alternative splicing (AS) and alternative polyadenylation (APA) events and long non-coding RNAs (lncRNAs), all of which reveal transcriptomic diversity and the complexity of gene regulation. Gnetum, a genus with ambiguous phylogenetic placement in seed plants, has a distinct stomatal structure and photosynthetic characteristics. In this study, a full-length transcriptome of Gnetum luofuense leaves at different developmental stages was sequenced with the latest PacBio Sequel platform. After correction by short reads generated by Illumina RNA-Seq, 80,496 full-length transcripts were obtained, of which 5269 reads were identified as isoforms of novel genes. Additionally, 1660 lncRNAs and 12,998 AS events were detected. In total, 5647 genes in the G. luofuense leaves had APA featured by at least one poly(A) site. Moreover, 67 and 30 genes from the bHLH gene family, which play an important role in stomatal development and photosynthesis, were identified from the G. luofuense genome and leaf transcripts, respectively. This leaf transcriptome supplements the reference genome of G. luofuense, and the AS events and lncRNAs detected provide valuable resources for future studies of investigating low photosynthetic capacity of Gnetum.
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Affiliation(s)
- Nan Deng
- Institute of Ecology, Hunan Academy of Forestry, Changsha 410004, China; (N.D.); (F.M.)
- Hunan Cili Forest Ecosystem State Research Station, Cili 417100, China
| | - Chen Hou
- School of life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Fengfeng Ma
- Institute of Ecology, Hunan Academy of Forestry, Changsha 410004, China; (N.D.); (F.M.)
| | - Caixia Liu
- Institute of Ecology, Hunan Academy of Forestry, Changsha 410004, China; (N.D.); (F.M.)
- Correspondence: (C.L.); (Y.T.)
| | - Yuxin Tian
- Institute of Ecology, Hunan Academy of Forestry, Changsha 410004, China; (N.D.); (F.M.)
- Hunan Cili Forest Ecosystem State Research Station, Cili 417100, China
- Correspondence: (C.L.); (Y.T.)
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Rudall PJ, Rice CL. Epidermal patterning and stomatal development in Gnetales. ANNALS OF BOTANY 2019; 124:149-164. [PMID: 31045221 PMCID: PMC6676381 DOI: 10.1093/aob/mcz053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND AND AIMS The gymnosperm order Gnetales, which has contentious phylogenetic affinities, includes three extant genera (Ephedra, Gnetum, Welwitschia) that are morphologically highly divergent and have contrasting ecological preferences: Gnetum occupies mesic tropical habitats, whereas Ephedra and Welwitschia occur in arid environments. Leaves are highly reduced in Ephedra, petiolate with a broad lamina in Gnetum and persistent and strap-like in Welwitschia. We investigate stomatal development and prepatterning stages in Gnetales, to evaluate the substantial differences among the three genera and compare them with other seed plants. METHODS Photosynthetic organs of representative species were examined using light microscopy, scanning electron microscopy and transmission electron microscopy. KEY RESULTS Stomata of all three genera possess lateral subsidiary cells (LSCs). LSCs of Ephedra are perigene cells derived from cell files adjacent to the stomatal meristemoids. In contrast, LSCs of Gnetum and Welwitschia are mesogene cells derived from the stomatal meristemoids; each meristemoid undergoes two mitoses to form a 'developmental triad', of which the central cell is the guard mother cell and the lateral pair are LSCs. Epidermal prepatterning in Gnetum undergoes a 'quartet' phase, in contrast with the linear development of Welwitschia. Quartet prepatterning in Gnetum resembles that of some angiosperms but they differ in later development. CONCLUSIONS Several factors underpin the profound and heritable differences observed among the three genera of Gnetales. Stomatal development in Ephedra differs significantly from that of Gnetum and Welwitschia, more closely resembling that of other extant gymnosperms. Differences in epidermal prepatterning broadly reflect differences in growth habit between the three genera.
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Affiliation(s)
| | - Callie L Rice
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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Widhelm TJ, Grewe F, Huang JP, Mercado-Díaz JA, Goffinet B, Lücking R, Moncada B, Mason-Gamer R, Lumbsch HT. Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota). Sci Rep 2019; 9:8968. [PMID: 31222061 PMCID: PMC6586878 DOI: 10.1038/s41598-019-45455-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 06/03/2019] [Indexed: 12/19/2022] Open
Abstract
In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
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Affiliation(s)
- Todd J Widhelm
- Field Museum, Science and Education, Chicago, 60605, USA.
- University of Illinois at Chicago, Biological Sciences, Chicago, 60607, USA.
| | - Felix Grewe
- Field Museum, Grainger Bioinformatics Center, Chicago, 60605, USA
| | - Jen-Pan Huang
- Field Museum, Science and Education, Chicago, 60605, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Bernard Goffinet
- University of Connecticut, Ecology and Evolutionary Biology, Storrs, 06268, USA
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Herbarium, Berlin, 14195, Germany
| | - Bibiana Moncada
- Universidad Distrital Francisco José de Caldas, Torre de Laboratorios, Herbario, Bogotá, 11021, Colombia
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9
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Caetano DS, O'Meara BC, Beaulieu JM. Hidden state models improve state-dependent diversification approaches, including biogeographical models. Evolution 2018; 72:2308-2324. [DOI: 10.1111/evo.13602] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/20/2018] [Accepted: 08/27/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Daniel S. Caetano
- Department of Biological Sciences; University of Arkansas; Fayetteville Arkansas 72701
| | - Brian C. O'Meara
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville Tennessee 37996-1610
| | - Jeremy M. Beaulieu
- Department of Biological Sciences; University of Arkansas; Fayetteville Arkansas 72701
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10
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Rothwell GW, Millay MA, Stockey RA. Resolving the overall pattern of marattialean fern phylogeny. AMERICAN JOURNAL OF BOTANY 2018; 105:1304-1314. [PMID: 30001474 DOI: 10.1002/ajb2.1115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/12/2018] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Recent clarification of the distribution of Marattiales through time provides the impetus for "total evidence" phylogenetic analyses of a major fern clade with a rich fossil record. These analyses serve as empirical tests for results from systematic analyses of living species and also of the belief that relationships among living species accurately reflect the overall pattern of phylogeny for clades with an extensive fossil record and a large percentage of extinction. METHODS Species of living and fossil Marattiaceae are analyzed employing a "total evidence approach" via maximum parsimony. Analyses were conducted using TNT implemented through WinClada. KEY RESULTS Systematic analyses of living species and of living + extinct species provide roughly concordant topologies for living taxa. However, living species of Marattiales are only one component of a much larger clade with two major subclades. One consists of Psaroniaceae and extends through time to at least the Early Cretaceous. The other consists of Marattiaceae and includes all living species. Various analyses support the generic-level clades of living species from earlier analyses, but the arrangement of such clades varies from analysis to analysis. CONCLUSIONS Marattiales is a monophyletic group that is extremely common in late Paleozoic and early Mesozoic deposits, with a stem group Psaroniaceae and a crown group Marattiaceae. Because Marattiaceae represents only a small component of overall marattialean diversity, living species alone neither account for evolutionary changes within the clade over time, nor accurately reflect the overall pattern of marattialean fern phylogeny.
