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Tyszka AS, Bretz EC, Robertson HM, Woodcock-Girard MD, Ramanauskas K, Larson DA, Stull GW, Walker JF. Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1125107. [PMID: 37063179 PMCID: PMC10098128 DOI: 10.3389/fpls.2023.1125107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.
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Affiliation(s)
- Alexa S. Tyszka
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Eric C. Bretz
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Holly M. Robertson
- Sainsbury Laboratory, School of Biological Sciences, University of Cambridge, Cambridge, England, United Kingdom
| | - Miles D. Woodcock-Girard
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Karolis Ramanauskas
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Drew A. Larson
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Gregory W. Stull
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Joseph F. Walker
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
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2
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Coiro M, Roberts EA, Hofmann CC, Seyfullah LJ. Cutting the long branches: Consilience as a path to unearth the evolutionary history of Gnetales. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1082639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Gnetales are one of the most fascinating groups within seed plants. Although the advent of molecular phylogenetics has generated some confidence in their phylogenetic placement of Gnetales within seed plants, their macroevolutionary history still presents many unknowns. Here, we review the reasons for such unknowns, and we focus the discussion on the presence of “long branches” both in their molecular and morphological history. The increased rate of molecular evolution and genome instability as well as the numerous unique traits (both reproductive and vegetative) in the Gnetales have been obstacles to a better understanding of their evolution. Moreover, the fossil record of the Gnetales, though relatively rich, has not yet been properly reviewed and investigated using a phylogenetic framework. Despite these apparent blocks to progress we identify new avenues to enable us to move forward. We suggest that a consilience approach, involving different disciplines such as developmental genetics, paleobotany, molecular phylogenetics, and traditional anatomy and morphology might help to “break” these long branches, leading to a deeper understanding of this mysterious group of plants.
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3
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Assembly and Annotation of Red Spruce ( Picea rubens) Chloroplast Genome, Identification of Simple Sequence Repeats, and Phylogenetic Analysis in Picea. Int J Mol Sci 2022; 23:ijms232315243. [PMID: 36499570 PMCID: PMC9739956 DOI: 10.3390/ijms232315243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/11/2022] Open
Abstract
We have sequenced the chloroplast genome of red spruce (Picea rubens) for the first time using the single-end, short-reads (44 bp) Illumina sequences, assembled and functionally annotated it, and identified simple sequence repeats (SSRs). The contigs were assembled using SOAPdenovo2 following the retrieval of chloroplast genome sequences using the black spruce (Picea mariana) chloroplast genome as the reference. The assembled genome length was 122,115 bp (gaps included). Comparatively, the P. rubens chloroplast genome reported here may be considered a near-complete draft. Global genome alignment and phylogenetic analysis based on the whole chloroplast genome sequences of Picea rubens and 10 other Picea species revealed high sequence synteny and conservation among 11 Picea species and phylogenetic relationships consistent with their known classical interrelationships and published molecular phylogeny. The P. rubens chloroplast genome sequence showed the highest similarity with that of P. mariana and the lowest with that of P. sitchensis. We have annotated 107 genes including 69 protein-coding genes, 28 tRNAs, 4 rRNAs, few pseudogenes, identified 42 SSRs, and successfully designed primers for 26 SSRs. Mononucleotide A/T repeats were the most common followed by dinucleotide AT repeats. A similar pattern of microsatellite repeats occurrence was found in the chloroplast genomes of 11 Picea species.
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4
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Wu C, Chaw S. Evolution of mitochondrial RNA editing in extant gymnosperms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1676-1687. [PMID: 35877596 PMCID: PMC9545813 DOI: 10.1111/tpj.15916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 06/01/2023]
Abstract
To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized mitochondrial genomes (mitogenomes), plastid genomes, RNA editing sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four of the five extant gymnosperm clades. The assembled mitogenomes vary in gene content due to massive gene losses in Gnetum and Conifer II clades. Mitochondrial gene expression levels also vary according to protein function, with the most highly expressed genes involved in the respiratory complex. We identified 9132 mitochondrial C-to-U editing sites, as well as 2846 P-class and 8530 PLS-class PPR proteins. Regains of editing sites were demonstrated in Conifer II rps3 transcripts whose corresponding mitogenomic sequences lack introns due to retroprocessing. Our analyses reveal that non-synonymous editing is efficient and results in more codons encoding hydrophobic amino acids. In contrast, synonymous editing, although performed with variable efficiency, can increase the number of U-ending codons that are preferentially utilized in gymnosperm mitochondria. The inferred loss-to-gain ratio of mitochondrial editing sites in gymnosperms is 2.1:1, of which losses of non-synonymous editing are mainly due to genomic C-to-T substitutions. However, such substitutions only explain a small fraction of synonymous editing site losses, indicating distinct evolutionary mechanisms. We show that gymnosperms have experienced multiple lineage-specific duplications in PLS-class PPR proteins. These duplications likely contribute to accumulated RNA editing sites, as a mechanistic correlation between RNA editing and PLS-class PPR proteins is statistically supported.
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Affiliation(s)
- Chung‐Shien Wu
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
| | - Shu‐Miaw Chaw
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
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5
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Liao Y, Liu Z, Gichira AW, Yang M, Mbichi RW, Meng L, Wan T. Deep evaluation of the evolutionary history of the Heat Shock Factor (HSF) gene family and its expansion pattern in seed plants. PeerJ 2022; 10:e13603. [PMID: 35966928 PMCID: PMC9373977 DOI: 10.7717/peerj.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
Heat shock factor (HSF) genes are essential in some of the basic developmental pathways in plants. Despite extensive studies on the structure, functional diversification, and evolution of HSF genes, their divergence history and gene duplication pattern remain unknown. To further illustrate the probable divergence patterns in these subfamilies, we analyzed the evolutionary history of HSF genes using phylogenetic reconstruction and genomic syntenic analyses, taking advantage of the increased sampling of genomic data from pteridophytes, gymnosperms and basal angiosperms. We identified a novel clade that includes HSFA2, HSFA6, HSFA7, and HSFA9 with a complex relationship, which is very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We hypothesized that HSFA9 derives from HSFA2 through gene duplication in eudicots at the ancestral state, and then expanded in a lineage-specific way. Our findings indicate that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in the most recent common ancestors of monocots. We also presumed that HSFC2 derives from HSFC1 in ancestral monocots. This work proposes that during the radiation of flowering plants, an era during which there was a differentiation of angiosperms, the size of the HSF gene family was also being adjusted with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication, gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying the evolutionary history of this multigene family.
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Affiliation(s)
- Yiying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Zhiming Liu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Andrew W. Gichira
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Min Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Ruth Wambui Mbichi
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Linping Meng
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Tao Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
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6
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Yang Y, Ferguson DK, Liu B, Mao KS, Gao LM, Zhang SZ, Wan T, Rushforth K, Zhang ZX. Recent advances on phylogenomics of gymnosperms and a new classification. PLANT DIVERSITY 2022; 44:340-350. [PMID: 35967253 PMCID: PMC9363647 DOI: 10.1016/j.pld.2022.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 05/30/2023]
Abstract
Living gymnosperms comprise four major groups: cycads, Ginkgo, conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes and single-copy nuclear genes, for reconstruction of solid phylogenetic trees. Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics. Here, we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms. This new classification includes three classes (Cycadopsida, Ginkgoopsida, and Pinopsida), five subclasses (Cycadidae, Ginkgoidae, Cupressidae, Pinidae, and Gnetidae), eight orders (Cycadales, Ginkgoales, Araucariales, Cupressales, Pinales, Ephedrales, Gnetales, and Welwitschiales), 13 families, and 86 genera. We also described six new tribes including Acmopyleae Y. Yang, Austrocedreae Y. Yang, Chamaecyparideae Y. Yang, Microcachrydeae Y. Yang, Papuacedreae Y. Yang, and Prumnopityeae Y. Yang, and made 27 new combinations in the genus Sabina.
