1
|
Zhang J, Chi X, Zhong J, Fernie A, Alseekh S, Huang L, Qian D. Extensive nrDNA ITS polymorphism in Lycium: Non-concerted evolution and the identification of pseudogenes. FRONTIERS IN PLANT SCIENCE 2022; 13:984579. [PMID: 36092433 PMCID: PMC9453804 DOI: 10.3389/fpls.2022.984579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/01/2022] [Indexed: 06/01/2023]
Abstract
The internal transcribed spacer (ITS) is one of the most extensively sequenced molecular markers in plant systematics due to its generally concerted evolution. While non-concerted evolution has been found in some plant taxa, such information is missing in Lycium. Molecular studies of six species and two variants of the genus Lycium revealed high levels of intra- and inter-individual polymorphism in the ITS, indicating non-concerted evolution. All genomic DNA ITS paralogues were identified as putative pseudogenes or functional paralogues through a series of comparisons of sequence features, including length and substitution variation, GC content, secondary structure stability, and the presence of conserved motifs in the 5.8S gene, and the rate of evolution. Approximately, 60% of ITS pseudogenes could be easily detected. Based on phylogenetic analysis, all pseudogenes were highly distinct from their corresponding functional copies, tended to evolve neutrally, and clustered randomly together in the evolutionary tree. The results probably suggest that this ITS non-concerted evolution is related to the recent divergence between tandem repeats within the Lycium genome and hybridization between species. Our study complements those of pseudogenes in plant taxa and provides a theoretical basis for the phylogeny and genetic origin of the genus Lycium while having important implications for the use of ITS molecular markers for phylogenetic reconstruction.
Collapse
Affiliation(s)
- Jiao Zhang
- Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiulian Chi
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Juying Zhong
- Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dan Qian
- Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
2
|
Cardoni S, Piredda R, Denk T, Grimm GW, Papageorgiou AC, Schulze E, Scoppola A, Salehi Shanjani P, Suyama Y, Tomaru N, Worth JRP, Cosimo Simeone M. 5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:909-926. [PMID: 34808015 PMCID: PMC9299691 DOI: 10.1111/tpj.15601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 11/02/2021] [Accepted: 11/18/2021] [Indexed: 05/31/2023]
Abstract
Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.
Collapse
Affiliation(s)
- Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Roberta Piredda
- Department of Veterinary MedicineUniversity of Bari ‘Aldo Moro’Valenzano70010Italy
| | - Thomas Denk
- Swedish Museum of Natural HistoryStockholm10405Sweden
| | | | | | | | - Anna Scoppola
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Parvin Salehi Shanjani
- Natural Resources Gene Bank, Research Institute of Forests and RangelandsAgricultural Research, Education and Extension OrganizationTehranIran
| | - Yoshihisa Suyama
- Graduate School of Agricultural ScienceTohoku UniversityOsakiMiyagi989‐6711Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaAichi464‐8601Japan
| | - James R. P. Worth
- Ecological Genetics LaboratoryForestry and Forest Products Research Institute (FFPRI)TsukubaIbaraki305‐8687Japan
| | - Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| |
Collapse
|
3
|
Lynch SC, Eskalen A, Gilbert GS. Host evolutionary relationships explain tree mortality caused by a generalist pest-pathogen complex. Evol Appl 2021; 14:1083-1094. [PMID: 33897822 PMCID: PMC8061262 DOI: 10.1111/eva.13182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
The phylogenetic signal of transmissibility (competence) and attack severity among hosts of generalist pests is poorly understood. In this study, we examined the phylogenetic effects on hosts differentially affected by an emergent generalist beetle-pathogen complex in California and South Africa. Host types (non-competent, competent and killed-competent) are based on nested types of outcomes of interactions between host plants, the beetles and the fungal pathogens. Phylogenetic dispersion analysis of each host type revealed that the phylogenetic preferences of beetle attack and fungal growth were a nonrandom subset of all available tree and shrub species. Competent hosts were phylogenetically narrower by 62 Myr than the set of all potential hosts, and those with devastating impacts were the most constrained by 107 Myr. Our results show a strong phylogenetic signal in the relative effects of a generalist pest-pathogen complex on host species, demonstrating that the strength of multi-host pest impacts in plants can be predicted by host evolutionary relationships. This study presents a unifying theoretical approach to identifying likely disease outcomes across multiple host-pest combinations.