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Affiliation(s)
- Gar W Rothwell
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - Michael A Millay
- Department of Environmental and Plant Biology, Ohio University Southern, Ironton, OH, 45638, USA
| | - Ruth A Stockey
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA
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11
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Hohmann N, Wolf EM, Rigault P, Zhou W, Kiefer M, Zhao Y, Fu CX, Koch MA. Ginkgo biloba's footprint of dynamic Pleistocene history dates back only 390,000 years ago. BMC Genomics 2018; 19:299. [PMID: 29703145 PMCID: PMC5921299 DOI: 10.1186/s12864-018-4673-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND At the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as sanctuary for Tertiary relict trees. Yet the status of these regions as refuge areas with naturally existing populations has been proven not earlier than one decade ago. Herein we elaborated the hypothesis that during the Pleistocene cooling periods G. biloba expanded its distribution range in China repeatedly. Whole plastid genomes were sequenced, assembled and annotated, and sequence data was analyzed in a phylogenetic framework of the entire gymnosperms to establish a robust spatio-temporal framework for gymnosperms and in particular for G. biloba Pleistocene evolutionary history. RESULTS Using a phylogenetic approach, we identified that Ginkgoatae stem group age is about 325 million years, whereas crown group radiation of extant Ginkgo started not earlier than 390,000 years ago. During repeated warming phases, Gingko populations were separated and isolated by contraction of distribution range and retreated into mountainous regions serving as refuge for warm-temperate deciduous forests. Diversification and phylogenetic splits correlate with the onset of cooling phases when Ginkgo expanded its distribution range and gene pools merged. CONCLUSIONS Analysis of whole plastid genome sequence data representing the entire spatio-temporal genetic variation of wild extant Ginkgo populations revealed the deepest temporal footprint dating back to approximately 390,000 years ago. Present-day directional West-East admixture of genetic diversity is shown to be the result of pronounced effects of the last cooling period. Our evolutionary framework will serve as a conceptual roadmap for forthcoming genomic sequence data, which can then provide deep insights into the demographic history of Ginkgo.
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Affiliation(s)
- Nora Hohmann
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.,Present address: Department of Environmental Sciences, Botany, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Eva M Wolf
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany
| | - Philippe Rigault
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.,GYDLE Inc., 1135 Grande Allée Ouest, Suite 220, QC, Québec, G1S 1E7, Canada
| | - Wenbin Zhou
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Markus Kiefer
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany
| | - Yunpeng Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Cheng-Xin Fu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Marcus A Koch
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.
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Abstract
Driven by limited resources and a sense of urgency, the prioritization of species for conservation has been a persistent concern in conservation science. Gymnosperms (comprising ginkgo, conifers, cycads, and gnetophytes) are one of the most threatened groups of living organisms, with 40% of the species at high risk of extinction, about twice as many as the most recent estimates for all plants (i.e. 21.4%). This high proportion of species facing extinction highlights the urgent action required to secure their future through an objective prioritization approach. The Evolutionary Distinct and Globally Endangered (EDGE) method rapidly ranks species based on their evolutionary distinctiveness and the extinction risks they face. EDGE is applied to gymnosperms using a phylogenetic tree comprising DNA sequence data for 85% of gymnosperm species (923 out of 1090 species), to which the 167 missing species were added, and IUCN Red List assessments available for 92% of species. The effect of different extinction probability transformations and the handling of IUCN data deficient species on the resulting rankings is investigated. Although top entries in our ranking comprise species that were expected to score well (e.g. Wollemia nobilis, Ginkgo biloba), many were unexpected (e.g. Araucaria araucana). These results highlight the necessity of using approaches that integrate evolutionary information in conservation science.
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13
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Gitzendanner MA, Soltis PS, Wong GKS, Ruhfel BR, Soltis DE. Plastid phylogenomic analysis of green plants: A billion years of evolutionary history. AMERICAN JOURNAL OF BOTANY 2018; 105:291-301. [PMID: 29603143 DOI: 10.1002/ajb2.1048] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/13/2017] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY For the past one billion years, green plants (Viridiplantae) have dominated global ecosystems, yet many key branches in their evolutionary history remain poorly resolved. Using the largest analysis of Viridiplantae based on plastid genome sequences to date, we examined the phylogeny and implications for morphological evolution at key nodes. METHODS We analyzed amino acid sequences from protein-coding genes from complete (or nearly complete) plastomes for 1879 taxa, including representatives across all major clades of Viridiplantae. Much of the data used was derived from transcriptomes from the One Thousand Plants Project (1KP); other data were taken from GenBank. KEY RESULTS Our results largely agree with previous plastid-based analyses. Noteworthy results include (1) the position of Zygnematophyceae as sister to land plants (Embryophyta), (2) a bryophyte clade (hornworts, mosses + liverworts), (3) Equisetum + Psilotaceae as sister to Marattiales + leptosporangiate ferns, (4) cycads + Ginkgo as sister to the remaining extant gymnosperms, within which Gnetophyta are placed within conifers as sister to non-Pinaceae (Gne-Cup hypothesis), and (5) Amborella, followed by water lilies (Nymphaeales), as successive sisters to all other extant angiosperms. Within angiosperms, there is support for Mesangiospermae, a clade that comprises magnoliids, Chloranthales, monocots, Ceratophyllum, and eudicots. The placements of Ceratophyllum and Dilleniaceae remain problematic. Within Pentapetalae, two major clades (superasterids and superrosids) are recovered. CONCLUSIONS This plastid data set provides an important resource for elucidating morphological evolution, dating divergence times in Viridiplantae, comparisons with emerging nuclear phylogenies, and analyses of molecular evolutionary patterns and dynamics of the plastid genome.
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Affiliation(s)
- Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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14
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Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ, Lohaus R, Liu ZJ, Xin HP, Gong YB, Liu Y, Wang WC, Chen LY, Yang Y, Kelly LJ, Yang J, Huang JL, Li Z, Liu P, Zhang L, Liu HM, Wang H, Deng SH, Liu M, Li J, Ma L, Liu Y, Lei Y, Xu W, Wu LQ, Liu F, Ma Q, Yu XR, Jiang Z, Zhang GQ, Li SH, Li RQ, Zhang SZ, Wang QF, Van de Peer Y, Zhang JB, Wang XM. A genome for gnetophytes and early evolution of seed plants. NATURE PLANTS 2018; 4:82-89. [PMID: 29379155 DOI: 10.1038/s41477-017-0097-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 12/27/2017] [Indexed: 05/07/2023]
Abstract
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms.