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Affiliation(s)
- Yong Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, 159 Longpan Road, Nanjing Forestry University, Nanjing 210037, China
| | | | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Kang-Shan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China
| | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, FairyLake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | | | - Zhi-Xiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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7
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Roemer RB, Irene Terry L, Booth DT, Walter GH. Insights from an ancient gymnosperm lineage: ambient temperature and light and the timing of thermogenesis in cycad cones. AMERICAN JOURNAL OF BOTANY 2022; 109:151-165. [PMID: 35025111 DOI: 10.1002/ajb2.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/08/2021] [Indexed: 06/14/2023]
Abstract
PREMISE Although maintaining the appropriate mid-day timing of the diel thermogenic events of cones of the dioecious cycads Macrozamia lucida and M. macleayi is central to the survival of both plant and pollinator in this obligate pollination mutualism, the nature of the underlying mechanism remains obscure. We investigated whether it is under circadian control. Circadian mechanisms control the timing of many ecologically important processes in angiosperms, yet only a few gymnosperms have been studied in this regard. METHODS We subjected cones to different ambient temperature and lighting regimens (constant temperature and darkness; stepwise cool/warm ambient temperatures in constant darkness; stepwise dark/light exposures at constant temperature) to determine whether the resulting timing of their thermogenic events was consistent with circadian control. RESULTS Cones exposed to constant ambient temperature and darkness generated multiple temperature peaks endogenously, with an average interpeak-temperature period of 20.7 (±0.20) h that is temperature-compensated (Q10 = 1.02). Exposure to 24-h ambient temperature cycles (12 h cool/12 h warm, constant darkness) yielded an interpeak-temperature period of 24.0 (±0.05) h, accurately and precisely replicating the ambient temperature period. Exposure to 24-h photo-cycles (12 h light/12 h dark, constant ambient temperature) yielded a shorter, more variable interpeak-temperature period of 23 (±0.23) h. CONCLUSIONS Our results indicate that cycad cone thermogenesis is under circadian clock control and differentially affected by ambient temperature and light cycles. Our data from cycads (an ancient gymnosperm lineage) adds to what little is known about circadian timing in gymnosperms, which have rarely been studied from the circadian perspective.
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Affiliation(s)
- Robert B Roemer
- Department of Mechanical Engineering, University of Utah, 1543 Rio Tinto Kennecott Mechanical Engineering Bldg., 1495 E., 100 S., Salt Lake City, UT, 84112, USA
| | - L Irene Terry
- School of Biological Sciences, University of Utah, 257 S. 1400 E., Salt Lake City, UT, 84112, USA
| | - David T Booth
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Gimme H Walter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
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8
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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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9
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Kordyum EL, Mosyakin SL. Endosperm of Angiosperms and Genomic Imprinting. Life (Basel) 2020; 10:E104. [PMID: 32635326 PMCID: PMC7400472 DOI: 10.3390/life10070104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
Modern ideas about the role of epigenetic systems in the regulation of gene expression allow us to understand the mechanisms of vital activities in plants, such as genomic imprinting. It is important that genomic imprinting is known first and foremost for the endosperm, which not only provides an embryo with necessary nutrients, but also plays a special biological role in the formation of seeds and fruits. Available data on genomic imprinting in the endosperm have been obtained only for the triploid endosperm in model plants, which develops after double fertilization in a Polygonum-type embryo sac, the most common type among angiosperms. Here we provide a brief overview of a wide diversity of embryo sacs and endosperm types and ploidy levels, as well as their distribution in the angiosperm families, positioned according to the Angiosperm Phylogeny Group IV (APG IV) phylogenetic classification. Addition of the new, non-model taxa to study gene imprinting in seed development will extend our knowledge about the epigenetic mechanisms underlying angiosperm fertility.
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Affiliation(s)
- Elizabeth L. Kordyum
- Institute of Botany, National Academy of Sciences of Ukraine, 01004 Kyiv, Ukraine; or
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10
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Salzman S, Crook D, Crall JD, Hopkins R, Pierce NE. An ancient push-pull pollination mechanism in cycads. SCIENCE ADVANCES 2020; 6:eaay6169. [PMID: 32582845 PMCID: PMC7292639 DOI: 10.1126/sciadv.aay6169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 04/17/2020] [Indexed: 05/25/2023]
Abstract
Most cycads engage in brood-site pollination mutualisms, yet the mechanism by which the Cycadales entice pollination services from diverse insect mutualists remains unknown. Here, we characterize a push-pull pollination mechanism between a New World cycad and its weevil pollinators that mirrors the mechanism between a distantly related Old World cycad and its thrips pollinators. The behavioral convergence between weevils and thrips, combined with molecular phylogenetic dating and a meta-analysis of thermogenesis and coordinated patterns of volatile attraction and repulsion suggest that a push-pull pollination mutualism strategy is ancestral in this ancient, dioecious plant group. Hence, it may represent one of the earliest insect/plant pollination mechanisms, arising long before the evolution of visual floral signaling commonly used by flowering plants.
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Affiliation(s)
- Shayla Salzman
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Damon Crook
- USDA-APHIS-PPQ CPHST, Otis Laboratory, Building 1398, Otis ANGB, MA 02542, USA
| | - James D. Crall
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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11
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Herrera F, Shi G, Mays C, Ichinnorov N, Takahashi M, Bevitt JJ, Herendeen PS, Crane PR. Reconstructing Krassilovia mongolica supports recognition of a new and unusual group of Mesozoic conifers. PLoS One 2020; 15:e0226779. [PMID: 31940374 PMCID: PMC6961850 DOI: 10.1371/journal.pone.0226779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/03/2019] [Indexed: 11/19/2022] Open
Abstract
Previously unrecognized anatomical features of the cone scales of the enigmatic Early Cretaceous conifer Krassilovia mongolica include the presence of transversely oriented paracytic stomata, which is unusual for all other extinct and extant conifers. Identical stomata are present on co-occurring broad, linear, multiveined leaves assigned to Podozamites harrisii, providing evidence that K. mongolica and P. harrisii are the seed cones and leaves of the same extinct plant. Phylogenetic analyses of the relationships of the reconstructed Krassilovia plant place it in an informal clade that we name the Krassilovia Clade, which also includes Swedenborgia cryptomerioides-Podozamites schenkii, and Cycadocarpidium erdmanni-Podozamites schenkii. All three of these plants have linear leaves that are relatively broad compared to most living conifers, and that are also multiveined with transversely oriented paracytic stomata. We propose that these may be general features of the Krassilovia Clade. Paracytic stomata, and other features of this new group, recall features of extant and fossil Gnetales, raising questions about the phylogenetic homogeneity of the conifer clade similar to those raised by phylogenetic analyses of molecular data.
