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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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Ma LT, Lee YR, Liu PL, Cheng YT, Shiu TF, Tsao NW, Wang SY, Chu FH. Phylogenetically distant group of terpene synthases participates in cadinene and cedrane-type sesquiterpenes accumulation in Taiwania cryptomerioides. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110277. [PMID: 31623780 DOI: 10.1016/j.plantsci.2019.110277] [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: 05/17/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
Along with the species evolution, plants have evolved ways to produce a different collection of terpenoids to accommodate its biotic and abiotic environment, and terpene synthase (TPS) is one of the major contributors to various terpene compounds. The timber of a monotypic and relictual conifer species of Cupressace, Taiwania cryptomerioides, has excellent durability, and one of the essential factors for Taiwania to resist decay and insect pests is sesquiterpene. Compared to other conifers, Taiwania has much higher abundance of cadinene-type sesquiterpenes, and the presence of cedrene-type sesquiterpenes. To understand sesquiterpene biosynthesis in Taiwania, we functionally characterized 10 T. cryptomerioides TPSs (TcTPSs) in vivo or in planta, which could catalyze sesquiterpene formation and potentially are involved in biosynthesis of diverse sesquiterpenoids in Taiwania. The distant phylogenetic relationship and the intron loss event of TcTPSs correlate to the differentiation of chemical profile Taiwania compared to other conifers. Furthermore, we identified TcTPS3 and TcTPS12 as δ-cadinene synthase, and TcTPS6 as cedrol synthase, which demonstrates the important contributions of dynamic evolution in TPSs to the chemical diversity in plants. Combining with functional characterization and comparison of catalytic residues, we conclude at least three catalytic routes for sesquiterpene biosynthesis in this species, and the skeleton diversity has been expended in T. cryptomeriodes.
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Affiliation(s)
- Li-Ting Ma
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Ru Lee
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan
| | - Pi-Ling Liu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan
| | - Yang-Tui Cheng
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan
| | - Tz-Fan Shiu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan
| | - Nai-Wen Tsao
- Department of Forestry, National Chung-Hsing University, Taichung 402, Taiwan
| | - Sheng-Yang Wang
- Department of Forestry, National Chung-Hsing University, Taichung 402, Taiwan
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei 10617, Taiwan.
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53
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Shao CC, Shen TT, Jin WT, Mao HJ, Ran JH, Wang XQ. Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae). Mol Phylogenet Evol 2019; 141:106610. [DOI: 10.1016/j.ympev.2019.106610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023]
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Hanlon VCT, Otto SP, Aitken SN. Somatic mutations substantially increase the per-generation mutation rate in the conifer Picea sitchensis. Evol Lett 2019; 3:348-358. [PMID: 31388445 PMCID: PMC6675141 DOI: 10.1002/evl3.121] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/14/2019] [Accepted: 05/21/2019] [Indexed: 12/11/2022] Open
Abstract
The rates and biological significance of somatic mutations have long been a subject of debate. Somatic mutations in plants are expected to accumulate with vegetative growth and time, yet rates of somatic mutations are unknown for conifers, which can reach exceptional sizes and ages. We investigated somatic mutation rates in the conifer Sitka spruce (Picea sitchensis (Bong.) Carr.) by analyzing a total of 276 Gb of nuclear DNA from the tops and bottoms of 20 old‐growth trees averaging 76 m in height. We estimate a somatic base substitution rate of 2.7 × 10−8 per base pair within a generation. To date, this is one of the highest estimated per‐generation rates of mutation among eukaryotes, indicating that somatic mutations contribute substantially to the total per‐generation mutation rate in conifers. Nevertheless, as the sampled trees are centuries old, the per‐year rate is low in comparison with nontree taxa. We argue that although somatic mutations raise genetic load in conifers, they generate important genetic variation and enable selection both among cell lineages within individual trees and among offspring.
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Affiliation(s)
- Vincent C T Hanlon
- Faculty of Forestry Department of Forest and Conservation Sciences University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Sarah P Otto
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Sally N Aitken
- Faculty of Forestry Department of Forest and Conservation Sciences University of British Columbia Vancouver BC V6T 1Z4 Canada
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Wang W, Wan T, Becher H, Kuderova A, Leitch IJ, Garcia S, Leitch AR, Kovařík A. Remarkable variation of ribosomal DNA organization and copy number in gnetophytes, a distinct lineage of gymnosperms. ANNALS OF BOTANY 2019; 123:767-781. [PMID: 30265284 PMCID: PMC6526317 DOI: 10.1093/aob/mcy172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 09/04/2018] [Indexed: 05/10/2023]
Abstract
INTRODUCTION Gnetophytes, comprising the genera Ephedra, Gnetum and Welwitschia, are an understudied, enigmatic lineage of gymnosperms with a controversial phylogenetic relationship to other seed plants. Here we examined the organization of ribosomal DNA (rDNA) across representative species. METHODS We applied high-throughput sequencing approaches to isolate and reconstruct rDNA units and to determine their intragenomic homogeneity. In addition, fluorescent in situ hybridization and Southern blot hybridization techniques were used to reveal the chromosome and genomic organization of rDNA. KEY RESULTS The 5S and 35S rRNA genes were separate (S-type) in Gnetum montanum, Gnetum gnemon and Welwitschia mirabilis and linked (L-type) in Ephedra altissima. There was considerable variability in 5S rDNA abundance, ranging from as few as ~4000 (W. mirabilis) to >100 000 (G. montanum) copies. A similar large variation was also observed in 5S rDNA locus numbers (two to 16 sites per diploid cell). 5S rRNA pseudogenes were interspersed between functional genes forming a single unit in E. altissima and G. montanum. Their copy number was comparable or even higher than that of functional 5S rRNA genes. In E. altissima internal transcribed spacers of 35S rDNA were long and intrinsically repetitive while in G. montanum and W. mirabilis they were short without the subrepeats. CONCLUSIONS Gnetophytes are distinct from other gymnosperms and angiosperms as they display surprisingly large variability in rDNA organization and rDNA copy and locus numbers between genera, with no relationship between copy numbers and genome sizes apparent. Concerted evolution of 5S rDNA units seems to have led to the amplification of 5S pseudogenes in both G. montanum and E. altissima. Evolutionary patterns of rDNA show both gymnosperm and angiosperm features underlining the diversity of the group.