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Affiliation(s)
- Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
| | - Zhi-Ming Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ling-Fei Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China
| | - Hai-Ping Xin
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Wen-Cai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ling-Yun Chen
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ji Yang
- Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Jin-Ling Huang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ping Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Li Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Hong-Mei Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Hui Wang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Shu-Han Deng
- Novogene Bioinformatics Institute, Beijing, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ji Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yan Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yang Lei
- Novogene Bioinformatics Institute, Beijing, China
| | - Wei Xu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ling-Qing Wu
- Novogene Bioinformatics Institute, Beijing, China
| | - Fan Liu
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
| | - Qian Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xin-Ran Yu
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui-Qiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China.
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Centre for Plant Systems Biology, VIB, Ghent, Belgium.
- Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
| | - Jin-Bo Zhang
- Novogene Bioinformatics Institute, Beijing, China.
| | - Xiao-Ming Wang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
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15
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Barker MS. A Gneato nuclear genome. NATURE PLANTS 2018; 4:63-64. [PMID: 29379154 DOI: 10.1038/s41477-018-0102-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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16
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Li Z, De La Torre AR, Sterck L, Cánovas FM, Avila C, Merino I, Cabezas JA, Cervera MT, Ingvarsson PK, Van de Peer Y. Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants. Genome Biol Evol 2017; 9:1130-1147. [PMID: 28460034 PMCID: PMC5414570 DOI: 10.1093/gbe/evx070] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2017] [Indexed: 01/02/2023] Open
Abstract
Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.
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Affiliation(s)
- Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium
| | - Amanda R De La Torre
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Sciences, University of California-Davis, Davis, CA
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, Málaga, Spain
| | - Concepción Avila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, Málaga, Spain
| | - Irene Merino
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | | | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium.,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, South Africa
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17
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Gachet MS, Schubert A, Calarco S, Boccard J, Gertsch J. Targeted metabolomics shows plasticity in the evolution of signaling lipids and uncovers old and new endocannabinoids in the plant kingdom. Sci Rep 2017; 7:41177. [PMID: 28120902 PMCID: PMC5264637 DOI: 10.1038/srep41177] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/16/2016] [Indexed: 12/28/2022] Open
Abstract
The remarkable absence of arachidonic acid (AA) in seed plants prompted us to systematically study the presence of C20 polyunsaturated fatty acids, stearic acid, oleic acid, jasmonic acid (JA), N-acylethanolamines (NAEs) and endocannabinoids (ECs) in 71 plant species representative of major phylogenetic clades. Given the difficulty of extrapolating information about lipid metabolites from genetic data we employed targeted metabolomics using LC-MS/MS and GC-MS to study these signaling lipids in plant evolution. Intriguingly, the distribution of AA among the clades showed an inverse correlation with JA which was less present in algae, bryophytes and monilophytes. Conversely, ECs co-occurred with AA in algae and in the lower plants (bryophytes and monilophytes), thus prior to the evolution of cannabinoid receptors in Animalia. We identified two novel EC-like molecules derived from the eicosatetraenoic acid juniperonic acid, an omega-3 structural isomer of AA, namely juniperoyl ethanolamide and 2-juniperoyl glycerol in gymnosperms, lycophytes and few monilophytes. Principal component analysis of the targeted metabolic profiles suggested that distinct NAEs may occur in different monophyletic taxa. This is the first report on the molecular phylogenetic distribution of apparently ancient lipids in the plant kingdom, indicating biosynthetic plasticity and potential physiological roles of EC-like lipids in plants.
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Affiliation(s)
- María Salomé Gachet
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Alexandra Schubert
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Serafina Calarco
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Julien Boccard
- School of Pharmaceutical Science, University of Geneva, University of Lausanne, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
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18
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Rothwell GW, Stockey RA. Phylogenetic diversification of Early Cretaceous seed plants: The compound seed cone of Doylea tetrahedrasperma. AMERICAN JOURNAL OF BOTANY 2016; 103:923-937. [PMID: 27208360 DOI: 10.3732/ajb.1600030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 03/07/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Discovery of cupulate ovules of Doylea tetrahedrasperma within a compact, compound seed cone highlights the rich diversity of fructification morphologies, pollination biologies, postpollination enclosure of seeds, and systematic diversity of Early Cretaceous gymnosperms. METHODS Specimens were studied using the cellulose acetate peel technique, three-dimensional reconstructions (in AVIZO), and morphological phylogenetic analyses (in TNT). KEY RESULTS Doylea tetrahedrasperma has bract/fertile short shoot complexes helically arranged within a compact, compound seed cone. Complexes diverge from the axis as a single unit and separate distally into a free bract tip and two sporophylls. Each sporophyll bears a single, abaxial seed, recurved toward the cone axis, that is enveloped after pollinaton by sporophyll tissue, forming a closed cupule. Ovules are pollinated by bisaccate grains captured by micropylar pollination horns. CONCLUSIONS The unique combination of characters shown by D. tetrahedrasperma includes the presence of cupulate seeds borne in conifer-like compound seed cones, an ovuliferous scale analogue structurally equivalent to the ovulate stalk of Ginkgo biloba, gymnospermous pollination, and nearly complete enclosure of mature seeds. These features characterize the Doyleales ord. nov., clearly distinguish it from the seed fern order Corystospermales, and allow for recognition of another recently described Early Cretaceous seed plant as a second species in genus Doylea. A morphological phylogenetic analysis highlights systematic relationships of the Doyleales ord. nov. and emphasizes the explosive phylogenetic diversification of gymnosperms that was underway at the time when flowering plants may have originated and/or first began to radiate.
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Affiliation(s)
- Gar W Rothwell
- Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331, USA Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701, USA
| | - Ruth A Stockey
- Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331, USA
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19
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Hou C, Wikström N, Rydin C. The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:330-331. [PMID: 26713841 DOI: 10.3109/19401736.2015.1122768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study presents the chloroplast genome of Ephedra foeminea, an entomophilous gymnosperm, sister to the remaining (wind-pollinated) species of Ephedra (Ephedraceae, Gnetales). Based on the reference-guided assembly, the length of the chloroplast genome was estimated to be 109 584 bp, comprising a large single copy region of 60 027 bp, a small single copy 8079 bp, and inverted repeat regions of 20 739 bp. In total, 118 genes were detected, including 73 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene density is 1.076 (genes/kb) and the GC content is 36.7%. The genomic sequence of the entomophilous, Mediterranean species E. foeminea, differs from that of the anemophilous, Asian species E. equisetina by 1018 point mutations and 1334 indels. The detected variation is useful for future development of new plastid markers for phylogenetic purposes. Our phylogenetic analysis based on 55 protein-coding chloroplast genes resolve Ephedra as monophyletic and sister to a Gnetum-Welwitschia clade. The Gnetales are sister to Cupressophytes.