Collapse
Affiliation(s)
- Shannon Colleen Lynch
- Department of Environmental StudiesUniversity of California Santa CruzSanta CruzCaliforniaUSA
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Akif Eskalen
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Gregory S. Gilbert
- Department of Environmental StudiesUniversity of California Santa CruzSanta CruzCaliforniaUSA
| |
Collapse
|
4
|
Urban allergy review: Allergic rhinitis and asthma with plane tree sensitization (Review). Exp Ther Med 2021; 21:275. [PMID: 33603882 DOI: 10.3892/etm.2021.9706] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/06/2020] [Indexed: 12/23/2022] Open
Abstract
Respiratory allergies represent a major public health issue in the modern world. Pollens are among the most significant causes of seasonal allergic rhinitis, with pollens of wind-pollinated trees representing an important cause. Members of the Platanaceae family (Platanus acerifolia, Platanus orientalis) are well-recognized sources of allergenic pollens worldwide, due to their high capacity of sensitization and widespread usage as ornamental urban trees. Air pollution, characteristic to all important urban conglomerates in the world and provoked by diesel exhaust gases, industrial and domestic fumes, and biogenic volatile organic compounds represents another major public health issue. Plane trees, along with other species of trees, are one of the main sources of volatile compounds. Recent studies have demonstrated a strong correlation between air pollution and respiratory allergies, with airway chemical compounds intensifying the capacity of sensitization to allergenic pollens. This study presents an overview of the known negative elements on public health of the Platanus family.
Collapse
|
5
|
Gong L, Shi W, Yang M, Luo H. Variations in the conserved 18S and 5.8S reveal the putative pseudogenes in 18S-ITS1-5.8S rDNA of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae). Biochem Biophys Res Commun 2020; 534:233-239. [PMID: 33276952 DOI: 10.1016/j.bbrc.2020.11.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 11/26/2022]
Abstract
Many early studies of ribosomal RNA gene (rDNA) suggested that rDNA tandem repeats within species are homogeneous. However, increasing number of reports have found intra-individual rDNA polymorphism across a range of taxa. Here, we reported a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in the genome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae), indicating a non-concerted evolution manner. Sequence alignments found two distinct types of 18S and 5.8S (Type A and B) and five types of ITS1 sequence (Type A - E) coexisted in the genome differing in length, GC content, secondary structure stability and minimum free energy. Based on the unique features of pseudogene and comparison of the conserved 18S rDNA sequence and 5.8S secondary structure of 22 flatfishes revealed that Type B sequences of 18S, 5.8S and their linked ITS1 were putative pseudogenes. So far, detection of rRNA pseudogenes from the multiple rDNA copies has been an intricate puzzle. Our results, as a result, provide a new ideal for rRNA pseudogene identification.
Collapse
Affiliation(s)
- Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, 316022, Zhoushan, China; Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, China.
| | - Wei Shi
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Min Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Hairong Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| |
Collapse
|
6
|
Buck R, Hyasat S, Hossfeld A, Flores-Rentería L. Patterns of hybridization and cryptic introgression among one- and four-needled pinyon pines. ANNALS OF BOTANY 2020; 126:401-411. [PMID: 32222765 PMCID: PMC7424738 DOI: 10.1093/aob/mcaa045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/27/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Pinyon pine hybridization is widely acknowledged, but the frequency of and contributors to such interspecific mating remain largely unstudied. Pinus quadrifolia has three to four needles per fascicle, suggesting that it is a result of hybridization between the five-needled P. juarezensis and the single-needled P. monophylla. In this study we address the taxonomic validity of P. juarezensis, the hybrid origin of P. quadrifolia and the presence of hybridization and intermediate morphology as a result of interspecific hybridization in this complex. METHODS We address these questions by combining a genomic and morphological approach. We generated 1868 single nucleotide polymorphisms (SNPs) to detect genetic clusters using principal co-ordinates analyis, discriminant analysis of principal components, fastSTRUCTURE and ADMIXTURE analyses, and performed a morphological analysis of the leaves. KEY RESULTS We found that the five-needled pinyons did not differ genetically from the four-needled P. quadrifolia, reducing the status of P. juarezensis to P. quadrifolia. We also found no evidence that P. quadrifolia is of hybrid origin from P. juarezensis × P. monophylla but is instead a genetically distinct species with natural needle number variation that has yet to be explained. Hybridization does occur in this complex, but mostly between P. quadrifolia and P. californiarum, and less commonly between P. quadrifolia and P. monophylla. Interestingly, some hybrid derivatives were detected between both single-needled taxa, P. monophylla and P. californiarum, a hybrid combination that has not yet been proposed. Hybrids have intermediate morphology when they have similar genetic contributions from both parental species; however, when one parent contributes more, hybrid derivatives resemble the parent with higher genetic contribution, resulting in cryptic introgression. CONCLUSIONS Our detailed sampling across the distribution of this complex allows us to describe the patterns of hybridization among these taxa, resolves an ancient taxonomic conflict and provides insights into the challenges of exclusively using morphological traits when identifying these taxa with cryptic hybridization and variable morphology.