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Affiliation(s)
- Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzen, PR China
- Sino-Africa Joint Research Center, Chinese Academy of Science, Wuhan, PR China
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Alena Kuderova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, Parc de Montjuïc, Barcelona, Catalonia, Spain
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- For correspondence. E-mail
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Liu YY, Jin WT, Wei XX, Wang XQ. Cryptic speciation in the Chinese white pine (Pinus armandii): Implications for the high species diversity of conifers in the Hengduan Mountains, a global biodiversity hotspot. Mol Phylogenet Evol 2019; 138:114-125. [PMID: 31112783 DOI: 10.1016/j.ympev.2019.05.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 03/19/2019] [Accepted: 05/17/2019] [Indexed: 12/30/2022]
Abstract
Conifers are the largest and ecologically and economically most important component group of the gymnosperms. Despite their slow rate of molecular evolution, rapid and recent diversification was unexpectedly prevalent in this ancient group in the Hengduan Mountains, a world's biodiversity hotspot and gymnosperm diversity center in Southwest China. In this study, we investigated the underlying mechanisms and disentangled the interactions of geography and ecology in speciation and evolution in Pinus armandii, an important forest tree species endemic to China, by integrating analyses of population transcriptomics, population genetics and ecological niche modeling. Many lines of evidence suggest that cryptic speciation has occurred in P. armandii. During the process, geologically induced formation of Mount Gongga and other massive peaks might trigger the initial vicariance isolation of the northern and southern subdivisions, and ecologically based selection then reinforced their differentiation and local adaptation. Our ecological niche analysis and earlier reciprocal transplant experiments in P. armandii provided convincing evidences for the critical role of ecology in the process of speciation. These findings suggest that both geography and ecology contributed significantly to the abundance of very recent and rapid species divergences, which promoted the rising of the extremely high conifer diversity in the Hengduan Mountains.
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Affiliation(s)
- Yan-Yan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiao-Xin Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Wu X, Liu X, Kodrul T, Quan C, Jin J. Dacrycarpus pattern shedding new light on the early floristic exchange between Asia and Australia. Natl Sci Rev 2019; 6:1086-1090. [PMID: 34691981 PMCID: PMC8291558 DOI: 10.1093/nsr/nwz060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xinkai Wu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, China
| | - Xiaoyan Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, China
| | - Tatiana Kodrul
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, China
- Geological Institute, Russian Academy of Sciences, Russia
| | - Cheng Quan
- School of Earth Science and Resources, Chang’an University, China
| | - Jianhua Jin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, China
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Ran JH, Shen TT, Wang MM, Wang XQ. Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. Proc Biol Sci 2019; 285:rspb.2018.1012. [PMID: 29925623 DOI: 10.1098/rspb.2018.1012] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/24/2018] [Indexed: 02/04/2023] Open
Abstract
After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has not been resolved, and the phylogenetic placement of Gnetales remains one of the most controversial issues in seed plant evolution. To resolve the deep phylogeny of seed plants and to address the sources of phylogenetic conflict, we conducted a phylotranscriptomic study with a sampling of all 13 families of gymnosperms and main lineages of angiosperms. Multiple datasets containing up to 1 296 042 sites across 1308 loci were analysed, using concatenation and coalescence approaches. Our study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis. Cycads plus Ginkgo is sister to the remaining gymnosperms. We also found that Gnetales and angiosperms have similar molecular evolutionary rates, which are much higher than those of other gymnosperms. This implies that Gnetales and angiosperms might have experienced similar selective pressures in evolutionary histories. Convergent molecular evolution or homoplasy is partially responsible for the phylogenetic conflicts in seed plants. Our study provides a robustly reconstructed backbone phylogeny that is important for future molecular and morphological studies of seed plants, in particular gymnosperms, in the light of evolution.
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Affiliation(s)
- Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Ting-Ting Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Ming-Ming Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China .,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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Mao K, Ruhsam M, Ma Y, Graham SW, Liu J, Thomas P, Milne RI, Hollingsworth PM. A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae. ANNALS OF BOTANY 2019; 123:153-167. [PMID: 30124771 PMCID: PMC6344097 DOI: 10.1093/aob/mcy152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/21/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS Rapid evolutionary divergence and reticulate evolution may result in phylogenetic relationships that are difficult to resolve using small nucleotide sequence data sets. Next-generation sequencing methods can generate larger data sets that are better suited to solving these puzzles. One major and long-standing controversy in conifers concerns generic relationships within the subfamily Cupressoideae (105 species, approx. 1/6 of all conifers) of Cupressaceae, in particular the relationship between Juniperus, Cupressus and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) clade. Here we attempt to resolve this question using transcriptome-derived data. METHODS Transcriptome sequences of 20 species from Cupressoideae were collected. Using MarkerMiner, single-copy nuclear (SCN) genes were extracted. These were applied to estimate phylogenies based on concatenated data, species trees and a phylogenetic network. We further examined the effect of alternative backbone topologies on downstream analyses, including biogeographic inference and dating analysis. RESULTS Based on the 73 SCN genes (>200 000 bp total alignment length) we considered, all tree-building methods lent strong support for the relationship (HCX, (Juniperus, Cupressus)); however, strongly supported conflicts among individual gene trees were also detected. Molecular dating suggests that these three lineages shared a most recent common ancestor approx. 60 million years ago (Mya), and that Juniperus and Cupressus diverged about 56 Mya. Ancestral area reconstructions (AARs) suggest an Asian origin for the entire clade, with subsequent dispersal to North America, Europe and Africa. CONCLUSIONS Our analysis of SCN genes resolves a controversial phylogenetic relationship in the Cupressoideae, a major clade of conifers, and suggests that rapid evolutionary divergence and incomplete lineage sorting probably acted together as the source for conflicting phylogenetic inferences between gene trees and between our robust results and recently published studies. Our updated backbone topology has not substantially altered molecular dating estimates relative to previous studies; however, application of the latest AAR approaches has yielded a clearer picture of the biogeographic history of Cupressoideae.