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Affiliation(s)
- Chen Hou
- a Department of Ecology, Environment and Plant Sciences , Stockholm University , Stockholm , Sweden
| | - Niklas Wikström
- b Bergius Foundation, the Royal Swedish Academy of Sciences and Department of Ecology, Environment and Plant Sciences , Stockholm University , Stockholm , Sweden
| | - Catarina Rydin
- b Bergius Foundation, the Royal Swedish Academy of Sciences and Department of Ecology, Environment and Plant Sciences , Stockholm University , Stockholm , Sweden
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20
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Jud NA. Fossil evidence for a herbaceous diversification of early eudicot angiosperms during the Early Cretaceous. Proc Biol Sci 2015; 282:20151045. [PMID: 26336172 PMCID: PMC4571693 DOI: 10.1098/rspb.2015.1045] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 08/12/2015] [Indexed: 11/12/2022] Open
Abstract
Eudicot flowering plants comprise roughly 70% of land plant species diversity today, but their early evolution is not well understood. Fossil evidence has been largely restricted to their distinctive tricolpate pollen grains and this has limited our understanding of the ecological strategies that characterized their primary radiation. I describe megafossils of an Early Cretaceous eudicot from the Potomac Group in Maryland and Virginia, USA that are complete enough to allow reconstruction of important life-history traits. I draw on quantitative and qualitative analysis of functional traits, phylogenetic analysis and sedimentological evidence to reconstruct the biology of this extinct species. These plants were small and locally rare but widespread, fast-growing herbs. They had complex leaves and they were colonizers of bright, wet, disturbance-prone habitats. Other early eudicot megafossils appear to be herbaceous rather than woody, suggesting that this habit was characteristic of their primary radiation. A mostly herbaceous initial diversification of eudicots could simultaneously explain the heretofore sparse megafossil record as well as their rapid diversification during the Early Cretaceous because the angiosperm capacity for fast reproduction and fast evolution is best expressed in herbs.
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Affiliation(s)
- Nathan A Jud
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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21
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Ma L, Hatlen A, Kelly LJ, Becher H, Wang W, Kovarik A, Leitch IJ, Leitch AR. Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway. Genome Biol Evol 2015; 7:2648-62. [PMID: 26338185 PMCID: PMC4607528 DOI: 10.1093/gbe/evv171] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The RNA-directed DNA methylation (RdDM) pathway can be divided into three phases: 1) small interfering RNA biogenesis, 2) de novo methylation, and 3) chromatin modification. To determine the degree of conservation of this pathway we searched for key genes among land plants. We used OrthoMCL and the OrthoMCL Viridiplantae database to analyze proteomes of species in bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms. We also analyzed small RNA size categories and, in two gymnosperms, cytosine methylation in ribosomal DNA. Six proteins were restricted to angiosperms, these being NRPD4/NRPE4, RDM1, DMS3 (defective in meristem silencing 3), SHH1 (SAWADEE homeodomain homolog 1), KTF1, and SUVR2, although we failed to find the latter three proteins in Fritillaria persica, a species with a giant genome. Small RNAs of 24 nt in length were abundant only in angiosperms. Phylogenetic analyses of Dicer-like (DCL) proteins showed that DCL2 was restricted to seed plants, although it was absent in Gnetum gnemon and Welwitschia mirabilis. The data suggest that phases (1) and (2) of the RdDM pathway, described for model angiosperms, evolved with angiosperms. The absence of some features of RdDM in F. persica may be associated with its large genome. Phase (3) is probably the most conserved part of the pathway across land plants. DCL2, involved in virus defense and interaction with the canonical RdDM pathway to facilitate methylation of CHH, is absent outside seed plants. Its absence in G. gnemon, and W. mirabilis coupled with distinctive patterns of CHH methylation, suggest a secondary loss of DCL2 following the divergence of Gnetales.
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Affiliation(s)
- Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Andrea Hatlen
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
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22
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Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms. Syst Biol 2015; 64:869-78. [DOI: 10.1093/sysbio/syv027] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/28/2015] [Indexed: 11/14/2022] Open
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23
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Trembath-Reichert E, Wilson JP, McGlynn SE, Fischer WW. Four hundred million years of silica biomineralization in land plants. Proc Natl Acad Sci U S A 2015; 112:5449-54. [PMID: 25825729 PMCID: PMC4418875 DOI: 10.1073/pnas.1500289112] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biomineralization plays a fundamental role in the global silicon cycle. Grasses are known to mobilize significant quantities of Si in the form of silica biominerals and dominate the terrestrial realm today, but they have relatively recent origins and only rose to taxonomic and ecological prominence within the Cenozoic Era. This raises questions regarding when and how the biological silica cycle evolved. To address these questions, we examined silica abundances of extant members of early-diverging land plant clades, which show that silica biomineralization is widespread across terrestrial plant linages. Particularly high silica abundances are observed in lycophytes and early-diverging ferns. However, silica biomineralization is rare within later-evolving gymnosperms, implying a complex evolutionary history within the seed plants. Electron microscopy and X-ray spectroscopy show that the most common silica-mineralized tissues include the vascular system, epidermal cells, and stomata, which is consistent with the hypothesis that biomineralization in plants is frequently coupled to transpiration. Furthermore, sequence, phylogenetic, and structural analysis of nodulin 26-like intrinsic proteins from diverse plant genomes points to a plastic and ancient capacity for silica accumulation within terrestrial plants. The integration of these two comparative biology approaches demonstrates that silica biomineralization has been an important process for land plants over the course of their >400 My evolutionary history.
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Affiliation(s)
| | | | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125; Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
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24
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Cardoso GC, Cortesão M, García C. Ecological Marginalization Facilitated Diversification in Conifers. Evol Biol 2015. [DOI: 10.1007/s11692-015-9306-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Friedman WE. Development and evolution of the female gametophyte and fertilization process in Welwitschia mirabilis (Welwitschiaceae). AMERICAN JOURNAL OF BOTANY 2015; 102:312-24. [PMID: 25667083 DOI: 10.3732/ajb.1400472] [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] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY The female gametophyte of Welwitschia has long been viewed as highly divergent from other members of the Gnetales and, indeed, all other seed plants. However, the formation of female gametes and the process of fertilization have never been observed. METHODS Standard histological techniques were applied to study gametophyte development and the fertilization process in Welwitschia. KEY RESULTS In Welwitschia, fertilization events occur when pollen tubes with binucleate sperm cells grow down through the nucellus and encounter prothallial tubes, free nuclear tubular extensions of the micropylar end of the female gametophyte that grow up through the nucellus. Entry of a binucleate sperm cell into a vacuolate prothallial tube appears to stimulate the rapid coagulation of cytoplasm around a single female nucleus, which differentiates into an egg cell. One sperm nucleus enters the female gamete, while the second sperm nucleus remains outside and ultimately degenerates. Only a single fertilization event occurs per mating pair of pollen tube and prothallial tube. CONCLUSIONS Welwitschia lacks the gnetalean pattern of regular double fertilization, as found in Ephedra and Gnetum, involving sperm from a single pollen tube to yield two zygotes. Moreover, an analysis of character evolution indicates that the female gametophyte of Welwitschia is highly apomorphic both among seed plants, and specifically within Gnetales, but also shares several key synapomorphies with its sister taxon Gnetum. Finally, the biological role of prothallial tubes in Welwitschia is examined from the perspectives of gamete competition and kin conflict.