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Affiliation(s)
- Fabiany Herrera
- Chicago Botanic Garden, Glencoe, Illinois, United States of America
| | - Gongle Shi
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, People’s Republic of China
| | - Chris Mays
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
- School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria, Australia
| | - Niiden Ichinnorov
- Institute of Paleontology and Geology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Masamichi Takahashi
- Department of Environmental Sciences, Faculty of Science, Niigata University, Nishi-ku, Niigata, Japan
| | - Joseph J. Bevitt
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | | | - Peter R. Crane
- Oak Spring Garden Foundation, Upperville, Virginia, United States of America
- School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut, United States of America
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12
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Smith SA, Walker-Hale N, Walker JF, Brown JW. Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants. Syst Biol 2019; 69:579-592. [DOI: 10.1093/sysbio/syz078] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 10/16/2019] [Accepted: 11/18/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a data set in order to resolve recalcitrant relationships and, importantly, identify what the data set is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant data set. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific data set to address deep phylogenetic relationships while also identifying the inferential boundaries of the data set. [Angiosperms; coalescent; gene-tree conflict; genomics; phylogenetics; phylogenomics.]
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
| | - Nathanael Walker-Hale
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, Cambridge, UK
| | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA
- Sainsbury Laboratory (SLCU), University of Cambrige, Bateman St, Cambridge CB2 1LR, Cambridge, UK
| | - Joseph W Brown
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, Sheffield, UK
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13
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Sudianto E, Chaw SM. Two Independent Plastid accD Transfers to the Nuclear Genome of Gnetum and Other Insights on Acetyl-CoA Carboxylase Evolution in Gymnosperms. Genome Biol Evol 2019; 11:1691-1705. [PMID: 30924880 PMCID: PMC6595918 DOI: 10.1093/gbe/evz059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2019] [Indexed: 12/26/2022] Open
Abstract
Acetyl-CoA carboxylase (ACCase) is the key regulator of fatty acid biosynthesis. In most plants, ACCase exists in two locations (cytosol and plastids) and in two forms (homomeric and heteromeric). Heteromeric ACCase comprises four subunits, three of them (ACCA-C) are nuclear encoded (nr) and the fourth (ACCD) is usually plastid encoded. Homomeric ACCase is encoded by a single nr-gene (ACC). We investigated the ACCase gene evolution in gymnosperms by examining the transcriptomes of newly sequenced Gnetum ula, combined with 75 transcriptomes and 110 plastomes of other gymnosperms. AccD-coding sequences are elongated through the insertion of repetitive DNA in four out of five cupressophyte families (except Sciadopityaceae) and were functionally transferred to the nucleus of gnetophytes and Sciadopitys. We discovered that, among the three genera of gnetophytes, only Gnetum has two copies of nr-accD. Furthermore, using protoplast transient expression assays, we experimentally verified that the nr-accD precursor proteins in Gnetum and Sciadopitys can be delivered to the plastids. Of the two nr-accD copies of Gnetum, one dually targets plastids and mitochondria, whereas the other potentially targets plastoglobuli. The distinct transit peptides, gene architectures, and flanking sequences between the two Gnetum accDs suggest that they have independent origins. Our findings are the first account of two distinctly targeted nr-accDs of any green plants and the most comprehensive analyses of ACCase evolution in gymnosperms to date.
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Affiliation(s)
- Edi Sudianto
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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15
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Abstract
Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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16
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Sello S, Meneghesso A, Alboresi A, Baldan B, Morosinotto T. Plant biodiversity and regulation of photosynthesis in the natural environment. PLANTA 2019; 249:1217-1228. [PMID: 30607502 DOI: 10.1007/s00425-018-03077-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
Investigation of photosynthesis regulation in different plant groups exposed to variable conditions showed that all species have similar photosynthetic electron transport modulation while excess energy dissipation is species specific. Photosynthesis is regulated in response to dynamic environmental conditions to satisfy plant metabolic demands while also avoiding possible over-excitation of the electron transport chain and the generation of harmful reactive oxygen species. Photosynthetic organisms evolved several mechanisms to modulate light harvesting and electron transport efficiency to respond to conditions changing at different timescales, going from fast sun flecks to slow seasonal variations. These regulatory mechanisms changed during evolution of photosynthetic organisms, also adapting to various ecological niches, making the investigation of plant biodiversity highly valuable to uncover conserved traits and plasticity of photosynthetic regulation and complement studies on model species. In this work, a set of plants belonging to different genera of angiosperms, gymnosperms, ferns and lycophytes were investigated by monitoring their photosynthetic parameters in different seasons looking for common trends and differences. In all plants, analysed photosynthetic electron transport rate was found to be modulated by growth light intensity, ensuring a balance between available energy and photochemical capacity. Growth light also influenced the threshold where heat dissipation of excitation energy, a mechanism called non-photochemical quenching (NPQ), was activated. On the contrary, NPQ amplitude did not correlate with light intensity experienced by the plants but was a species-specific feature. The zeaxanthin-dependent component of NPQ, qZ, was found to be the most variable in different plants and its modulation influenced the intensity and the kinetic properties of the response.
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Affiliation(s)
- Simone Sello
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy
- Botanical Garden, University of Padova, 35123, Padua, Italy
| | - Andrea Meneghesso
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy
| | - Alessandro Alboresi
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy
- Botanical Garden, University of Padova, 35123, Padua, Italy
| | - Barbara Baldan
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy
- Botanical Garden, University of Padova, 35123, Padua, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy.
- Botanical Garden, University of Padova, 35123, Padua, Italy.
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17
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Dörken VM, Nimsch H, Rudall PJ. Origin of the Taxaceae aril: evolutionary implications of seed-cone teratologies in Pseudotaxus chienii. ANNALS OF BOTANY 2019; 123:133-143. [PMID: 30137225 PMCID: PMC6344100 DOI: 10.1093/aob/mcy150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/20/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Fleshy structures that promote biotic dispersal by ingestion have evolved many times in seed plants. Within the yew family Taxaceae sensu lato (six genera, including Cephalotaxus), it remains controversial whether the characteristic fleshy structure surrounding the seed is interpreted as a novel outgrowth of the base of the ovule (i.e. an aril) or a fleshy seed coat that is entirely derived from the integument (i.e. a sarcotesta). This paper presents a detailed study of both wild-type and teratological seed cones of Pseudotaxus chienii, including morphology, anatomy and ontogeny. METHODS Wild-type and teratological seed cones were investigated with the classical paraffin technique and subsequent astrablue/safranin staining and scanning electron microscopy. KEY RESULTS The wild-type seed cone of Pseudotaxus possesses a fleshy white aril that is cup-like and not entirely fused to the seed. In the teratological seed cones investigated, the aril was bilobed and consisted of two free halves. In both wild-type and teratological cones, the aril was initiated as two lateral primordia in a transverse plane, but in wild-type cones the two primordia became extended into a ring primordium, which grew apically, leading to the cup-like shape. The teratological seed cones lacked a ring primordium and the two lateral aril lobes remained free throughout their entire ontogeny, alternating with the scale-like leaves inserted below them on the same branch; in some cases, these leaves also became fleshy. CONCLUSIONS Based on the ontogeny and arrangement of the two fleshy aril lobes in the teratological seed cones of Pseudotaxus, we suggest that the typical aril of Taxaceae could be readily interpreted as a fused pair of strongly swollen leaves rather than a modified integument. Our investigations of the cup-like aril of Pseudotaxus demonstrate a similarity not only with other Taxaceae but also with relatively distantly related conifers such as Phyllocladus (Podocarpaceae).