Collapse
Affiliation(s)
- Ryan Buck
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Sandra Hyasat
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alice Hossfeld
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | |
Collapse
|
7
|
Molecular and morphological evidence for hybrid origin and matroclinal inheritance of an endangered wild rose, Rosa × pseudobanksiae (Rosaceae) from China. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01227-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
8
|
Gong L, Shi W, Yang M, Kong X. Marked intra-genomic variation and pseudogenes in the ITS1-5.8S-ITS2 rDNA of Symphurus plagiusa (Pleuronectiformes: Cynoglossidae). ANIM BIOL 2018. [DOI: 10.1163/15707563-17000134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The eukaryotic ribosomal DNA (rDNA) cluster consists of multiple copies of three genes (18S, 5.8S, and 28S rDNA) and two internal transcribed spacers (ITS1 and ITS2). In recent years, an increasing number of rDNA sequence polymorphisms have been identified in numerous species. In the present study, we provide 33 complete ITS (ITS1-5.8S-ITS2) sequences from two Symphurus plagiusa individuals. To the best of our knowledge, these sequences are the first detailed information on ITS sequences in Pleuronectiformes. Here, two divergent types (Type A and B) of the ITS1-5.8S-ITS2 rDNA sequence were found, which mainly differ in sequence length, GC content, nucleotide diversity (π), secondary structure and minimum free energy. The ITS1-5.8S-ITS2 rDNA sequence of Type B was speculated to be a putative pseudogene according to pseudogene identification criteria. Cluster analysis showed that sequences from the same type clustered into one group and two major groups were formed. The high degree of ITS1-5.8S-ITS2 sequence polymorphism at the intra-specific level indicated that the S. plagiusa genome has evolved in a non-concerted evolutionary manner. These results not only provide useful data for ribosomal pseudogene identification, but also further contribute to the study of rDNA evolution in teleostean genomes.
Collapse
Affiliation(s)
- Li Gong
- 1National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022, Zhoushan, China
- 2National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Wei Shi
- 3Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510000, Guangzhou, China
- 4South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, 510000, Guangzhou, China
| | - Min Yang
- 3Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510000, Guangzhou, China
- 4South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, 510000, Guangzhou, China
| | - Xiaoyu Kong
- 3Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510000, Guangzhou, China
- 4South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, 510000, Guangzhou, China
| |
Collapse
|
9
|
Mujtaba M, Sargin I, Akyuz L, Ceter T, Kaya M. Newly isolated sporopollenin microcages from Platanus orientalis pollens as a vehicle for controlled drug delivery. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 77:263-270. [DOI: 10.1016/j.msec.2017.02.176] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/19/2016] [Accepted: 02/06/2017] [Indexed: 10/19/2022]
|
10
|
Tsopelas P, Santini A, Wingfield MJ, Wilhelm de Beer Z. Canker Stain: A Lethal Disease Destroying Iconic Plane Trees. PLANT DISEASE 2017; 101:645-658. [PMID: 30678566 DOI: 10.1094/pdis-09-16-1235-fe] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Europe, both Oriental plane and London plane trees are seriously threatened by the invasive fungal pathogen Ceratocystis platani (Walter) Engelbr. & T.C. Harr., the causal agent of canker stain disease (CSD) of plane trees. The fungus is considered to be indigenous to North America and was accidently introduced into Europe during World War II, where it continues to spread clonally. The impact of CSD in Europe can be compared with notorious tree diseases such as Dutch elm disease, chestnut blight, and more recently Ash dieback, which have all caused devastating losses to natural woody ecosystems and ornamental trees. In Italy and France, C. platani has caused widespread mortality to London plane trees and the pathogen has also been recorded in Switzerland and Spain. However, the most dramatic impact of the disease has been in Greece in natural stands of Oriental plane. The objective of this feature article is to review current knowledge regarding CSD and to highlight the dramatic and devastating nature of the disease. An important aim is also to highlight the risk of C. platani spreading northward in Europe and eastward to Asia in the natural and cultivated range of oriental and London plane.