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Affiliation(s)
- William E Friedman
- Department of Organismic and Evolutionary Biology, 26 Oxford Street, Harvard University, Cambridge, Massachusetts 02138 USA; and Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, Massachusetts 02131 USA
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Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GKS, Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A 2014; 111:E4859-68. [PMID: 25355905 PMCID: PMC4234587 DOI: 10.1073/pnas.1323926111] [Citation(s) in RCA: 767] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
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Affiliation(s)
- Norman J Wickett
- Chicago Botanic Garden, Glencoe, IL 60022; Program in Biological Sciences, Northwestern University, Evanston, IL 60208;
| | - Siavash Mirarab
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Nam Nguyen
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Tandy Warnow
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Naim Matasci
- iPlant Collaborative, Tucson, AZ 85721; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Matthew A Gitzendanner
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611
| | - Brad R Ruhfel
- Department of Biology and Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475; Florida Museum of Natural History, Gainesville, FL 32611
| | - Eric Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | - Joshua P Der
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | | | - Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, MA 02138
| | | | - Douglas E Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | - Pamela S Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | | | - Carl J Rothfels
- Department of Biology, Duke University, Durham, NC 27708; Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Lisa Pokorny
- Department of Biology, Duke University, Durham, NC 27708; Department of Biodiversity and Conservation, Real Jardín Botánico-Consejo Superior de Investigaciones Cientificas, 28014 Madrid, Spain
| | | | | | | | - Barbara Surek
- Botanical Institute, Universität zu Köln, Cologne D-50674, Germany
| | - Juan Carlos Villarreal
- Department fur Biologie, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universitat, 80638 Munich, Germany
| | - Béatrice Roure
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7
| | - Hervé Philippe
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7; CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | | | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
| | - Toni M Kutchan
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | | | - Jun Wang
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Yong Zhang
- CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | - Zhijian Tian
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Zhixiang Yan
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiaolei Wu
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiao Sun
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9; BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1
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Evolution and biogeography of gymnosperms. Mol Phylogenet Evol 2014; 75:24-40. [DOI: 10.1016/j.ympev.2014.02.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022]
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Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol 2014; 14:23. [PMID: 24533922 PMCID: PMC3933183 DOI: 10.1186/1471-2148-14-23] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 01/13/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. RESULTS We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. CONCLUSIONS Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.
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Affiliation(s)
- Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475, USA
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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Gernandt DS, Pérez-de la Rosa JA. Biodiversidad de Pinophyta (coníferas) en México. REV MEX BIODIVERS 2014. [DOI: 10.7550/rmb.32195] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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On the origin and evolution of plant brassinosteroid receptor kinases. J Mol Evol 2013; 78:118-29. [PMID: 24370731 DOI: 10.1007/s00239-013-9609-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/18/2013] [Indexed: 12/19/2022]
Abstract
Brassinosteroid (BR) signaling pathway is so far the best-understood receptor-kinase signaling pathway in plants. In Arabidopsis, the activation of this pathway requires binding of BRs to the receptor kinase BRASSINOSTEROID-INSENSITIVE I (AtBRI1). Although the function of AtBRI1 has been extensively studied, it is not known when the binding function emerged and how this important component of BR signaling pathway and related genes (the BRI1-BRL gene family) have evolved in plants. We define BRI1-BRL genes in sequenced plant genomes, construct profiles for critical protein domains, scan them against all accessible plant gene/EST resources, and reveal the evolution of domain configuration of this family. We also investigate its evolutionary pattern through phylogenetic analysis. The complete BR receptor domain configuration originates through two domain gain events in the ancestral receptor-like kinase: first juxtamembrane domain gained during the early diversification of land plants, and then island domain (ID) acquired in the common ancestor of angiosperms and gymnosperms after its divergence from spike moss. The 70 amino acid ID has characteristic sequences of BRI1-BRL family and this family keeps relative stable copy numbers during the history of angiosperms and the majority of duplications and losses have occurred in terminal taxa in current taxon sampling. This study reveals important events shaping structural and functional characteristics of plant BR receptors. It answers the question of how and when BR receptors originates, which provide insights into the origin and evolution of the BR signaling pathway.
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31
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Leslie AB, Glasspool I, Herendeen PS, Ichinnorov N, Knopf P, Takahashi M, Crane PR. Pinaceae-like reproductive morphology in Schizolepidopsis canicularis sp. nov. from the Early Cretaceous (Aptian-Albian) of Mongolia. AMERICAN JOURNAL OF BOTANY 2013; 100:2426-2436. [PMID: 24285570 DOI: 10.3732/ajb.1300173] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Seed cone scales assigned to the genus Schizolepidopsis are widespread in Late Triassic to Cretaceous Eurasian deposits. They have been linked to the conifer family Pinaceae based on associated vegetative remains, but their exact affinities are uncertain. Recently discovered material from the Early Cretaceous of Mongolia reveals important new information concerning Schizolepidopsis cone scales and seeds, and provides support for a relationship between the genus and extant Pinaceae. METHODS Specimens were collected from Early Cretaceous (probable Aptian-Albian) lignite deposits in central Mongolia. Lignite samples were disaggregated, cleaned in hydrofluoric acid, and washed in water. Specimens were selected for further study using light and electron microscopy. KEY RESULTS Schizolepidopsis canicularis seed cones consist of loosely arranged, bilobed ovulate scales subtended by a small bract. A single inverted seed with an elongate micropyle is borne on each lobe of the ovulate scale. Each seed has a wing formed by the separation of the adaxial surface of the ovulate scale. CONCLUSIONS Schizolepidopsis canicularis produced winged seeds that formed in a manner that is unique to Pinaceae among extant conifers. We do not definitively place this species in Pinaceae pending more complete information concerning its pollen cones and vegetative remains. Nevertheless, this material suggests that Schizolepidopsis may be important for understanding the early evolution of Pinaceae, and may potentially help reconcile the appearance of the family in the fossil record with results based on phylogenetic analyses of molecular data.
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Affiliation(s)
- Andrew B Leslie
- Yale School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, Connecticut 06511 USA
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32
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Xi Z, Rest JS, Davis CC. Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS One 2013; 8:e80870. [PMID: 24278335 PMCID: PMC3836751 DOI: 10.1371/journal.pone.0080870] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 10/15/2013] [Indexed: 12/29/2022] Open
Abstract
The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods.