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Affiliation(s)
- Veit Martin Dörken
- University of Konstanz, Department of Biology, Konstanz, Germany
- For correspondence. E-mail
| | - Hubertus Nimsch
- Forestry Arboretum Freiburg-Günterstal, Bollschweil, Germany
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18
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Singh SP, Inderjit , Singh JS, Majumdar S, Moyano J, Nuñez MA, Richardson DM. Insights on the persistence of pines ( Pinus species) in the Late Cretaceous and their increasing dominance in the Anthropocene. Ecol Evol 2018; 8:10345-10359. [PMID: 30398478 PMCID: PMC6206191 DOI: 10.1002/ece3.4499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/21/2018] [Accepted: 08/04/2018] [Indexed: 01/03/2023] Open
Abstract
Although gymnosperms were nearly swept away by the rise of the angiosperms in the Late Cretaceous, conifers, and pines (Pinus species) in particular, survived and regained their dominance in some habitats. Diversification of pines into fire-avoiding (subgenus Haploxylon) and fire-adapted (subgenus Diploxylon) species occurred in response to abiotic and biotic factors in the Late Cretaceous such as competition with emerging angiosperms and changing fire regimes. Adaptations/traits that evolved in response to angiosperm-fuelled fire regimes and stressful environments in the Late Cretaceous were key to pine success and are also contributing to a new "pine rise" in some areas in the Anthropocene. Human-mediated activities exert both positive and negative impacts of range size and expansion and invasions of pines. Large-scale afforestation with pines, human-mediated changes to fire regimes, and other ecosystem processes are other contributing factors. We discuss traits that evolved in response to angiosperm-mediated fires and stressful environments in the Cretaceous and that continue to contribute to pine persistence and dominance and the numerous ways in which human activities favor pines.
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Affiliation(s)
| | - Inderjit
- Department of Environmental StudiesCentre for Environmental Management of Degraded Ecosystems (CEMDE)University of DelhiDelhiIndia
| | | | - Sudipto Majumdar
- Department of Environmental StudiesCentre for Environmental Management of Degraded Ecosystems (CEMDE)University of DelhiDelhiIndia
| | - Jaime Moyano
- Grupo de Ecologia de InvasionesINIBIOMACONICET/Universidad Nacional del ComahueBarilocheArgentina
| | - Martin A. Nuñez
- Grupo de Ecologia de InvasionesINIBIOMACONICET/Universidad Nacional del ComahueBarilocheArgentina
| | - David M. Richardson
- Department of Botany and ZoologyCentre for Invasion BiologyStellenbosch UniversityMatielandSouth Africa
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19
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Leslie AB, Beaulieu J, Holman G, Campbell CS, Mei W, Raubeson LR, Mathews S. An overview of extant conifer evolution from the perspective of the fossil record. AMERICAN JOURNAL OF BOTANY 2018; 105:1531-1544. [PMID: 30157290 DOI: 10.1002/ajb2.1143] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 05/29/2018] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY Conifers are an important living seed plant lineage with an extensive fossil record spanning more than 300 million years. The group therefore provides an excellent opportunity to explore congruence and conflict between dated molecular phylogenies and the fossil record. METHODS We surveyed the current state of knowledge in conifer phylogenetics to present a new time-calibrated molecular tree that samples ~90% of extant species diversity. We compared phylogenetic relationships and estimated divergence ages in this new phylogeny with the paleobotanical record, focusing on clades that are species-rich and well known from fossils. KEY RESULTS Molecular topologies and estimated divergence ages largely agree with the fossil record in Cupressaceae, conflict with it in Araucariaceae, and are ambiguous in Pinaceae and Podocarpaceae. Molecular phylogenies provide insights into some fundamental questions in conifer evolution, such as the origin of their seed cones, but using them to reconstruct the evolutionary history of specific traits can be challenging. CONCLUSIONS Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.
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Affiliation(s)
- Andrew B Leslie
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, 80 Waterman Street, Providence, Rhode Island, 02912, USA
| | - Jeremy Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Garth Holman
- School of Biology and Ecology, University of Maine, Orono, Maine, 04469, USA
| | | | - Wenbin Mei
- Department of Plant Sciences, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
| | - Linda R Raubeson
- Department of Biological Sciences, Central Washington University, 400 E. University Way, Ellensburg, Washington, 98926, USA
| | - Sarah Mathews
- CSIRO National Research Collections Australia, Australian National Herbarium, Canberra, ACT, 2601, Australia
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20
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Gernandt DS, Reséndiz Arias C, Terrazas T, Aguirre Dugua X, Willyard A. Incorporating fossils into the Pinaceae tree of life. AMERICAN JOURNAL OF BOTANY 2018; 105:1329-1344. [PMID: 30091785 DOI: 10.1002/ajb2.1139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/12/2018] [Indexed: 05/27/2023]
Abstract
PREMISE OF THE STUDY Pinaceae have a rich but enigmatic early fossil record, much of which is represented by permineralized seed cones. Our incomplete knowledge of morphology and anatomy in living and extinct species poses an important barrier to understanding their phylogenetic relationships and timing of diversification. METHODS We expanded a morphology matrix to 46 fossil and 31 extant Pinaceae species, mainly adding characters from stem and leaf anatomy and seed cones. Using parsimony and Bayesian inference, we compared phylogenetic relationships for extant taxa with and without fossils from the morphology matrix combined with an alignment of plastid gene sequences. KEY RESULTS Combined analysis of morphological and molecular characters resulted in a phylogeny of extant Pinaceae that was robust at all nodes except those relating to the interrelationships of Pinus, Picea, and Cathaya and the position of Cedrus. Simultaneous analysis of all fossil and extant species did not result in changes in the relationships among the extant species but did greatly reduce branch support. We found that the placement of most fossils was sensitive to the method of phylogenetic reconstruction when analyzing them singly with the extant species. CONCLUSIONS A robust phylogenetic hypothesis for the main lineages of Pinaceae is emerging. Most Early Cretaceous fossils are stem or crown lineages of Pinus, but close relationships also were found between fossils and several other extant genera. The phylogenetic position of fossils broadly supports the existence of extant genera in the Lower Cretaceous.