Collapse
Affiliation(s)
- Panaghiotis Tsopelas
- Hellenic Agricultural Organization "Demeter," Institute of Mediterranean Forest Ecosystems, Athens, Greece
| | - Alberto Santini
- C.N.R. Institute for Sustainable Plant Protection, Firenze, Italy
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Αgricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - Z Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Αgricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| |
Collapse
|
11
|
Flores-Rentería L, Rymer PD, Riegler M. Unpacking boxes: Integration of molecular, morphological and ecological approaches reveals extensive patterns of reticulate evolution in box eucalypts. Mol Phylogenet Evol 2017; 108:70-87. [DOI: 10.1016/j.ympev.2017.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 11/26/2022]
|
12
|
Against all odds: reconstructing the evolutionary history of Scrophularia (Scrophulariaceae) despite high levels of incongruence and reticulate evolution. ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0316-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Xu B, Zeng XM, Gao XF, Jin DP, Zhang LB. ITS non-concerted evolution and rampant hybridization in the legume genus Lespedeza (Fabaceae). Sci Rep 2017; 7:40057. [PMID: 28051161 PMCID: PMC5209741 DOI: 10.1038/srep40057] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/30/2016] [Indexed: 12/27/2022] Open
Abstract
The internal transcribed spacer (ITS) as one part of nuclear ribosomal DNA is one of the most extensively sequenced molecular markers in plant systematics. The ITS repeats generally exhibit high-level within-individual homogeneity, while relatively small-scale polymorphism of ITS copies within individuals has often been reported in literature. Here, we identified large-scale polymorphism of ITS copies within individuals in the legume genus Lespedeza (Fabaceae). Divergent paralogs of ITS sequences, including putative pseudogenes, recombinants, and multiple functional ITS copies were sometimes detected in the same individual. Thirty-seven ITS pseudogenes could be easily detected according to nucleotide changes in conserved 5.8S motives, the significantly lower GC contents in at least one of three regions, and the lost ability of 5.8S rDNA sequence to fold into a conserved secondary structure. The distribution patterns of the putative functional clones were highly different between the traditionally recognized two subgenera, suggesting different rates of concerted evolution in two subgenera which could be attributable to their different extents/frequencies of hybridization, confirmed by our analysis of the single-copy nuclear gene PGK. These findings have significant implications in using ITS marker for reconstructing phylogeny and studying hybridization.
Collapse
MESH Headings
- Base Composition
- Cluster Analysis
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Evolution, Molecular
- Lespedeza/classification
- Lespedeza/genetics
- Nucleic Acid Hybridization
- Phylogeny
- Polymorphism, Genetic
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Xiao-Mao Zeng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Dong-Pil Jin
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Li-Bing Zhang
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166, USA
| |
Collapse
|
14
|
Johnson MG, Lang K, Manos P, Golet GH, Schierenbeck KA. Evidence for genetic erosion of a California native tree, Platanus racemosa, via recent, ongoing introgressive hybridization with an introduced ornamental species. CONSERV GENET 2016. [DOI: 10.1007/s10592-015-0808-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
15
|
Asam C, Hofer H, Wolf M, Aglas L, Wallner M. Tree pollen allergens-an update from a molecular perspective. Allergy 2015; 70:1201-11. [PMID: 26186076 PMCID: PMC5102629 DOI: 10.1111/all.12696] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2015] [Indexed: 12/30/2022]
Abstract
It is estimated that pollen allergies affect approximately 40% of allergic individuals. In general, tree pollen allergies are mainly elicited by allergenic trees belonging to the orders Fagales, Lamiales, Proteales, and Pinales. Over 25 years ago, the gene encoding the major birch pollen allergen Bet v 1 was the first such gene to be cloned and its product characterized. Since that time, 53 tree pollen allergens have been identified and acknowledged by the WHO/IUIS allergen nomenclature subcommittee. Molecule‐based profiling of allergic sensitization has helped to elucidate the immunological connections of allergen cross‐reactivity, whereas advances in biochemistry have revealed structural and functional aspects of allergenic proteins. In this review, we provide a comprehensive overview of the present knowledge of the molecular aspects of tree pollen allergens. We analyze the geographic distribution of allergenic trees, discuss factors pivotal for allergic sensitization, and describe the role of tree pollen panallergens. Novel allergenic tree species as well as tree pollen allergens are continually being identified, making research in this field highly competitive and instrumental for clinical applications.