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Affiliation(s)
- Kangshan 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, Sichuan, China
| | | | - Yazhen Ma
- 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, Sichuan, China
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jianquan Liu
- 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, Sichuan, China
| | | | - Richard I Milne
- Institute of Molecular Plant Science, School of Biological Science, University of Edinburgh, Edinburgh, UK
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Yin Q, Chen S, Guo W, Huang Y, Huang Y, Zhou R, Fan Q, Liao W. Pronounced genetic differentiation in Fokienia hodginsii revealed by simple sequence repeat markers. Ecol Evol 2018; 8:10938-10951. [PMID: 30519418 PMCID: PMC6262914 DOI: 10.1002/ece3.4560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 08/16/2018] [Accepted: 08/29/2018] [Indexed: 11/13/2022] Open
Abstract
Fokienia hodginsii is a Tertiary relict conifer of the monotypic genus Fokienia (Cupressaceae s.l.). Currently, the species is distributed in southern China, northern Vietnam, and northern Laos and listed as a "near threatened" species by the IUCN. In this study, a total of 427 individuals of F. hodginsii were sampled from China and Vietnam to characterize its genetic diversity and population differentiation. Based on the profiles of 12 simple sequence repeat (SSR) markers, we observed a high level of genetic diversity in F. hodginsii at the species level (H e =0.635), albeit slightly lower than that of its sister species Chamaecyparis obtusa. Signals of bottleneck events were detected in the populations GXDMS, GXHJ, V-PXB, and V-HB, probably due to Pleistocene glaciations or overexploitation in recent years. Pronounced genetic differentiation (F st = 0.157) was found in this species. The inbreeding index (F is = 0.176 ± 0.024) indicated that F. hodginsii has a mixed mating system. Significant correlation was found between the pairwise genetic differentiation and geographic distance (r = 0.882, p = 0.01), suggesting that genetic differentiation among the populations follows the model of isolation by distance (IBD). STRUCTURE analysis and principal coordinate analysis revealed that these populations were divided into four groups: the western China group located mainly in the Yunnan-Guizhou Plateau, the central China group located mostly in the Luoxiao Mountains and Nanling Mountains, the eastern China group located in the Wuyi Mountains and the Vietnam group containing two populations in Vietnam. The different terrains and elevations of populations may be the most likely factors leading to the differentiation between the western China group and the central China group, while the geographic isolation caused by the lack of appropriate habitats may greatly contribute to the differentiation between the central China group and the eastern China group. Based on the results, some conservation suggestions for this species are provided, such as establishing seed orchards and multiple nature reserves.
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Affiliation(s)
- Qianyi Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSun Yat‐sen UniversityGuangzhouChina
| | - Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSun Yat‐sen UniversityGuangzhouChina
| | - Wei Guo
- Department of Horticulture and Landscape ArchitectureZhongkai University of Agriculture and EngineeringGuangzhouChina
| | - Yanshuang Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSun Yat‐sen UniversityGuangzhouChina
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSun Yat‐sen UniversityGuangzhouChina
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSun Yat‐sen UniversityGuangzhouChina
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSun Yat‐sen UniversityGuangzhouChina
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSun Yat‐sen UniversityGuangzhouChina
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61
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From America to Eurasia: a multigenomes history of the genus Abies. Mol Phylogenet Evol 2018; 125:14-28. [DOI: 10.1016/j.ympev.2018.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 11/24/2022]
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62
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Xiang KL, Erst AS, Xiang XG, Jabbour F, Wang W. Biogeography of Coptis Salisb. (Ranunculales, Ranunculaceae, Coptidoideae), an Eastern Asian and North American genus. BMC Evol Biol 2018; 18:74. [PMID: 29793422 PMCID: PMC5968522 DOI: 10.1186/s12862-018-1195-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous studies have favored dispersal (colonization) over vicariance (past fragmentation) events to explain eastern Asian-North American distribution patterns. In plants, however the disjunction between eastern Asia and western North America has been rarely examined using the integration of phylogenetic, molecular dating, and biogeographical methods. Meanwhile, the biogeographic patterns within eastern Asia remain poorly understood. The goldthread genus Coptis Salisb. includes 15 species disjunctly distributed in North America, Japan, mainland China, and Taiwan. We present a dated phylogeny for Coptis under the optimal clock model and infer its historical biogeography by comparing different biogeographic models. RESULTS The split of Coptis and Xanthorhiza Marshall occurred in the middle Miocene (ca. 15.47 Ma). Coptis started their diversification in the early late Miocene (ca. 9.55 Ma). A late Miocene vicariance event resulted in the eastern Asian and western North American disjunction in the genus. Within eastern Asia, dispersals from mainland Asia to Japan and from Japan to Taiwan occurred at ca. 4.85 Ma and at ca. 1.34 Ma, respectively. CONCLUSIONS Our analyses provide evidence that both vicariance and dispersal events have played important roles in shaping the current distribution and endemism of Coptis, likely resulting from eustatic sea-level changes, mountain formation processes and an increasing drier and cooler climate from the middle Miocene onwards.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Andrey S Erst
- Central Siberian Botanical Garden of the Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia.,Laboratory of Systematics and Phylogeny of Plants, Tomsk State University, Tomsk, 634050, Russia
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Florian Jabbour
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, 75005, Paris, France
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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63
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Wan T, Liu ZM, Li LF, Leitch AR, Leitch IJ, Lohaus R, Liu ZJ, Xin HP, Gong YB, Liu Y, Wang WC, Chen LY, Yang Y, Kelly LJ, Yang J, Huang JL, Li Z, Liu P, Zhang L, Liu HM, Wang H, Deng SH, Liu M, Li J, Ma L, Liu Y, Lei Y, Xu W, Wu LQ, Liu F, Ma Q, Yu XR, Jiang Z, Zhang GQ, Li SH, Li RQ, Zhang SZ, Wang QF, Van de Peer Y, Zhang JB, Wang XM. A genome for gnetophytes and early evolution of seed plants. NATURE PLANTS 2018; 4:82-89. [PMID: 29379155 DOI: 10.1038/s41477-017-0097-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 12/27/2017] [Indexed: 05/07/2023]
Abstract
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms.