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Affiliation(s)
- David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Cecelic Reséndiz Arias
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Teresa Terrazas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Xitlali Aguirre Dugua
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Ann Willyard
- Biology Department, Hendrix College, Conway, AR, 72032, USA
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21
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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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22
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Puebla GG, Iglesias A, Gómez MA, Prámparo MB. Fossil record of Ephedra in the Lower Cretaceous (Aptian), Argentina. JOURNAL OF PLANT RESEARCH 2017; 130:975-988. [PMID: 28528483 DOI: 10.1007/s10265-017-0953-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 04/21/2017] [Indexed: 06/07/2023]
Abstract
Fossil plants from the Lower Cretaceous (upper Aptian) of the La Cantera Formation, Argentina, are described. The fossils studied represent a leafy shooting system with several orders of articulated and striated axes and attached leaves with unequivocal ephedroid affinity. We also found associated remains of ovulate cones with four whorls of sterile bracts, which contain two female reproductive units (FRU). Ovulate cone characters fit well within the genus Ephedra. Special characters in the ovulate cones including an outer seed envelope with two types of trichomes, allowed us to consider our remains as a new Ephedra species. Abundant dispersed ephedroid pollen obtained from the macrofossil-bearing strata also confirms the abundance of Ephedraceae in the basin. The co-occurrence of abundant fossil of Ephedra (adapted to dry habitats) associated with thermophilic cheirolepideacean conifer pollen (Classopollis) in the unit would suggest marked seasonality at the locality during the Early Cretaceous. Furthermore, the floristic association is linked to dry sensitive rocks in the entire section. The macro- and microflora from San Luis Basin are similar in composition to several Early Cretaceous floras from the Northern Gondwana floristic province, but it may represent one of the southernmost records of an arid biome in South America.
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Affiliation(s)
- Gabriela G Puebla
- Unidad de Paleopalinología, Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales Centro Científico Tecnológico, UNCuyo-CONICET, Av. Adrián Ruiz Leal s/n-C.C.131, 5500, Mendoza, Argentina.
| | - Ari Iglesias
- Instituto de Investigaciones en Biodiversidad y Medioambiente UNCO-CONICET, Quintral 1250, 8400, San Carlos de Bariloche, Río Negro, Argentina
| | - María A Gómez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis CONICET, Chacabuco 913, 5700, San Luis, Argentina
| | - Mercedes B Prámparo
- Unidad de Paleopalinología, Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales Centro Científico Tecnológico, UNCuyo-CONICET, Av. Adrián Ruiz Leal s/n-C.C.131, 5500, Mendoza, Argentina
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23
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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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24
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Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E. Evidence for an ancient whole genome duplication in the cycad lineage. PLoS One 2017; 12:e0184454. [PMID: 28886111 PMCID: PMC5590961 DOI: 10.1371/journal.pone.0184454] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/24/2017] [Indexed: 11/26/2022] Open
Abstract
Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome duplications have been reported for most gymnosperm lineages as well, some are still contested and need to be confirmed. For instance, data for ginkgo, but particularly cycads have remained inconclusive so far, likely due to the quality of the data available and flaws in the analysis. We extracted and sequenced RNA from both the cycad Encephalartos natalensis and Ginkgo biloba. This was followed by transcriptome assembly, after which these data were used to build paralog age distributions. Based on these distributions, we identified remnants of an ancient whole genome duplication in both cycads and ginkgo. The most parsimonious explanation would be that this whole genome duplication event was shared between both species and had occurred prior to their divergence, about 300 million years ago.
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Affiliation(s)
- Danielle Roodt
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Riaan L. Swanepoel
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
| | - Yves Van de Peer
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- * E-mail:
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Vajda V, Pucetaite M, McLoughlin S, Engdahl A, Heimdal J, Uvdal P. Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships. Nat Ecol Evol 2017; 1:1093-1099. [DOI: 10.1038/s41559-017-0224-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/24/2017] [Indexed: 01/07/2023]
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Qu XJ, Jin JJ, Chaw SM, Li DZ, Yi TS. Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae). Sci Rep 2017; 7:41005. [PMID: 28120880 PMCID: PMC5264392 DOI: 10.1038/srep41005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 12/12/2016] [Indexed: 11/18/2022] Open
Abstract
Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The phylogenetic relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer stem branches than those of HCX, so their sister relationships may be attributed to LBA. We used multiple measures including data filtering and modifying, evolutionary model selection and coalescent phylogenetic reconstruction to alleviate the LBA artifact. Data filtering by strictly removing unreliable aligned regions and removing substitution saturation genes and rapidly evolving sites could significantly reduce branch lengths of subclades J and C and recovered a relationship of J (C, HCX). In addition, using coalescent phylogenetic reconstruction could elucidate the LBA artifact and recovered J (C, HCX). However, some valid methods for other taxa were inefficient in alleviating the LBA artifact in J-C-HCX. Different strategies should be carefully considered and justified to reduce LBA in phylogenetic reconstruction of different groups. Three subclades of J-C-HCX were estimated to have experienced ancient rapid divergence within a short period, which could be another major obstacle in resolving relationships. Furthermore, our plastid phylogenomic analyses fully resolved the intergeneric relationships of Cupressoideae.
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Affiliation(s)
- Xiao-Jian Qu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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Relative strength of fine-scale spatial genetic structure in paternally vs biparentally inherited DNA in a dioecious plant depends on both sex proportions and pollen-to-seed dispersal ratio. Heredity (Edinb) 2016; 117:449-459. [PMID: 27577692 DOI: 10.1038/hdy.2016.65] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 11/08/2022] Open
Abstract
In plants, the spatial genetic structure (SGS) is shaped mainly by gene dispersal and effective population density. Among additional factors, the mode of DNA inheritance and dioecy influence SGS. However, their joint impact on SGS remains unclear, especially in the case of paternally inherited DNA. Using theoretical approximations and computer simulations, here we showed that the relative intensity of SGS measured in paternally and biparentally inherited DNA in a dioecious plant population depends on both the proportion of males and the pollen-to-seed dispersal ratio. As long as males do not prevail in a population, SGS is more intense in paternally than biparentally inherited DNA. When males prevail, the intensity of SGS in paternally vs biparentally inherited DNA depends on the compound effect of sex proportions and the pollen-to-seed dispersal ratio. To empirically validate our predictions, we used the case of Taxus baccata, a dioecious European tree. First, we showed that mitochondrial DNA (mtDNA) in T. baccata is predominantly (98%) paternally inherited. Subsequently, using nuclear DNA (nuDNA) and mitochondrial microsatellite data, we compared the fine-scale SGS intensity at both marker types in two natural populations. The population with equal sex proportions showed stronger SGS in mtDNA than in nuDNA. On the other hand, we found lower SGS intensity in mtDNA than in nuDNA in the population with 67% males. Thus, the empirical results provided good support for the theoretical predictions, suggesting that knowledge about SGS in paternally vs biparentally inherited DNA may provide insight into effective sex proportions within dioecious populations.
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Abstract
Many genes in the plastid genomes (plastomes) of plants are organized as gene clusters, in which genes are co-transcribed, resembling bacterial operons. These plastid operons are highly conserved, even among conifers, whose plastomes are highly rearranged relative to other seed plants. We have determined the complete plastome sequence of Sciadopitys verticillata (Japanese umbrella pine), the sole member of Sciadopityaceae. The Sciadopitys plastome is characterized by extensive inversions, pseudogenization of four tRNA genes after tandem duplications, and a unique pair of 370-bp inverted repeats involved in the formation of isomeric plastomes. We showed that plastomic inversions in Sciadopitys have led to shuffling of the remote conserved operons, resulting in the birth of four chimeric gene clusters. Our data also demonstrated that the relocated genes can be co-transcribed in these chimeric gene clusters. The plastome of Sciadopitys advances our current understanding of how the conifer plastomes have evolved toward increased diversity and complexity.