Collapse
Affiliation(s)
- C. Asam
- Department of Molecular Biology University of Salzburg Salzburg Austria
| | - H. Hofer
- Department of Molecular Biology University of Salzburg Salzburg Austria
| | - M. Wolf
- Department of Molecular Biology University of Salzburg Salzburg Austria
| | - L. Aglas
- Department of Molecular Biology University of Salzburg Salzburg Austria
| | - M. Wallner
- Department of Molecular Biology University of Salzburg Salzburg Austria
| |
Collapse
|
16
|
Su X, Wu G, Li L, Liu J. Species delimitation in plants using the Qinghai-Tibet Plateau endemic Orinus (Poaceae: Tridentinae) as an example. ANNALS OF BOTANY 2015; 116:35-48. [PMID: 25987712 PMCID: PMC4479750 DOI: 10.1093/aob/mcv062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/27/2014] [Accepted: 03/31/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Accurate identification of species is essential for the majority of biological studies. However, defining species objectively and consistently remains a challenge, especially for plants distributed in remote regions where there is often a lack of sufficient previous specimens. In this study, multiple approaches and lines of evidence were used to determine species boundaries for plants occurring in the Qinghai-Tibet Plateau, using the genus Orinus (Poaceae) as a model system for an integrative approach to delimiting species. METHODS A total of 786 individuals from 102 populations of six previously recognized species were collected for niche, morphological and genetic analyses. Three plastid DNA regions (matK, rbcL and trnH-psbA) and one nuclear DNA region [internal transcribed space (ITS)] were sequenced. KEY RESULTS Whereas six species had been previously recognized, statistical analyses based on character variation, molecular data and niche differentiation identified only two well-delimited clusters, together with a third possibly originating from relatively recent hybridization between, or historical introgression from, the other two. CONCLUSIONS Based on a principle of integrative species delimitation to reconcile different sources of data, the results provide compelling evidence that the six previously recognized species of the genus Orinus that were examined should be reduced to two, with new circumscriptions, and a third, identified in this study, should be described as a new species. This empirical study highlights the value of applying genetic differentiation, morphometric statistics and ecological niche modelling in an integrative approach to re-circumscribing species boundaries. The results produce relatively objective, operational and unbiased taxonomic classifications of plants occurring in remote regions.
Collapse
Affiliation(s)
- Xu Su
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Guili Wu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Lili Li
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| |
Collapse
|
17
|
Discovery of unusual anatomical and continuous characters in the evolutionary history of Conostegia (Miconieae: Melastomataceae). Mol Phylogenet Evol 2015; 82 Pt A:289-313. [DOI: 10.1016/j.ympev.2014.09.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 11/19/2022]
|
18
|
Galián JA, Rosato M, Rosselló JA. Incomplete sequence homogenization in 45S rDNA multigene families: intermixed IGS heterogeneity within the single NOR locus of the polyploid species Medicago arborea (Fabaceae). ANNALS OF BOTANY 2014; 114:243-51. [PMID: 24925322 PMCID: PMC4111382 DOI: 10.1093/aob/mcu115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/02/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Ribosomal sequences have become the classical example of the genomic homogenization of nuclear multigene families. Despite theoretical advantages and modelling predictions that support concerted evolution of the 45S rDNA, several reports have found intragenomic polymorphisms. However, the origins and causes of these rDNA polymorphisms are difficult to assess because seed plants show a wide range of 45S rDNA loci number variation, especially in polyploids. Medicago arborea is a tetraploid species that has a single 45S rDNA locus. This feature makes this species a suitable case study to assess the fate of ribosomal IGS homogenization in polyploid species showing nucleolus organizer region (NOR) reduction. METHODS The intergenic spacer (IGS) region was amplified by long PCR and the fragments were cloned and sequenced by a primer-walking strategy. The physical mapping of the whole and partial IGS variants was assessed by fluorescent in situ hybridization (FISH) and fibre-FISH methods on mitotic chromosomes and extended DNA fibres, respectively. KEY RESULTS Two IGS fragments of 4·8 and 3·5 kb were obtained showing structural features of functional sequences. The shorter variant appears to be a truncated copy of the 4·8 kb fragment that lacks the duplication of the transcription initiation site region and the entire D region. The physical localization of the two IGS variants on metaphase chromosomes and extended DNA fibres using FISH corroborated their joint presence within the same locus. In addition, no spatial structure of the two variants was detected within the NOR. CONCLUSIONS The results suggest that full sequence homogenization is not operating within the NOR locus of M. arborea. The structure of the NOR locus reported here departs from the models of IGS heterogeneity present in plants and caution against assuming the widespread belief that intragenomic ribosomal heterogeneity is mainly due to sequence variation between paralogous loci.