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Affiliation(s)
- Tao Wan
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
| | - Zhi-Ming Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ling-Fei Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China
| | - Hai-Ping Xin
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Wen-Cai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ling-Yun Chen
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ji Yang
- Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Jin-Ling Huang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ping Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Li Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Hong-Mei Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Hui Wang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Shu-Han Deng
- Novogene Bioinformatics Institute, Beijing, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ji Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yan Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yang Lei
- Novogene Bioinformatics Institute, Beijing, China
| | - Wei Xu
- Novogene Bioinformatics Institute, Beijing, China
| | - Ling-Qing Wu
- Novogene Bioinformatics Institute, Beijing, China
| | - Fan Liu
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China
| | - Qian Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xin-Ran Yu
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Centre of China and Orchid Conservation and Research Centre, Shenzhen, China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui-Qiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Centre, Chinese Academy of Science, Wuhan, China.
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Centre for Plant Systems Biology, VIB, Ghent, Belgium.
- Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
| | - Jin-Bo Zhang
- Novogene Bioinformatics Institute, Beijing, China.
| | - Xiao-Ming Wang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
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64
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Lin CT, Chung KF. Phylogenetic Classification of Seed Plants of Taiwan. BOTANICAL STUDIES 2017; 58:52. [PMID: 29159759 PMCID: PMC5696268 DOI: 10.1186/s40529-017-0206-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/10/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Biological classification, the hierarchical arrangement of scientific names of organisms, constitutes the core infrastructure of biological databases. For an efficient management of biological databases, adopting a stable and universal biological classification system is crucial. Currently in Taiwan Biodiversity Information Facility (TaiBIF; http://taibif.tw/ ), the national portal website that integrates Taiwan's biodiversity information databases, angiosperms are arranged according to Cronquist's System of Classification, which is not compatible with current trend of the Angiosperm Phylogeny Group (APG) classification. To consolidate the function and management of the database, TaiBIF is moving to adopt the APG IV classification and Christenhusz et al. (Phytotaxa 19:55-70, 2011)'s classification of gymnosperms, which we summarize as the Phylogenetic Classification of Seed Plants of Taiwan. RESULTS The Phylogenetic Classification of Seed Plants of Taiwan places gymnosperms in five families [vs. eight families in the Flora of Taiwan (FOT)] and angiosperms in 210 families (vs. 193 families in FOT). Three FOT gymnosperm families are synonymized in current treatment. Of the 210 APG IV families, familial circumscriptions of 114 families are identical with FOT and 50 families are recircumscription of FOT, with 46 families newly added. Of the 29 FOT families not included in current classification, two families are excluded and 27 families are synonymized. CONCLUSIONS The adoption of the Phylogenetic Classification of Seed Plants of Taiwan in TaiBIF will provide better service and efficient management of the nation's biodiversity information databases.
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Affiliation(s)
- Cheng-Tao Lin
- Department of Biological Resources, National Chiayi University, Chiayi, 60004 Taiwan
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
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65
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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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66
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De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK. Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants. Mol Biol Evol 2017; 34:1363-1377. [PMID: 28333233 PMCID: PMC5435085 DOI: 10.1093/molbev/msx069] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.
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Affiliation(s)
- Amanda R De La Torre
- Department of Plant Sciences, University of California-Davis, Davis, CA.,Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Zhen Li
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, South Africa
| | - 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
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67
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Liu Y, El-Kassaby YA. Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories. FRONTIERS IN PLANT SCIENCE 2017; 8:1719. [PMID: 29046688 PMCID: PMC5632664 DOI: 10.3389/fpls.2017.01719] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18-24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration. We applied diverse profiling methods to examine sRNA and miRNA features, including size distribution, sequence conservation and reproduction-specific regulation, as well as to predict their putative targets. The top 27 most abundant miRNAs were highly overlapped between the two species (e.g., miR166,-319 and-396), but in P. glauca, they were less abundant and significantly less correlated with seed-set phases. The most abundant sRNAs in libraries were deeply conserved miRNAs in the plant kingdom for Arabidopsis but long sRNAs (24-nt) for P. glauca. We also found significant difference in normalized expression between populations for population-specific sRNAs but not for lineage-specific ones. Moreover, lineage-specific sRNAs were enriched in the 21-nt size class. This pattern is consistent in both species and alludes to a specific type of sRNAs (e.g., miRNA, tasiRNA) being selected for. In addition, we deemed 24 and 9 sRNAs in P. glauca and Arabidopsis, respectively, as sRNA candidates targeting known adaptive genes. Temperature had significant influence on selected gene and miRNA expression at seed development in both species. This study increases our integrated understanding of sRNA evolution and its potential link to genomic architecture (e.g., sRNA derivation from genome and sRNA-mediated genomic events) and organismal complexity (e.g., association between different sRNA expression and their functionality).