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Affiliation(s)
- Chih-Yao Hsu
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan Genome and Systems Biology Degree Program, National Taiwan University & Academia Sinica, Daan District, Taipei 10617, Taiwan
| | - Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan
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Fu YB, Dong Y, Yang MH. Multiplexed shotgun sequencing reveals congruent three-genome phylogenetic signals for four botanical sections of the flax genus Linum. Mol Phylogenet Evol 2016; 101:122-132. [PMID: 27165939 DOI: 10.1016/j.ympev.2016.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/02/2016] [Accepted: 05/06/2016] [Indexed: 12/11/2022]
Abstract
A genome-wide detection of phylogenetic signals by next generation sequencing (NGS) has recently emerged as a promising genomic approach for phylogenetic analysis of non-model organisms. Here we explored the use of a multiplexed shotgun sequencing method to assess the phylogenetic relationships of 18 Linum samples representing 16 species within four botanical sections of the flax genus Linum. The whole genome DNAs of 18 Linum samples were fragmented, tagged, and sequenced using an Illumina MiSeq. Acquired sequencing reads per sample were further separated into chloroplast, mitochondrial and nuclear sequence reads. SNP calls upon genome-specific sequence data sets revealed 6143 chloroplast, 2673 mitochondrial, and 19,562 nuclear SNPs. Phylogenetic analyses based on three-genome SNP data sets with and without missing observations showed congruent three-genome phylogenetic signals for four botanical sections of the Linum genus. Specifically, two major lineages showing a separation of Linum-Dasylinum sections and Linastrum-Syllinum sections were confirmed. The Linum section displayed three major branches representing two major evolutionary stages leading to cultivated flax. Cultivated flax and its immediate progenitor were formed as its own branch, genetically more closely related to L. decumbens and L. grandiflorum with chromosome count of eight, and distantly apart from six other species with chromosome count of nine. Five species of the Linastrum and Syllinum sections were genetically more distant from cultivated flax, but they appeared to be more closely related to each other, even with variable chromosome counts. These findings not only provide the first evidence of congruent three-genome phylogenetic pathways within the Linum genus, but also demonstrate the utility of the multiplexed shotgun sequencing in acquisition of three-genome phylogenetic signals of non-model organisms.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, AAFC Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N0X2, Canada.
| | - Yibo Dong
- Plant Gene Resources of Canada, AAFC Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N0X2, Canada
| | - Mo-Hua Yang
- Plant Gene Resources of Canada, AAFC Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N0X2, Canada; College of Forestry, Central South University of Forestry & Technology, Changsha, Hunan, China
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Lin X, Faridi N, Casola C. An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers. Genome Biol Evol 2016; 8:1252-66. [PMID: 27190138 PMCID: PMC4860704 DOI: 10.1093/gbe/evw076] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants.
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Affiliation(s)
- Xuan Lin
- Department of Ecosystem Science and Management, Texas A&M University
| | - Nurul Faridi
- Department of Ecosystem Science and Management, Texas A&M University Southern Institute of Forest Genetics, USDA Forest Service Southern Research Station, Saucier, Mississippi
| | - Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University
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Kouřil R, Nosek L, Bartoš J, Boekema EJ, Ilík P. Evolutionary loss of light-harvesting proteins Lhcb6 and Lhcb3 in major land plant groups--break-up of current dogma. THE NEW PHYTOLOGIST 2016; 210:808-814. [PMID: 27001142 DOI: 10.1111/nph.13947] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/25/2016] [Indexed: 06/05/2023]
Abstract
Photosynthesis in plants and algae relies on the coordinated function of photosystems (PS) I and II. Their efficiency is augmented by finely-tuned light-harvesting proteins (Lhcs) connected to them. The most recent Lhcs (in evolutionary terms), Lhcb6 and Lhcb3, evolved during the transition of plants from water to land and have so far been considered to be an essential characteristic of land plants. We used single particle electron microscopy and sequence analysis to study architecture and composition of PSII supercomplex from Norway spruce and related species. We have found that there are major land plant families that lack functional lhcb6 and lhcb3 genes, which notably changes the organization of PSII supercomplexes. The Lhcb6 and Lhcb3 proteins have been lost in the gymnosperm genera Picea and Pinus (family Pinaceae) and Gnetum (Gnetales). We also revealed that the absence of these proteins in Norway spruce modifies the PSII supercomplex in such a way that it resembles its counterpart in the alga Chlamydomonas reinhardtii, an evolutionarily older organism. Our results break a deep-rooted concept of Lhcb6 and Lhcb3 proteins being the essential characteristic of land plants, and beg the question of what the evolutionary benefit of their loss could be.
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Affiliation(s)
- Roman Kouřil
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Lukáš Nosek
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
| | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Egbert J Boekema
- Electron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG Groningen, the Netherlands
| | - Petr Ilík
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc, Czech Republic
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Valverde A, De Maayer P, Oberholster T, Henschel J, Louw MK, Cowan D. Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil. PLoS One 2016; 11:e0153353. [PMID: 27064484 PMCID: PMC4827806 DOI: 10.1371/journal.pone.0153353] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/29/2016] [Indexed: 11/24/2022] Open
Abstract
Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few “species” (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small ‘core’ rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth.
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Affiliation(s)
- Angel Valverde
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- * E-mail:
| | - Pieter De Maayer
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Tanzelle Oberholster
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Joh Henschel
- Namib Ecological Restoration and Monitoring Unit, Gobabeb Research and Training Centre, Walvis Bay, Namibia
- SAEON Arid Lands Node, Hadison Park, Kimberly, South Africa
| | | | - Don Cowan
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Ishishita K, Suetsugu N, Hirose Y, Higa T, Doi M, Wada M, Matsushita T, Gotoh E. Functional characterization of blue-light-induced responses and PHOTOTROPIN 1 gene in Welwitschia mirabilis. JOURNAL OF PLANT RESEARCH 2016; 129:175-87. [PMID: 26858202 DOI: 10.1007/s10265-016-0790-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/04/2016] [Indexed: 05/05/2023]
Abstract
The blue light (BL) receptor phototropin (phot) is specifically found in green plants; it regulates various BL-induced responses such as phototropism, chloroplast movement, stomatal opening, and leaf flattening. In Arabidopsis thaliana, two phototropins--phot1 and phot2--respond to blue light in overlapping but distinct ways. These BL-receptor-mediated responses enhance the photosynthetic activity of plants under weak light and minimize photodamage under strong light conditions. Welwitschia mirabilis Hook.f. found in the Namib Desert, and it has adapted to severe environmental stresses such as limiting water and strong sunlight. Although the plant has physiologically and ecologically unique features, it is unknown whether phototropin is functional in this plant. In this study, we assessed the functioning of phot-mediated BL responses in W. mirabilis. BL-dependent phototropism and stomatal opening was observed but light-dependent chloroplast movement was not detected. We performed a functional analysis of the PHOT1 gene of W. mirabilis, WmPHOT1, in Arabidopsis thaliana. We generated transgenic A. thaliana lines expressing WmPHOT1 in a phot1 phot2 double mutant background. Several Wmphot1 transgenic plants showed normal growth, although phot1 phot2 double mutant plants showed stunted growth. Furthermore, Wmphot1 transgenic plants showed normal phot1-mediated responses including phototropism, chloroplast accumulation, stomatal opening, and leaf flattening, but lacked the chloroplast avoidance response that is specifically mediated by phot2. Thus, our findings indicate that W. mirabilis possesses typical phot-mediated BL responses that were at least partially mediated by functional phototropin 1, an ortholog of Atphot1.