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Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Joshua S. Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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Little SA, Jacobs B, McKechnie SJ, Cooper RL, Christianson ML, Jernstedt JA. Branch architecture in Ginkgo biloba: wood anatomy and long shoot-short shoot interactions. AMERICAN JOURNAL OF BOTANY 2013; 100:1923-1935. [PMID: 24061214 DOI: 10.3732/ajb.1300123] [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: 06/02/2023]
Abstract
PREMISE Ginkgo, centrally placed in seed plant phylogeny, is considered important in many phylogenetic and evolutionary studies. Shoot dimorphism of Ginkgo has been long noted, but no work has yet been done to evaluate the relationships between overall branch architecture and wood ring characters, shoot growth, and environmental conditions. • METHODS Branches, sampled from similar canopy heights, were mapped with the age of each long shoot segment determined by counting annual leaf-scar series on its short shoots. Transverse sections were made for each long shoot segment and an adjacent short shoot; wood ring thickness, number of rings, and number of tracheids/ring were determined. Using branch maps, we identified wood rings for each long shoot segment to year and developmental context of each year (distal short shoot growth only vs. at least one distal long shoot). Climate data were also analyzed in conjunction with developmental context. • KEY RESULTS Significantly thicker wood rings occur in years with distal long shoot development. The likelihood that a branch produced long shoots in a given year was lower with higher maximum annual temperature. Annual maximum temperature was negatively correlated with ring thickness in microsporangiate trees only. Annual minimum temperatures were correlated differently with ring thickness of megasporangiate and microsporangiate trees, depending on the developmental context. There were no significant effects associated with precipitation. • CONCLUSIONS Overall, developmental context alone predicts wood ring thickness about as well as models that include temperature. This suggests that although climatic factors may be strongly correlated with wood ring data among many gymnosperm taxa, at least for Ginkgo, correlations with climate data are primarily due to changes in proportions of shoot developmental types (LS vs. SS) across branches.
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Affiliation(s)
- Stefan A Little
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, California 95616, USA
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Marazzi B, Bronstein JL, Koptur S. The diversity, ecology and evolution of extrafloral nectaries: current perspectives and future challenges. ANNALS OF BOTANY 2013; 111:1243-50. [PMID: 23704115 PMCID: PMC3662527 DOI: 10.1093/aob/mct109] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plants in over one hundred families in habitats worldwide bear extrafloral nectaries (EFNs). EFNs display a remarkable diversity of evolutionary origins, as well as diverse morphology and location on the plant. They secrete extrafloral nectar, a carbohydrate-rich food that attracts ants and other arthropods, many of which protect the plant in return. By fostering ecologically important protective mutualisms, EFNs play a significant role in structuring both plant and animal communities. And yet researchers are only now beginning to appreciate their importance and the range of ecological, evolutionary and morphological diversity that EFNs exhibit. SCOPE This Highlight features a series of papers that illustrate some of the newest directions in the study of EFNs. Here, we introduce this set of papers by providing an overview of current understanding and new insights on EFN diversity, ecology and evolution. We highlight major gaps in our current knowledge, and outline future research directions. CONCLUSIONS Our understanding of the roles EFNs play in plant biology is being revolutionized with the use of new tools from developmental biology and genomics, new modes of analysis allowing hypothesis-testing in large-scale phylogenetic frameworks, and new levels of inquiry extending to community-scale interaction networks. But many central questions remain unanswered; indeed, many have not yet been asked. Thus, the EFN puzzle remains an intriguing challenge for the future.
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Affiliation(s)
- Brigitte Marazzi
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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Zimmer EA, Wen J. Reprint of: using nuclear gene data for plant phylogenetics: progress and prospects. Mol Phylogenet Evol 2013; 66:539-50. [PMID: 23375140 DOI: 10.1016/j.ympev.2013.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022]
Abstract
The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.
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Affiliation(s)
- Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation. Heredity (Edinb) 2013; 111:23-33. [PMID: 23512008 PMCID: PMC3692318 DOI: 10.1038/hdy.2013.11] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either
separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA
locus encoding 18S–5.8S–26S genes (L-type arrangement). Here we used Southern
blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA
genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and
Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the
35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo
(∼30% of the species analysed), while the remaining exhibit separate
organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short
tandems embedded in the 26S–18S rDNA intergenic spacer (IGS). The 5S transcript may
be encoded by the same (Ginkgo, Ephedra) or opposite
(Podocarpus) DNA strand as the 18S–5.8S–26S genes. In addition,
pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have
been largely homogenised across the genomes. Phylogenetic relationships based on the
comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at
least three times in the course of gymnosperm evolution. Frequent transpositions and
rearrangements of basic units indicate relatively relaxed selection pressures imposed on
genomic organisation of 5S genes in plants.
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Zimmer EA, Wen J. Using nuclear gene data for plant phylogenetics: Progress and prospects. Mol Phylogenet Evol 2012; 65:774-85. [DOI: 10.1016/j.ympev.2012.07.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 10/28/2022]
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Abstract
Fundamental differences in the distribution of oceans and landmasses in the Northern and Southern Hemispheres potentially impact patterns of biological diversity in the two areas. The evolutionary history of conifers provides an opportunity to explore these dynamics, because the majority of extant conifer species belong to lineages that have been broadly confined to the Northern or Southern Hemisphere during the Cenozoic. Incorporating genetic information with a critical review of fossil evidence, we developed an age-calibrated phylogeny sampling ∼80% of living conifer species. Most extant conifer species diverged recently during the Neogene within clades that generally were established during the later Mesozoic, but lineages that diversified mainly in the Southern Hemisphere show a significantly older distribution of divergence ages than their counterparts in the Northern Hemisphere. Our tree topology and divergence times also are best fit by diversification models in which Northern Hemisphere conifer lineages have higher rates of species turnover than Southern Hemisphere lineages. The abundance of recent divergences in northern clades may reflect complex patterns of migration and range shifts during climatic cycles over the later Neogene leading to elevated rates of speciation and extinction, whereas the scattered persistence of mild, wetter habitats in the Southern Hemisphere may have favored the survival of older lineages.
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Hsieh YSY, Harris PJ. Structures of xyloglucans in primary cell walls of gymnosperms, monilophytes (ferns sensu lato) and lycophytes. PHYTOCHEMISTRY 2012; 79:87-101. [PMID: 22537406 DOI: 10.1016/j.phytochem.2012.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/16/2012] [Accepted: 03/22/2012] [Indexed: 05/02/2023]
Abstract
Little is known about the structures of the xyloglucans in the primary cell walls of vascular plants (tracheophytes) other than angiosperms. Xyloglucan structures were examined in 13 species of gymnosperms, 13 species of monilophytes (ferns sensu lato), and two species of lycophytes. Wall preparations were obtained, extracted with 6 M sodium hydroxide, and the extracts treated with a xyloglucan-specific endo-(1→4)-β-glucanase preparation. The oligosaccharides released were analysed by matrix-assisted laser-desorption ionisation time-of-flight mass spectrometry and by high-performance anion-exchange chromatography. The xyloglucan oligosaccharide profiles from the gymnosperm walls were similar to those from the walls of most eudicotyledons and non-commelinid monocotyledons, indicating that the xyloglucans were fucogalactoxyloglucans, containing the fucosylated units XXFG and XLFG. The xyloglucan oligosaccharide profiles for six of the monilophyte species were similar to those of the gymnosperms, indicating they were also fucogalactoxyloglucans. Phylogenetically, these monilophyte species were from both basal and more derived orders. However, the profiles for the other monilophyte species showed various significant differences, including additional oligosaccharides. In three of the species, these additional oligosaccharides contained arabinosyl residues which were most abundant in the profile of Equisetum hyemale. The two species of lycophytes examined, Selaginella kraussiana and Lycopodium cernuum, had quite different xyloglucan oligosaccharide profiles, but neither were fucogalactoxyloglucans. The S. kraussiana profile had abundant oligosaccharides containing arabinosyl residues. The L. cernuum profile indicated the xyloglucan had a very complex structure.