Collapse
Affiliation(s)
- José A Galián
- Jardín Botánico, ICBiBE, Universidad de Valencia, c/Quart 80, E-46008, Valencia, Spain
| | - Marcela Rosato
- Jardín Botánico, ICBiBE, Universidad de Valencia, c/Quart 80, E-46008, Valencia, Spain
| | - Josep A Rosselló
- Jardín Botánico, ICBiBE, Universidad de Valencia, c/Quart 80, E-46008, Valencia, Spain Marimurtra Bot. Garden, Carl Faust Fdn, PO Box 112, E-17300 Blanes, Catalonia, Spain
| |
Collapse
|
19
|
Malé PJG, Bardon L, Besnard G, Coissac E, Delsuc F, Engel J, Lhuillier E, Scotti-Saintagne C, Tinaut A, Chave J. Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Mol Ecol Resour 2014; 14:966-75. [DOI: 10.1111/1755-0998.12246] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/09/2014] [Accepted: 02/22/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Pierre-Jean G. Malé
- UMR 5174 Laboratoire Évolution & Diversité Biologique; CNRS; Université Paul Sabatier; ENFA; 118 route de Narbonne F-31062 Toulouse France
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto ON M5S 3G5 Canada
| | - Léa Bardon
- UMR 5174 Laboratoire Évolution & Diversité Biologique; CNRS; Université Paul Sabatier; ENFA; 118 route de Narbonne F-31062 Toulouse France
| | - Guillaume Besnard
- UMR 5174 Laboratoire Évolution & Diversité Biologique; CNRS; Université Paul Sabatier; ENFA; 118 route de Narbonne F-31062 Toulouse France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine CNRS; UMR5553; Université Joseph Fourier; BP 53 F-38041 Grenoble Cedex 9 France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution; UMR 5554-CNRS; Université Montpellier 2; Place Eugène Bataillon Montpellier France
| | - Julien Engel
- UMR ECOFOG; INRA; Université Antilles-Guyane; CNRS; CIRAD; AgroParisTech; Campus agronomique BP 709 F-97387 Kourou Cedex France
| | - Emeline Lhuillier
- INRA; UAR 1209 Département de Génétique Animale; INRA Auzeville; F-31326 Castanet-Tolosan France
- GeT-PlaGe; Genotoul; INRA Auzeville; F-31326 Castanet-Tolosan France
| | - Caroline Scotti-Saintagne
- UMR ECOFOG; INRA; Université Antilles-Guyane; CNRS; CIRAD; AgroParisTech; Campus agronomique BP 709 F-97387 Kourou Cedex France
| | - Alexandra Tinaut
- UMR ECOFOG; INRA; Université Antilles-Guyane; CNRS; CIRAD; AgroParisTech; Campus agronomique BP 709 F-97387 Kourou Cedex France
| | - Jérôme Chave
- UMR 5174 Laboratoire Évolution & Diversité Biologique; CNRS; Université Paul Sabatier; ENFA; 118 route de Narbonne F-31062 Toulouse France
| |
Collapse
|
20
|
Multiple ITS copies reveal extensive hybridization within Rheum (Polygonaceae), a genus that has undergone rapid radiation. PLoS One 2014; 9:e89769. [PMID: 24587023 PMCID: PMC3937351 DOI: 10.1371/journal.pone.0089769] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 01/25/2014] [Indexed: 11/24/2022] Open
Abstract
Background During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual. Methodology/Principal Findings In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively. Conclusions These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation.
Collapse
|
21
|
|
22
|
De Castro O, Di Maio A, Lozada García JA, Piacenti D, Vázquez-Torres M, De Luca P. Plastid DNA sequencing and nuclear SNP genotyping help resolve the puzzle of central American Platanus. ANNALS OF BOTANY 2013; 112:589-602. [PMID: 23798602 PMCID: PMC3718222 DOI: 10.1093/aob/mct134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/23/2013] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Recent research on the history of Platanus reveals that hybridization phenomena occurred in the central American species. This study has two goals: to help resolve the evolutive puzzle of central American Platanus, and to test the potential of real-time polymerase chain reaction (PCR) for detecting ancient hybridization. METHODS Sequencing of a uniparental plastid DNA marker [psbA-trnH((GUG)) intergenic spacer] and qualitative and quantitative single nucleotide polymorphism (SNP) genotyping of biparental nuclear ribosomal DNA (nrDNA) markers [LEAFY intron 2 (LFY-i2) and internal transcribed spacer 2 (ITS2)] were used. KEY RESULTS Based on the SNP genotyping results, several Platanus accessions show the presence of hybridization/introgression, including some accessions of P. rzedowskii and of P. mexicana var. interior and one of P. mexicana var. mexicana from Oaxaca (= P. oaxacana). Based on haplotype analyses of the psbA-trnH spacer, five haplotypes were detected. The most common of these is present in taxa belonging to P. orientalis, P. racemosa sensu lato, some accessions of P. occidentalis sensu stricto (s.s.) from Texas, P. occidentalis var. palmeri, P. mexicana s.s. and P. rzedowskii. This is highly relevant to genetic relationships with the haplotypes present in P. occidentalis s.s. and P. mexicana var. interior. CONCLUSIONS Hybridization and introgression events between lineages ancestral to modern central and eastern North American Platanus species occurred. Plastid haplotypes and qualitative and quantitative SNP genotyping provide information critical for understanding the complex history of Mexican Platanus. Compared with the usual molecular techniques of sub-cloning, sequencing and genotyping, real-time PCR assay is a quick and sensitive technique for analysing complex evolutionary patterns.