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Affiliation(s)
- Kazuhiro Ishishita
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka, 812-8581, Japan
| | - Noriyuki Suetsugu
- Department of Biology, Faculty of Science, Kyushu University, Hakozaki, Fukuoka, 812-8581, Japan
- Department of Plant Gene and Totipotency, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Yuki Hirose
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka, 812-8581, Japan
| | - Takeshi Higa
- Department of Biology, Faculty of Science, Kyushu University, Hakozaki, Fukuoka, 812-8581, Japan
- Department of Plant Gene and Totipotency, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Michio Doi
- Faculty of Art and Science, Kyushu University, Motooka, Fukuoka, 819-0395, Japan
| | - Masamitsu Wada
- Department of Biology, Faculty of Science, Kyushu University, Hakozaki, Fukuoka, 812-8581, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan
| | - Tomonao Matsushita
- Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka, 812-8581, Japan
- PRESTO, JST, Saitama, 332-0012, Japan
| | - Eiji Gotoh
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka, 812-8581, Japan.
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Lora J, Hormaza JI, Herrero M. The Diversity of the Pollen Tube Pathway in Plants: Toward an Increasing Control by the Sporophyte. FRONTIERS IN PLANT SCIENCE 2016; 7:107. [PMID: 26904071 PMCID: PMC4746263 DOI: 10.3389/fpls.2016.00107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/20/2016] [Indexed: 05/06/2023]
Abstract
Plants, unlike animals, alternate multicellular diploid, and haploid generations in their life cycle. While this is widespread all along the plant kingdom, the size and autonomy of the diploid sporophyte and the haploid gametophyte generations vary along evolution. Vascular plants show an evolutionary trend toward a reduction of the gametophyte, reflected both in size and lifespan, together with an increasing dependence from the sporophyte. This has resulted in an overlooking of the importance of the gametophytic phase in the evolution of higher plants. This reliance on the sporophyte is most notorious along the pollen tube journey, where the male gametophytes have to travel a long way inside the sporophyte to reach the female gametophyte. Along evolution, there is a change in the scenery of the pollen tube pathway that favors pollen competition and selection. This trend, toward apparently making complicated what could be simple, appears to be related to an increasing control of the sporophyte over the gametophyte with implications for understanding plant evolution.
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Affiliation(s)
- Jorge Lora
- Department of Subtropical Fruit Crops, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora – University of Málaga – Consejo Superior de Investigaciones CientíficasMálaga, Spain
| | - José I. Hormaza
- Department of Subtropical Fruit Crops, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora – University of Málaga – Consejo Superior de Investigaciones CientíficasMálaga, Spain
| | - María Herrero
- Department of Pomology, Estación Experimental Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
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Ranade SS, García-Gil MR, Rosselló JA. Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes. Mol Genet Genomics 2016; 291:935-41. [PMID: 26732267 DOI: 10.1007/s00438-015-1159-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022]
Abstract
Many genes have been lost from the prokaryote plastidial genome during the early events of endosymbiosis in eukaryotes. Some of them were definitively lost, but others were relocated and functionally integrated to the host nuclear genomes through serial events of gene transfer during plant evolution. In gymnosperms, plastid genome sequencing has revealed the loss of ndh genes from several species of Gnetales and Pinaceae, including Norway spruce (Picea abies). This study aims to trace the ndh genes in the nuclear and organellar Norway spruce genomes. The plastid genomes of higher plants contain 11 ndh genes which are homologues of mitochondrial genes encoding subunits of the proton-pumping NADH-dehydrogenase (nicotinamide adenine dinucleotide dehydrogenase) or complex I (electron transport chain). Ndh genes encode 11 NDH polypeptides forming the Ndh complex (analogous to complex I) which seems to be primarily involved in chloro-respiration processes. We considered ndh genes from the plastidial genome of four gymnosperms (Cryptomeria japonica, Cycas revoluta, Ginkgo biloba, Podocarpus totara) and a single angiosperm species (Arabidopsis thaliana) to trace putative homologs in the nuclear and organellar Norway spruce genomes using tBLASTn to assess the evolutionary fate of ndh genes in Norway spruce and to address their genomic location(s), structure, integrity and functionality. The results obtained from tBLASTn were subsequently analyzed by performing homology search for finding ndh specific conserved domains using conserved domain search. We report the presence of non-functional plastid ndh gene fragments, excepting ndhE and ndhG genes, in the nuclear genome of Norway spruce. Regulatory transcriptional elements like promoters, TATA boxes and enhancers were detected in the upstream regions of some ndh fragments. We also found transposable elements in the flanking regions of few ndh fragments suggesting nuclear rearrangements in those regions. These evidences support the hypothesis that, at least in Picea, ndh translocations from the plastid to the nuclear genome have occurred, and that there might have been a functional machinery at some time during evolution to accommodate them within a nuclear-encoded environment, or attempts to form it.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden.
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Josep A Rosselló
- Jardí Botànic, Universidad de Valencia, c/Quart 80, 46008, Valencia, Spain
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Wang W, Ma L, Becher H, Garcia S, Kovarikova A, Leitch IJ, Leitch AR, Kovarik A. Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb. Chromosoma 2015; 125:683-99. [PMID: 26637996 PMCID: PMC5023732 DOI: 10.1007/s00412-015-0556-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/05/2015] [Indexed: 11/28/2022]
Abstract
In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes (<20 %) encode functional rRNA. The most common SNPs were C > T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.
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Affiliation(s)
- Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Sònia Garcia
- Laboratori de Botànica-Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Alena Kovarikova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic.
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Folk RA, Mandel JR, Freudenstein JV. A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500039. [PMID: 26312196 PMCID: PMC4542943 DOI: 10.3732/apps.1500039] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/09/2015] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera. METHODS Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based assembly was performed using genomic references; additionally, chloroplast and mitochondrial genomes were used as references for off-target reads. The data were aligned and subjected to coalescent and concatenated phylogenetic analyses to demonstrate support for major relationships. RESULTS Complete or nearly complete (>99%) sequences were assembled from essentially all loci from all taxa. Aligned introns showed a fourfold increase in divergence as opposed to exons. Concatenated analysis gave decisive support to all nodes, and support was also high and relationships mostly similar in the coalescent analysis. Organellar phylogenies were also well-supported and conflicted with the nuclear signal. DISCUSSION Our approach shows promise for resolving a recent radiation. Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.
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Affiliation(s)
- Ryan A. Folk
- Herbarium, The Ohio State University, Columbus, Ohio 43212 USA
- Author for correspondence:
| | - Jennifer R. Mandel
- Department of Biology, University of Memphis, Memphis, Tennessee 38152 USA
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Folk RA, Mandel JR, Freudenstein JV. A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae). APPLICATIONS IN PLANT SCIENCES 2015. [PMID: 26312196 DOI: 10.5061/dryad.4cn66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera. METHODS Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based assembly was performed using genomic references; additionally, chloroplast and mitochondrial genomes were used as references for off-target reads. The data were aligned and subjected to coalescent and concatenated phylogenetic analyses to demonstrate support for major relationships. RESULTS Complete or nearly complete (>99%) sequences were assembled from essentially all loci from all taxa. Aligned introns showed a fourfold increase in divergence as opposed to exons. Concatenated analysis gave decisive support to all nodes, and support was also high and relationships mostly similar in the coalescent analysis. Organellar phylogenies were also well-supported and conflicted with the nuclear signal. DISCUSSION Our approach shows promise for resolving a recent radiation. Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.