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68
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Jokipii‐Lukkari S, Sundell D, Nilsson O, Hvidsten TR, Street NR, Tuominen H. NorWood: a gene expression resource for evo-devo studies of conifer wood development. THE NEW PHYTOLOGIST 2017; 216:482-494. [PMID: 28186632 PMCID: PMC6079643 DOI: 10.1111/nph.14458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/22/2016] [Indexed: 05/04/2023]
Abstract
The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.
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Affiliation(s)
- Soile Jokipii‐Lukkari
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesSE‐901 84UmeåSweden
| | - David Sundell
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
| | - Ove Nilsson
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesSE‐901 84UmeåSweden
| | - Torgeir R. Hvidsten
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
- Department of Chemistry, Biotechnology and Food ScienceNorwegian University of Life Sciences1430ÅsNorway
| | - Nathaniel R. Street
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
| | - Hannele Tuominen
- Umeå Plant Science CentreDepartment of Plant PhysiologyUmeå UniversitySE‐901 87UmeåSweden
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69
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Wong KH, Tan WL, Xiao T, Tam JP. β-Ginkgotides: Hyperdisulfide-constrained peptides from Ginkgo biloba. Sci Rep 2017; 7:6140. [PMID: 28733600 PMCID: PMC5522442 DOI: 10.1038/s41598-017-06598-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/14/2017] [Indexed: 11/13/2022] Open
Abstract
Hyperdisulfide-constrained peptides are distinguished by their high stability and diverse functions. Thus far, these peptides have been reported from animals only but their occurrence in plants are rare. Here, we report the discovery, synthesis and characterization of a hyperdisulfide-constrained peptides family of approximately 2 kDa, β-ginkgotides (β-gB1 and β-gB2) from Ginkgo biloba. Proteomic analysis showed β-ginkgotides contain 18‒20 amino acids, of which 16 residues form a conserved six-cysteine core with a highly clustered cysteine spacing of C‒CC‒C‒CC, an arrangement that has not been reported in cysteine-rich peptides. Disulfide mapping revealed a novel disulfide connectivity of CysI‒IV, CysII‒VI and CysIII‒V. Oxidative folding of synthetic β-gB1 to the native form was obtained in 70% yield. The synthetic β-gB1 displays a compact structure with no regular secondary structural elements, as determined by NMR spectroscopy. Transcriptomic analysis showed precursor βgb1 has a four-domain architecture and revealed an additional 76 β-ginkgotide-like peptides in 59 different gymnosperms, but none in angiosperms. Phylogenetic clustering analysis demonstrated β-ginkgotides belong to a new cysteine-rich peptide family. β-Ginkgotide is resistant to thermal, chemical and proteolytic degradation. Together, β-ginkgotides represent the first-in-class hyperdisulfide-constrained peptide family from plants with a novel scaffold that could be useful for engineering metabolically stable peptidyl therapeutics.
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Affiliation(s)
- Ka H Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Wei Liang Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Tianshu Xiao
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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70
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Molecular phylogenetics and historical biogeography of Sorbus sensu stricto (Rosaceae). Mol Phylogenet Evol 2017; 111:76-86. [DOI: 10.1016/j.ympev.2017.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022]
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71
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He T, Lamont BB. Baptism by fire: the pivotal role of ancient conflagrations in evolution of the Earth's flora. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwx041] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Fire became a defining feature of the Earth's processes as soon as land plants evolved 420 million years ago and has played a major role in shaping the composition and physiognomy of many ecosystems ever since. However, there remains a general lack of appreciation of the place of fire in the origin, evolution, ecology and conservation of the Earth's biodiversity. We review the literature on the presence of fire throughout the Earth's history following the evolution of land plants and examine the evidence for the origin and evolution of adaptive functional traits, biomes and major plant groups in relation to fire. We show that: (1) fire activities have fluctuated throughout geological time due to variations in climate, and more importantly in atmospheric oxygen, as these affected fuel levels and flammability; (2) fire promoted the early evolution and spread of major terrestrial plant groups; (3) fire has shaped the floristics, structure and function of major global biomes; and (4) fire has initiated and maintained the evolution of a wide array of fire-adapted functional traits since the evolution of land plants. We conclude that fire has been a fundamental agent of natural selection on terrestrial plants throughout the history of life on the Earth's land surface. We suggest that a paradigm shift is required to reassess ecological and evolutionary theories that exclude a role for fire, and also there is a need to review fire-suppression policies on ecosystem management and biodiversity conservation in global fire-prone regions.
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Affiliation(s)
- Tianhua He
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
| | - Byron B Lamont
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
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72
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Qu XJ, Wu CS, Chaw SM, Yi TS. Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae). Genome Biol Evol 2017; 9:1110-1119. [PMID: 28431152 PMCID: PMC5408090 DOI: 10.1093/gbe/evx071] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae. Our PCR and read mapping analyses together suggested the existence of isomeric plastomes in eight of the ten sequenced Cupressoideae species. The isomeric plastomes were also detected in 176 individuals from nine wild populations of four Cupressoideae species. Within Calocedrus macrolepis, we discovered a new type of isomeric plastomes that was likely derived from homologous recombination mediated by an 11-bp repeat. We conclude that isomeric plastomes are commonly present in Cupressoideae, thereby contributing to increased plastomic complexity.