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Affiliation(s)
- Yves S Y Hsieh
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
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Klymiuk AA, Stockey RA. A lower Cretaceous (Valanginian) seed cone provides the earliest fossil record for Picea (Pinaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:1069-1082. [PMID: 22623610 DOI: 10.3732/ajb.1100568] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF STUDY Sequence analyses for Pinaceae have suggested that extant genera diverged in the late Mesozoic. While the fossil record indicates that Pinaceae was highly diverse during the Cretaceous, there are few records of living genera. This description of an anatomically preserved seed cone extends the fossil record for Picea A. Dietrich (Pinaceae) by ∼75 Ma. METHODS The specimen was collected from the Apple Bay locality of Vancouver Island (Lower Cretaceous, Valanginian) and is described from anatomical sections prepared using cellulose acetate peels. Cladistic analyses of fossil and extant pinaceous seed cones employed parsimony ratchet searches of an anatomical and morphological matrix. KEY RESULTS This new seed cone has a combination of characters shared only with the genus Picea A. Dietr. and is thus described as Picea burtonii Klymiuk et Stockey sp. nov. Bisaccate pollen attributable to Picea is found in the micropyles of several ovules, corroborating the designation of this cone as an early spruce. Cladistic analyses place P. burtonii with extant Picea and an Oligocene representative of the genus. Furthermore, our analyses indicate that Picea is sister to Cathaya Chun et Kuang, and P. burtonii helps to establish a minimum date for this node in hypotheses of conifer phylogeny. CONCLUSIONS As an early member of the extant genus Picea, this seed cone extends the fossil record of Picea to the Valanginian Stage of the Early Cretaceous, ca. 136 Ma, thereby resolving a ghost lineage predicted by molecular divergence analyses, and offers new insight into the evolution of Pinaceae.
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Affiliation(s)
- Ashley A Klymiuk
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta, Canada T6G 2E9.
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Escapa IH, Rothwell GW, Stockey RA, Cúneo NR. Seed cone anatomy of Cheirolepidiaceae (Coniferales): reinterpreting Pararaucaria patagonica Wieland. AMERICAN JOURNAL OF BOTANY 2012; 99:1058-1068. [PMID: 22665438 DOI: 10.3732/ajb.1100544] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Seed cone morphology and anatomy reflect some of the most important changes in the phylogeny and evolutionary biology of conifers. Reexamination of the enigmatic Jurassic seed cone Pararaucaria patagonica reveals previously unknown systematically informative characters that demonstrate affinities with the Cheirolepidiaceae. This paper documents, for the first time, internal anatomy for seed cones of this important extinct Mesozoic conifer family, which may represent the ghost lineage leading to modern Pinaceae. METHODS Morphology and anatomy of cones from the Jurassic La Matilde Formation in Patagonia are described from a combination of polished wafers and thin section preparations. New photographic techniques are employed to reveal histological details of thin sections in which organic cell wall remains are not preserved. Specific terminology for conifer seed cones is proposed to help clarify hypotheses of homology for the various structures of the cones. KEY RESULTS Specimens are demonstrated to have trilobed ovuliferous scale tips along with a seed enclosing pocket of ovuliferous scale tissue. Originally thought to represent a seed wing in P. patagonica, this pocket-forming tissue is comparable to the flap of tissue covering seeds of compressed cheirolepidiaceous cones and is probably the most diagnostic character for seed cones of the family. CONCLUSIONS Pararaucaria patagonica is assigned to Cheirolepidiaceae, documenting anatomical features for seed cones of the family and providing evidence for the antiquity of pinoid conifers leading to the origin of Pinaceae. A list of key morphological and anatomical characters for seed cones of Cheirolepidiaceae is developed to facilitate assignment of a much broader range of fossil remains to the family. This confirms the presence of Cheirolepidiaceae in the Jurassic of the Southern Hemisphere, which was previously suspected from palynological records.
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Affiliation(s)
- Ignacio H Escapa
- CONICET-Museo Paleontologico Egidio Feruglio, Av. Fontana 140, Trelew, Chubut 9100, Argentina.
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Rothwell GW, Mapes G, Stockey RA, Hilton J. The seed cone Eathiestrobus gen. nov.: fossil evidence for a Jurassic origin of Pinaceae. AMERICAN JOURNAL OF BOTANY 2012; 99:708-720. [PMID: 22491001 DOI: 10.3732/ajb.1100595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Pinaceae and nonpinoid species are sister groups within the conifer clade as inferred from molecular systematic comparisons of living species and therefore should have comparable geological ages. However, the fossil record for the nonpinoid lineage of extant conifer families is Triassic, nearly 100 million years older than the oldest widely accepted Lower Cretaceous record for Pinaceae. An anatomically preserved fossil conifer seed cone described here extends the stratigraphic range of Pinaceae nearly 30 million years, thus reducing the apparent discrepancy between evidence from the fossil record and inferences from systematic studies of living species. METHODS Material was prepared as serial thin sections by the cellulose acetate peel technique, mounted on microscope slides, and viewed and photographed using transmitted light. KEY RESULTS A large cylindrical cone consisting of bract-scale complexes that diverge from the cone axis in a helical phyllotaxis has bracts and scales that separate from each other in the midregion and are of equal length and of nearly equal width. The cone has two inverted and winged seeds that are attached to the adaxial surface of each cone scale and, thus, represents an early member of the Pinaceae. CONCLUSIONS Eathiestrobus mackenziei gen. et sp. nov. extends the fossil record for well-documented members of the family Pinaceae from the Lower Cretaceous to the Kimmeridgian Stage of the Upper Jurassic. This species also clarifies the set of characters that are diagnostic for seed cones of Pinaceae and reveals possible plesiomorphic characters for seed cones of the family.
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Affiliation(s)
- Gar W Rothwell
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701, USA.
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Early evolutionary colocalization of the nuclear ribosomal 5S and 45S gene families in seed plants: evidence from the living fossil gymnosperm Ginkgo biloba. Heredity (Edinb) 2012; 108:640-6. [PMID: 22354111 DOI: 10.1038/hdy.2012.2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In seed plants, the colocalization of the 5S loci within the intergenic spacer (IGS) of the nuclear 45S tandem units is restricted to the phylogenetically derived Asteraceae family. However, fluorescent in situ hybridization (FISH) colocalization of both multigene families has also been observed in other unrelated seed plant lineages. Previous work has identified colocalization of 45S and 5S loci in Ginkgo biloba using FISH, but these observations have not been confirmed recently by sequencing a 1.8 kb IGS. In this work, we report the presence of the 45S-5S linkage in G. biloba, suggesting that in seed plants the molecular events leading to the restructuring of the ribosomal loci are much older than estimated previously. We obtained a 6.0 kb IGS fragment showing structural features of functional sequences, and a single copy of the 5S gene was inserted in the same direction of transcription as the ribosomal RNA genes. We also obtained a 1.8 kb IGS that was a truncate variant of the 6.0 kb IGS lacking the 5S gene. Several lines of evidence strongly suggest that the 1.8 kb variants are pseudogenes that are present exclusively on the satellite chromosomes bearing the 45S-5S genes. The presence of ribosomal IGS pseudogenes best reconciles contradictory results concerning the presence or absence of the 45S-5S linkage in Ginkgo. Our finding that both ribosomal gene families have been unified to a single 45S-5S unit in Ginkgo indicates that an accurate reassessment of the organization of rDNA genes in basal seed plants is necessary.