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Affiliation(s)
- Ryan A Folk
- Herbarium, The Ohio State University, Columbus, Ohio 43212 USA
| | - Jennifer R Mandel
- Department of Biology, University of Memphis, Memphis, Tennessee 38152 USA
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Martín M, Marín D, Serrot PH, Sabater B. Evolutionary reversion of editing sites of ndh genes suggests their origin in the Permian-Triassic, before the increase of atmospheric CO2. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Goremykin VV, Nikiforova SV, Cavalieri D, Pindo M, Lockhart P. The Root of Flowering Plants and Total Evidence. Syst Biol 2015; 64:879-91. [DOI: 10.1093/sysbio/syv028] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
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Koh SH, Li H, Admiraal R, Jones MGK, Wylie SJ. Catharanthus mosaic virus: A potyvirus from a gymnosperm, Welwitschia mirabilis. Virus Res 2015; 203:41-6. [PMID: 25804761 DOI: 10.1016/j.virusres.2015.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/12/2015] [Accepted: 03/14/2015] [Indexed: 11/24/2022]
Abstract
A virus from a symptomatic plant of the gymnosperm Welwitschia mirabilis Hook. growing as an ornamental plant in a domestic garden in Western Australia was inoculated to a plant of Nicotiana benthamiana where it established a systemic infection. The complete genome sequence of 9636 nucleotides was determined using high-throughput and Sanger sequencing technologies. The genome sequence shared greatest identity (83% nucleotides and 91% amino acids) with available partial sequences of catharanthus mosaic virus, indicating that the new isolate belonged to that taxon. Analysis of the phylogeny of the complete virus sequence placed it in a monotypic group in the genus Potyvirus. This is the first record of a virus from W. mirabilis, the first complete genome sequence of catharanthus mosaic virus determined, and the first record from Australia. This finding illustrates the risk to natural and managed systems posed by the international trade in live plants and propagules, which enables viruses to establish in new regions and infect new hosts.
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Affiliation(s)
- Shu Hui Koh
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia; School of Engineering and Information Technology, Mathematics & Statistics, Murdoch University, Perth, Western Australia 6150, Australia.
| | - Hua Li
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Ryan Admiraal
- School of Engineering and Information Technology, Mathematics & Statistics, Murdoch University, Perth, Western Australia 6150, Australia
| | - Michael G K Jones
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Stephen J Wylie
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
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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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Ruhlman TA, Chang WJ, Chen JJW, Huang YT, Chan MT, Zhang J, Liao DC, Blazier JC, Jin X, Shih MC, Jansen RK, Lin CS. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. BMC PLANT BIOLOGY 2015; 15:100. [PMID: 25886915 PMCID: PMC4404220 DOI: 10.1186/s12870-015-0484-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/30/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes is widely distributed across diverse lineages of photoautotrophic seed plants and mutants/transgenics lacking NDH function demonstrate little difference from wild type under non-stressed conditions. This study analyzes large transcriptomic and genomic datasets to evaluate the persistence and loss of NDH expression across plants. RESULTS Nuclear expression profiles showed accretion of the NDH gene complement at key transitions in land plant evolution, such as the transition to land and at the base of the angiosperm lineage. While detection of transcripts for a selection of non-NDH, photosynthesis related proteins was independent of the state of NDH, coordinate, lineage-specific loss of plastid NDH genes and expression of nuclear-encoded NDH subunits was documented in Pinaceae, gnetophytes, Orchidaceae and Geraniales confirming the independent and complete loss of NDH in these diverse seed plant taxa. CONCLUSION The broad phylogenetic distribution of NDH loss and the subtle phenotypes of mutants suggest that the NDH complex is of limited biological significance in contemporary plants. While NDH activity appears dispensable under favorable conditions, there were likely sufficiently frequent episodes of abiotic stress affecting terrestrial habitats to allow the retention of NDH activity. These findings reveal genetic factors influencing plant/environment interactions in a changing climate through 450 million years of land plant evolution.
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Affiliation(s)
- Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan.
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
| | - Jin Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - De-Chih Liao
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
| | - John C Blazier
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
- Department of Biological Science, Biotechnology Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center of Academia Sinica, Agricultural Technology Building, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
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Wang B, Jiang B, Zhou Y, Su Y, Wang T. Higher substitution rates and lower dN/dS for the plastid genes in Gnetales than other gymnosperms. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Transcriptome profiling of khat (Catha edulis) and Ephedra sinica reveals gene candidates potentially involved in amphetamine-type alkaloid biosynthesis. PLoS One 2015; 10:e0119701. [PMID: 25806807 PMCID: PMC4373857 DOI: 10.1371/journal.pone.0119701] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/15/2015] [Indexed: 12/25/2022] Open
Abstract
Amphetamine analogues are produced by plants in the genus Ephedra and by khat (Catha edulis), and include the widely used decongestants and appetite suppressants (1S,2S)-pseudoephedrine and (1R,2S)-ephedrine. The production of these metabolites, which derive from L-phenylalanine, involves a multi-step pathway partially mapped out at the biochemical level using knowledge of benzoic acid metabolism established in other plants, and direct evidence using khat and Ephedra species as model systems. Despite the commercial importance of amphetamine-type alkaloids, only a single step in their biosynthesis has been elucidated at the molecular level. We have employed Illumina next-generation sequencing technology, paired with Trinity and Velvet-Oases assembly platforms, to establish data-mining frameworks for Ephedra sinica and khat plants. Sequence libraries representing a combined 200,000 unigenes were subjected to an annotation pipeline involving direct searches against public databases. Annotations included the assignment of Gene Ontology (GO) terms used to allocate unigenes to functional categories. As part of our functional genomics program aimed at novel gene discovery, the databases were mined for enzyme candidates putatively involved in alkaloid biosynthesis. Queries used for mining included enzymes with established roles in benzoic acid metabolism, as well as enzymes catalyzing reactions similar to those predicted for amphetamine alkaloid metabolism. Gene candidates were evaluated based on phylogenetic relationships, FPKM-based expression data, and mechanistic considerations. Establishment of expansive sequence resources is a critical step toward pathway characterization, a goal with both academic and industrial implications.
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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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Gramzow L, Weilandt L, Theißen G. MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants. ANNALS OF BOTANY 2014; 114:1407-29. [PMID: 24854168 PMCID: PMC4204780 DOI: 10.1093/aob/mcu066] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 03/10/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. METHODS The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. KEY RESULTS Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14-16 Type II MADS-box genes. CONCLUSIONS The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is the first that provides a comprehensive overview of MADS-box genes in conifers and thus will provide a framework for future work on MADS-box genes in seed plants.
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Affiliation(s)
- Lydia Gramzow
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Lisa Weilandt
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany
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Lu Y, Ran JH, Guo DM, Yang ZY, Wang XQ. Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes. PLoS One 2014; 9:e107679. [PMID: 25222863 PMCID: PMC4164646 DOI: 10.1371/journal.pone.0107679] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/19/2014] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.
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Affiliation(s)
- Ying Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Dong-Mei Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zu-Yu Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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