Collapse
Affiliation(s)
- Olga De Castro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Via Foria 223, Orto Botanico, 80139 Napoli, Italy.
| | | | | | | | | | | |
Collapse
|
23
|
Dkhar J, Kumaria S, Rao SR, Tandon P. New insights into character evolution, hybridization and diversity of IndianNymphaea(Nymphaeaceae): evidence from molecular and morphological data. SYST BIODIVERS 2013. [DOI: 10.1080/14772000.2013.773949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
24
|
SONG HUIXING, GAO SUPING, JIANG MINGYAN, LIU GUANGLI, YU XIAOFANG, CHEN QIBING. The evolution and utility of ribosomal ITS sequences in Bambusinae and related species: divergence, pseudogenes, and implications for phylogeny. J Genet 2012; 91:129-39. [DOI: 10.1007/s12041-012-0170-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
25
|
Kusumi J, Azuma H, Tzeng HY, Chou LS, Peng YQ, Nakamura K, Su ZH. Phylogenetic analyses suggest a hybrid origin of the figs (Moraceae: Ficus) that are endemic to the Ogasawara (Bonin) Islands, Japan. Mol Phylogenet Evol 2012; 63:168-79. [PMID: 22281208 DOI: 10.1016/j.ympev.2012.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 12/29/2011] [Accepted: 01/07/2012] [Indexed: 01/02/2023]
Abstract
The Ogasawara Islands are oceanic islands and harbor a unique endemic flora. There are three fig species (Ficus boninsimae, F. nishimurae and F. iidaiana) endemic to the Ogasawara Islands, and these species have been considered to be closely related to Ficus erecta, and to have diverged within the islands. However, this hypothesis remains uncertain. To investigate this issue, we assessed the phylogenetic relationships of the Ogasawara figs and their close relatives occurring in Japan, Taiwan and South China based on six plastid genome regions, nuclear ITS region and two nuclear genes. The plastid genome-based tree indicated a close relationship between the Ogasawara figs and F. erecta, whereas some of the nuclear gene-based trees suggested this relationship was not so close. In addition, the phylogenetic analyses of the pollinating wasps associated with these fig species based on the nuclear 28S rRNA and mitochondrial cytB genes suggested that the fig-pollinating wasps of F. erecta are not sister to those of the Ogasawara figs These results suggest the occurrence of an early hybridization event(s) in the lineage leading to the Ogasawara figs.
Collapse
Affiliation(s)
- Junko Kusumi
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | | | | | | | | | | | | |
Collapse
|
26
|
Peng YY, Baum BR, Ren CZ, Jiang QT, Chen GY, Zheng YL, Wei YM. The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae). Hereditas 2010; 147:183-204. [PMID: 21039456 DOI: 10.1111/j.1601-5223.2010.02172.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and these repeats often undergo rapid concerted evolution within and between arrays. Therefore, the rDNA ITS copies appear to be virtually identical and can sometimes be treated as a single gene. In this paper we examined ITS polymorphism within and among 13 diploid (A and C genomes), seven tetraploid (AB, AC and CC genomes) and four hexaploid (ACD genome) to infer the extent and direction of concerted evolution, and to reveal the phylogenetic and genome relationship among species of Avena. A total of 170 clones of the ITS1-5.8S-ITS2 fragment were sequenced to carry out haplotype and phylogenetic analysis. In addition, 111 Avena ITS sequences retrieved from GenBank were combined with 170 clones to construct a phylogeny and a network. We demonstrate the major divergence between the A and C genomes whereas the distinction among the A and B/D genomes was generally not possible. High affinity among the A(d) genome species A. damascena and the ACD genome species A. fatua was found, whereas the rest of the ACD genome hexaploids and the AACC tetraploids were highly affiliated with the A(l) genome diploid A. longiglumis. One of the AACC species A. murphyi showed the closest relationship with most of the hexaploid species. Both C(v) and C(p) genome species have been proposed as paternal donors of the C-genome carrying polyploids. Incomplete concerted evolution is responsible for the observed differences among different clones of a single Avena individual. The elimination of C-genome rRNA sequences and the resulting evolutionary inference of hexaploid species are discussed.
Collapse
Affiliation(s)
- Yuan-Ying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Ya'an, Sichuan, PR China
| | | | | | | | | | | | | |
Collapse
|
27
|
A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae). Mol Phylogenet Evol 2010; 55:911-28. [DOI: 10.1016/j.ympev.2009.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 11/17/2022]
|
28
|
Xiao LQ, Möller M, Zhu H. High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: Incomplete concerted evolution and the origin of pseudogenes. Mol Phylogenet Evol 2010; 55:168-177. [PMID: 19945537 DOI: 10.1016/j.ympev.2009.11.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 11/19/2009] [Accepted: 11/20/2009] [Indexed: 11/15/2022]
Affiliation(s)
- Long-Qian Xiao
- Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Kunming 650223, China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Michael Möller
- Royal Botanical Garden Edinburgh, Edinburg EH3 5LR, Scotland, United Kingdom
| | - Hua Zhu
- Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Kunming 650223, China.