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Affiliation(s)
- Xiao-Jian Qu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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73
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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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74
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Tedersoo L. Global Biogeography and Invasions of Ectomycorrhizal Plants: Past, Present and Future. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_20] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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75
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Wang Y, Liu X, Garzón‐Orduña IJ, Winterton SL, Yan Y, Aspöck U, Aspöck H, Yang D. Mitochondrial phylogenomics illuminates the evolutionary history of Neuropterida. Cladistics 2016; 33:617-636. [DOI: 10.1111/cla.12186] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2016] [Indexed: 01/19/2023] Open
Affiliation(s)
- Yuyu Wang
- Department of Entomology China Agricultural University Beijing 100193 China
- Department of Biological Sciences Vanderbilt University Nashville TN 37235 USA
| | - Xingyue Liu
- Department of Entomology China Agricultural University Beijing 100193 China
| | - Ivonne J. Garzón‐Orduña
- California Department of Food & Agriculture California State Collection of Arthropods 3294 Meadowview Rd Sacramento CA USA
| | - Shaun L. Winterton
- California Department of Food & Agriculture California State Collection of Arthropods 3294 Meadowview Rd Sacramento CA USA
| | - Yan Yan
- Department of Entomology China Agricultural University Beijing 100193 China
| | - Ulrike Aspöck
- Department of Entomology Natural History Museum Vienna Burgring 7 Vienna A‐1010 Austria
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine Medical Parasitology Medical University of Vienna Kinderspitalgasse 15 Vienna A‐1090 Austria
| | - Ding Yang
- Department of Entomology China Agricultural University Beijing 100193 China
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76
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Abstract
DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.
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77
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Semerikova SA, Semerikov VL. Phylogeny of firs (genus Abies, Pinaceae) based on multilocus nuclear markers (AFLP). RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416110132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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78
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Maherali H, Oberle B, Stevens PF, Cornwell WK, McGlinn DJ. Mutualism Persistence and Abandonment during the Evolution of the Mycorrhizal Symbiosis. Am Nat 2016; 188:E113-E125. [DOI: 10.1086/688675] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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79
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Lindquist E, Solymosi K, Aronsson H. Vesicles Are Persistent Features of Different Plastids. Traffic 2016; 17:1125-38. [PMID: 27405297 DOI: 10.1111/tra.12427] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 02/06/2023]
Abstract
Peripheral vesicles in plastids have been observed repeatedly, primarily in proplastids and developing chloroplasts, in which they are suggested to function in thylakoid biogenesis. Previous observations of vesicles in mature chloroplasts have mainly concerned low temperature pretreated plants occasionally treated with inhibitors blocking vesicle fusion. Here, we show that such vesicle-like structures occur not only in chloroplasts and proplastids, but also in etioplasts, etio-chloroplasts, leucoplasts, chromoplasts and even transforming desiccoplasts without any specific pretreatment. Observations are made both in C3 and C4 species, in different cell types (meristematic, epidermis, mesophyll, bundle sheath and secretory cells) and different organs (roots, stems, leaves, floral parts and fruits). Until recently not much focus has been given to the idea that vesicle transport in chloroplasts could be mediated by proteins, but recent data suggest that the vesicle system of chloroplasts has similarities with the cytosolic coat protein complex II system. All current data taken together support the idea of an ongoing, active and protein-mediated vesicle transport not only in chloroplasts but also in other plastids, obviously occurring regardless of chemical modifications, temperature and plastid developmental stage.
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Affiliation(s)
- Emelie Lindquist
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
| | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117, Budapest, Hungary
| | - Henrik Aronsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden.
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80
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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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81
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A global molecular phylogeny and timescale of evolution for Cryptocercus woodroaches. Mol Phylogenet Evol 2016; 98:201-9. [DOI: 10.1016/j.ympev.2016.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 01/27/2016] [Accepted: 02/07/2016] [Indexed: 11/21/2022]
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82
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Wu H, Ma Z, Wang MM, Qin AL, Ran JH, Wang XQ. A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features. Mol Ecol 2016; 25:1192-210. [PMID: 26800145 PMCID: PMC7168403 DOI: 10.1111/mec.13538] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
The origin and evolution of polyploids have been studied extensively in angiosperms and ferns but very rarely in gymnosperms. With the exception of three species of conifers, all natural polyploid species of gymnosperms belong to Ephedra, in which more than half of the species show polyploid cytotypes. Here, we investigated the origin and evolution of polyploids of Ephedra distributed in the Qinghai–Tibetan Plateau (QTP) and neighbouring areas. Flow cytometry (FCM) was used to measure the ploidy levels of the sampled species that are represented by multiple individuals from different populations, and then, two single‐copy nuclear genes (LFY and DDB2) and two chloroplast DNA fragments were used to unravel the possible origins and maternal donors of the polyploids. The results indicate that the studied polyploid species are allopolyploids, and suggest that allotetraploidy is a dominant mode of speciation in Ephedra. The high percentage of polyploids in the genus could be related to some of its biological attributes such as vegetative propagation, a relatively high rate of unreduced gamete formation, and a small genome size relative to most other gymnosperms. Significant ecological divergences between allotetraploids and their putative progenitors were detected by PCAs and anova and Tukey's tests, with the exception of E. saxatilis. The overlap of geographical distributions and ecological niches of some diploid species could have provided opportunities for interspecific hybridization and allopolyploid speciation.
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Affiliation(s)
- Hui Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhen Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ming-Ming Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ai-Li Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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83
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Gallien L, Saladin B, Boucher FC, Richardson DM, Zimmermann NE. Does the legacy of historical biogeography shape current invasiveness in pines? THE NEW PHYTOLOGIST 2016; 209:1096-105. [PMID: 26477339 DOI: 10.1111/nph.13700] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/02/2015] [Indexed: 05/12/2023]
Abstract
Why are some introduced species more successful at establishing and spreading than others? Until now, characteristics of extant species have been intensively investigated to answer this question. We propose to gain new insights on species invasiveness by exploring the long-term biogeographic and evolutionary history of lineages. We exemplify our approach using one of the best-studied invasive plant genera, Pinus. We notably estimated the historical biogeography of pines and the rates of trait evolution in pines. These estimates were analysed with regard to species invasiveness status. The results revealed that currently invasive species belong to lineages that were particularly successful at colonizing new regions in the past. We also showed that highly mobile lineages had faster rates of niche evolution, but that these rates are poor proxies for species adaptive potential in invaded regions (estimated by niche shift among native and invaded regions). In summary, working at the interface of ecology, historical biogeography and evolutionary history offers stimulating perspectives to improve our understanding of the drivers of invasion success.