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Tegeder M, Ward JM. Molecular Evolution of Plant AAP and LHT Amino Acid Transporters. FRONTIERS IN PLANT SCIENCE 2012; 3:21. [PMID: 22645574 PMCID: PMC3355764 DOI: 10.3389/fpls.2012.00021] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 01/19/2012] [Indexed: 05/17/2023]
Abstract
Nitrogen is an essential mineral nutrient and it is often transported within living organisms in its reduced form, as amino acids. Transport of amino acids across cellular membranes requires proteins, and here we report the phylogenetic analysis across taxa of two amino acid transporter families, the amino acid permeases (AAPs) and the lysine-histidine-like transporters (LHTs). We found that the two transporter families form two distinct groups in plants supporting the concept that both are essential. AAP transporters seem to be restricted to land plants. They were found in Selaginella moellendorffii and Physcomitrella patens but not in Chlorophyte, Charophyte, or Rhodophyte algae. AAPs were strongly represented in vascular plants, consistent with their major function in phloem (vascular tissue) loading of amino acids for sink nitrogen supply. LHTs on the other hand appeared prior to land plants. LHTs were not found in chlorophyte algae Chlamydomonas reinhardtii and Volvox carterii. However, the characean alga Klebsormidium flaccidum encodes KfLHT13 and phylogenetic analysis indicates that it is basal to land plant LHTs. This is consistent with the hypothesis that characean algae are ancestral to land plants. LHTs were also found in both S. moellendorffii and P. patens as well as in monocots and eudicots. To date, AAPs and LHTs have mainly been characterized in Arabidopsis (eudicots) and these studies provide clues to the functions of the newly identified homologs.
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Affiliation(s)
- Mechthild Tegeder
- School of Biological Sciences, Washington State UniversityPullman, WA, USA
| | - John M. Ward
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
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Sims HJ. The evolutionary diversification of seed size: using the past to understand the present. Evolution 2012; 66:1636-49. [PMID: 22519796 DOI: 10.1111/j.1558-5646.2011.01527.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Devonian origin of seed plants and subsequent morphological diversification of seeds during the late Paleozoic represents an adaptive radiation into unoccupied ecological niche space. A plant's seed size is correlated with its life-history strategy, growth form, and seed dispersal syndrome. The fossil record indicates that the oldest seed plants had relatively small seeds, but the Mississippian seed size envelope increased significantly with the diversification of larger seeded lineages. Fossil seeds equivalent to the largest extant gymnosperm seeds appeared by the Pennsylvanian, concurrent with morphological diversification of growth forms and dispersal syndromes as well as the clade's radiation into new environments. Wang's Analysis of Skewness indicates that the evolutionary trend of increasing seed size resulted from primarily passive processes in Pennsylvanian seed plants. The distributions of modern angiosperms indicate a more diverse system of active and some passive processes, unbounded by Paleozoic limits; multiple angiosperm lineages independently evolved though the upper and lower bounds. Quantitative measures of preservation suggest that, although our knowledge of Paleozoic seeds is far from complete, the evolutionary trend in seed size is unlikely to be an artifact of taphonomy.
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Affiliation(s)
- Hallie J Sims
- Department of Geoscience, University of Iowa, Iowa City, Iowa 52242, USA.
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Jansen RK, Ruhlman TA. Plastid Genomes of Seed Plants. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_5] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, DeSalle R. A functional phylogenomic view of the seed plants. PLoS Genet 2011; 7:e1002411. [PMID: 22194700 PMCID: PMC3240601 DOI: 10.1371/journal.pgen.1002411] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 10/21/2011] [Indexed: 12/01/2022] Open
Abstract
A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.
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Affiliation(s)
- Ernest K. Lee
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Angelica Cibrian-Jaramillo
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Cullman Program in Molecular Systematics, The New York Botanical Garden, Bronx, New York, United States of America
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Sergios-Orestis Kolokotronis
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Manpreet S. Katari
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | | | - Michael Ott
- Department of Computer Science, Technische Universität München, Munich, Germany
| | - Joanna C. Chiu
- Department of Entomology, University of California Davis, Davis, California, United States of America
| | - Damon P. Little
- Cullman Program in Molecular Systematics, The New York Botanical Garden, Bronx, New York, United States of America
| | - Dennis Wm. Stevenson
- Cullman Program in Molecular Systematics, The New York Botanical Garden, Bronx, New York, United States of America
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Gloria Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
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Crisp MD, Cook LG. Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms. THE NEW PHYTOLOGIST 2011; 192:997-1009. [PMID: 21895664 DOI: 10.1111/j.1469-8137.2011.03862.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We test the widely held notion that living gymnosperms are 'ancient' and 'living fossils' by comparing them with their sister group, the angiosperms. This perception derives partly from the lack of gross morphological differences between some Mesozoic gymnosperm fossils and their living relatives (e.g. Ginkgo, cycads and dawn redwood), suggesting that the rate of evolution of gymnosperms has been slow. We estimated the ages and diversification rates of gymnosperm lineages using Bayesian relaxed molecular clock dating calibrated with 21 fossils, based on the phylogenetic analysis of alignments of matK chloroplast DNA (cpDNA) and 26S nuclear ribosomal DNA (nrDNA) sequences, and compared these with published estimates for angiosperms. Gymnosperm crown groups of Cenozoic age are significantly younger than their angiosperm counterparts (median age: 32 Ma vs 50 Ma) and have long unbranched stems, indicating major extinctions in the Cenozoic, in contrast with angiosperms. Surviving gymnosperm genera have diversified more slowly than angiosperms during the Neogene as a result of their higher extinction rate. Compared with angiosperms, living gymnosperm groups are not ancient. The fossil record also indicates that gymnosperms suffered major extinctions when climate changed in the Oligocene and Miocene. Extant gymnosperm groups occupy diverse habitats and some probably survived after making adaptive shifts.
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Affiliation(s)
- Michael D Crisp
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
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Rooting phylogenies using gene duplications: An empirical example from the bees (Apoidea). Mol Phylogenet Evol 2011; 60:295-304. [DOI: 10.1016/j.ympev.2011.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 04/26/2011] [Accepted: 05/03/2011] [Indexed: 12/23/2022]
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