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Affiliation(s)
- Laure Gallien
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Bianca Saladin
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Florian C Boucher
- Institute of Systematic Botany, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - David M Richardson
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, 7602, Matieland, South Africa
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84
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Mitochondrial introgression and complex biogeographic history of the genus Picea. Mol Phylogenet Evol 2015; 93:63-76. [DOI: 10.1016/j.ympev.2015.07.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 07/18/2015] [Accepted: 07/25/2015] [Indexed: 11/18/2022]
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85
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Uddenberg D, Akhter S, Ramachandran P, Sundström JF, Carlsbecker A. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology. FRONTIERS IN PLANT SCIENCE 2015; 6:970. [PMID: 26579190 PMCID: PMC4630563 DOI: 10.3389/fpls.2015.00970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/22/2015] [Indexed: 05/20/2023]
Abstract
Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.
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Affiliation(s)
- Daniel Uddenberg
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Shirin Akhter
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Prashanth Ramachandran
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Jens F. Sundström
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Annelie Carlsbecker
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
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86
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Assessing 62 Chinese Fir (Cunninghamia lanceolata) Breeding Parents in a 12-Year Grafted Clone Test. FORESTS 2015. [DOI: 10.3390/f6103799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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87
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de Miguel M, Bartholomé J, Ehrenmann F, Murat F, Moriguchi Y, Uchiyama K, Ueno S, Tsumura Y, Lagraulet H, de Maria N, Cabezas JA, Cervera MT, Gion JM, Salse J, Plomion C. Evidence of intense chromosomal shuffling during conifer evolution. Genome Biol Evol 2015; 7:2799-2809. [PMID: 26400405 PMCID: PMC4684699 DOI: 10.1093/gbe/evv185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkage mapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma: Pinaceae and Cupressaceae. We propose for the first time a model based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n = 12) and Cupressaceae (with n = 11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes.
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Affiliation(s)
- Marina de Miguel
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Jérôme Bartholomé
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - François Ehrenmann
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Yoshinari Moriguchi
- Niigata University, Graduate School of Science and Technology, 8050, Igarashi 2-Nocho, Nishi-ku, Niigata 950-2181, Japan
| | - Kentaro Uchiyama
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tsukuba, Ibaraki 305-8687, Japan
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tsukuba, Ibaraki 305-8687, Japan
| | - Yoshihiko Tsumura
- University of Tsukuba, Faculty of Life & Environmental Sciences, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hélène Lagraulet
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Nuria de Maria
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - José-Antonio Cabezas
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - Maria-Teresa Cervera
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - Jean Marc Gion
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France CIRAD, UMR AGAP, F-33612 Cestas, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Christophe Plomion
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
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88
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Cui YM, Sun B, Wang HF, Ferguson DK, Wang YF, Li CS, Yang J, Ma QW. Exploring the Formation of a Disjunctive Pattern between Eastern Asia and North America Based on Fossil Evidence from Thuja (Cupressaceae). PLoS One 2015; 10:e0138544. [PMID: 26393513 PMCID: PMC4579098 DOI: 10.1371/journal.pone.0138544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/01/2015] [Indexed: 11/19/2022] Open
Abstract
Thuja, a genus of Cupressaceae comprising five extant species, presently occurs in both East Asia (3 species) and North America (2 species) and has a long fossil record from Paleocene to Pleistocene in the Northern Hemisphere. Two distinct hypotheses have been proposed to account for the origin and present distribution of this genus. Here we recognize and describe T. sutchuenensis Franch., a new fossil Thuja from the late Pliocene sediments of Zhangcun, Shanxi, North China, based on detailed comparisons with all living species and other fossil ones, integrate the global fossil records of this genus plotted in a set of paleomaps from different time intervals, which show that Thuja probably first appeared at high latitudes of North America in or before the Paleocene. This genus reached Greenland in the Paleocene, then arrived in eastern Asia in the Miocene via the land connection between East Asia and western North America. In the late Pliocene, it migrated into the interior of China. With the Quaternary cooling and drying, Thuja gradually retreated southwards to form today's disjunctive distribution between East Asia and North America.
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Affiliation(s)
- Yi-Ming Cui
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nan Xin Cun, Xiangshan, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Bin Sun
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nan Xin Cun, Xiangshan, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Hai-Feng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nan Xin Cun, Xiangshan, Beijing, 100093, China
| | - David Kay Ferguson
- Department of Paleontology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Yu-Fei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nan Xin Cun, Xiangshan, Beijing, 100093, China
- * E-mail: (Y-FW); (JY)
| | - Cheng-Sen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nan Xin Cun, Xiangshan, Beijing, 100093, China
| | - Jian Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nan Xin Cun, Xiangshan, Beijing, 100093, China
- * E-mail: (Y-FW); (JY)
| | - Qing-Wen Ma
- Beijing Museum of Natural History, Beijing, 100050, China
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89
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Liu J, Zhou W, Gong X. Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China. FRONTIERS IN PLANT SCIENCE 2015; 6:696. [PMID: 26442013 PMCID: PMC4562272 DOI: 10.3389/fpls.2015.00696] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/21/2015] [Indexed: 06/02/2023]
Abstract
Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.
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Affiliation(s)
- Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Wei Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Yunnan Key Laboratory for Wild Plant ResourcesKunming, China
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90
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da Silva JAT, Karimi J, Mohsenzadeh S, Dobranszki J. Allelopathic Potential of Select Gymnospermous Trees. ACTA ACUST UNITED AC 2015. [DOI: 10.7747/jfes.2015.31.2.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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91
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Abstract
Plastid-to-nucleus DNA transfer provides a rich genetic resource to the complexity of plant nuclear genome architecture. To date, the evolutionary route of nuclear plastid DNA (nupt) remain unknown in conifers. We have sequenced the complete plastomes of two yews, Amentotaxus formosana and Taxus mairei (Taxaceae of coniferales). Our comparative genomic analyses recovered an evolutionary scenario for plastomic reorganization from ancestral to extant plastomes in the three sampled Taxaceae genera, Amentotaxus, Cephalotaxus, and Taxus. Specific primers were designed to amplify nonsyntenic regions between ancestral and extant plastomes, and 12.6 kb of nupts were identified based on phylogenetic analyses. These nupts have significantly accumulated GC-to-AT mutations, reflecting a nuclear mutational environment shaped by spontaneous deamination of 5-methylcytosin. The ancestral initial codon of rps8 is retained in the T. nupts, but its corresponding extant codon is mutated and requires C-to-U RNA-editing. These findings suggest that nupts can help recover scenarios of the nucleotide mutation process. We show that the Taxaceae nupts we retrieved may have been retained because the Cretaceous and they carry information of both ancestral genomic organization and nucleotide composition, which offer clues for understanding the plastome evolution in conifers.
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Affiliation(s)
- Chih-Yao Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
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92
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Hao ZZ, Liu YY, Nazaire M, Wei XX, Wang XQ. Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (Pinus): implications for Northern Hemisphere biogeography. Mol Phylogenet Evol 2015; 87:65-79. [PMID: 25800283 DOI: 10.1016/j.ympev.2015.03.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/24/2015] [Accepted: 03/14/2015] [Indexed: 01/15/2023]
Abstract
Climatic changes and tectonic events in the Cenozoic have greatly influenced the evolution and geographic distribution of the temperate flora. Such consequences should be most evident in plant groups that are ancient, widespread, and diverse. As one of the most widespread genera of trees, Pinus provides a good model for investigating the history of species diversification and biogeographic disjunction in the Northern Hemisphere. In this study, we reconstructed the phylogeny and investigated the evolutionary and biogeographic history of sect. Quinquefoliae (Pinus), a species-rich lineage disjunctly distributed in Asia, Europe and North America, based on complete taxon sampling and by using nine DNA fragments from chloroplast (cp), mitochondrial (mt) and nuclear genomes. The monophyly of the three subsections, Krempfianae, Gerardianae, and Strobus, is well-supported by cpDNA and nuclear gene phylogenies. However, neither subsect. Gerardianae nor subsect. Strobus forms a monophyletic group in the mtDNA phylogeny, in which sect. Quinquefoliae was divided into two major clades, one consisting of the North American and northeastern Asian species as well as the European P. peuce of subsect. Strobus, and the other comprising the remaining Eurasian species belonging to three subsections. The significant topological incongruence among the gene trees, in conjunction with divergence time estimation and ancestral area reconstruction, indicates that both ancient and relatively recent introgressive hybridization events occurred in the evolution of sect. Quinquefoliae, particularly in northeastern Asia and northwestern North America. In addition, the phylogenetic analysis suggests that the species of subsect. Strobus from subtropical eastern Asia and neighboring areas may have a single origin, although species non-monophyly is very widespread in the nuclear gene trees. Moreover, our study seems to support a Tethyan origin of sect. Quinquefoliae given the distributions and phylogenetic positions of subsects. Krempfianae and Gerardianae, and also highlights the importance of active mountain buildings and climatic changes during the Late Neogene in shaping the species diversity and geographic distribution of Pinus.
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Affiliation(s)
- Zhen-Zhen Hao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yan-Yan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mare Nazaire
- Rancho Santa Ana Botanic Garden, Claremont, CA 91711, USA
| | - Xiao-Xin Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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93
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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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94
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Qiu C, Shen Z, Peng P, Mao L, Zhang X. How does contemporary climate versus climate change velocity affect endemic plant species richness in China? ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0640-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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95
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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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96
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Wang B, Wang XR. Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus. Mol Phylogenet Evol 2014; 80:20-30. [PMID: 25106134 DOI: 10.1016/j.ympev.2014.07.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/18/2014] [Accepted: 07/24/2014] [Indexed: 11/28/2022]
Abstract
The evolution of the mitochondrial (mt) genome is far from being fully understood. Systematic investigations into the modes of inheritance, rates and patterns of recombination, nucleotide substitution, and structural changes in the mt genome are still lacking in many groups of plants. In this study, we sequenced >11kbp mtDNA segments from multiple accessions of 36 pine species to characterize the evolutionary patterns of mtDNA in the genus Pinus. We found extremely low substitution rates and complex repetitive sequences scattered across different genome regions, as well as chimeric structures that were probably generated by multiple intergenomic recombinations. The mtDNA-based phylogeny of the genus differed from that based on chloroplast and nuclear DNA in the placement of several groups of species. Such discordances suggest a series of mtDNA capture events during past range shifts of the pine species and that both vertical and horizontal inheritance are implicated in the evolution of mtDNA in Pinus. MtDNA dating revealed that most extant lineages of the genus originated during Oligocene-Miocene radiation and subgenus Strobus diversified earlier than subgenus Pinus. Our findings illustrate a reticular evolutionary pathway for the mt genome through capture and recombination in the genus Pinus, and provide new insights into the evolution of the genus.
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Affiliation(s)
- Baosheng Wang
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden.
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden
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