| |
Collapse
|
29
|
Bao Y, Wendel JF, Ge S. Multiple patterns of rDNA evolution following polyploidy in Oryza. Mol Phylogenet Evol 2009; 55:136-142. [PMID: 19857580 DOI: 10.1016/j.ympev.2009.10.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 10/06/2009] [Accepted: 10/18/2009] [Indexed: 10/20/2022]
Abstract
Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and hence are ubiquitous and present in high copy number. Ribosomal rDNA repeats often undergo rapid concerted evolution within and between arrays. Interspecific hybridization merges divergent repeat types in a single nucleus, setting in motion evolutionary processes leading to coexistence, maintenance of paralogs, origin of novel sequence variants, loss of arrays, or inter-array sequence homogenization via concerted evolution. Here we examined ITS polymorphism within and among six Oryza tetraploids of varying genomic composition to infer the extent and direction of concerted evolution following allopolyploid speciation. We demonstrate that different polyploids have experienced varying fates, including maintenance or homogenization of divergent arrays, even among allopolyploids having the same genomic origins but in different geographic locations. Bidirectional concerted evolution, in which arrays become homogenized to alternative progenitor diploid types in different allopolyploid derivatives, is evident among species in one clade. Our results exemplify the panoply of outcomes for ribosomal DNA evolution following allopolyploid speciation.
Collapse
Affiliation(s)
- Ying Bao
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, PR China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.
| | - Jonathan F Wendel
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, United States
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| |
Collapse
|
30
|
Garcia-Jacas N, Soltis PS, Font M, Soltis DE, Vilatersana R, Susanna A. The polyploid series of Centaurea toletana: glacial migrations and introgression revealed by nrDNA and cpDNA sequence analyzes. Mol Phylogenet Evol 2009; 52:377-94. [PMID: 19306936 DOI: 10.1016/j.ympev.2009.03.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Revised: 03/08/2009] [Accepted: 03/10/2009] [Indexed: 11/17/2022]
Abstract
The polyploid series of Centaurea toletana comprises diploid, tetraploid, and hexaploid cytotypes. Previous studies suggested that the tetraploid was an autopolyploid, while the hexaploid was an allopolyploid and should be considered a different species, C. argecillensis. Sequencing of the ITS and rps4-trnT-trnL, ycf3-trnS, and rpL16 regions, and extensive cloning and sequencing of the ETS region have revealed that many diploid individuals and populations show different ribotypes, likely resulting from ancient hybridization events. Ribotypes found in the diploid populations are also present in tetraploid populations. The extreme difficulties in classifying the tetraploid as auto- or allopolyploid are discussed. The hexaploid C. argecillensis also shows many different ribotypes, including a ribotype not found in the diploids and making an autopolyploid origin unlikely. The pattern of introgression and gene flow implicates several species from the Iberian Peninsula and the High Atlas Mountains in Morocco as genetic donors in ancient hybridization events. This long-reaching network of hybridization may trace its origin to the climatic history of the western Mediterranean during the Neogene.
Collapse
Affiliation(s)
- Núria Garcia-Jacas
- Botanic Institute of Barcelona (CSIC-ICUB), Passeig del Migdia, s.n., E-08038 Barcelona, Spain.
| | | | | | | | | | | |
Collapse
|
31
|
Feild TS, Chatelet DS, Brodribb TJ. Ancestral xerophobia: a hypothesis on the whole plant ecophysiology of early angiosperms. GEOBIOLOGY 2009; 7:237-64. [PMID: 19260972 DOI: 10.1111/j.1472-4669.2009.00189.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Today, angiosperms are fundamental players in the diversity and biogeochemical functioning of the planet. Yet despite the omnipresence of angiosperms in today's ecosystems, the basic evolutionary understanding of how the earliest angiosperms functioned remains unknown. Here we synthesize ecophysiological, paleobotanical, paleoecological, and phylogenetic lines of evidence about early angiosperms and their environments. In doing so, we arrive at a hypothesis that early angiosperms evolved in evermoist tropical terrestrial habitats, where three of their emblematic innovations - including net-veined leaves, xylem vessels, and flowers - found ecophysiological advantages. However, the adaptation of early angiosperm ecophysiology to wet habitats did not initially promote massive diversification and ecological dominance. Instead, wet habitats were permissive for the ecological roothold of the clade, a critical phase of early diversification that entailed experimentation with a range of functional innovations in the leaves, wood, and flowers. Later, our results suggest that some of these innovations were co-opted gradually for new roles in the evolution of greater productivity and drought tolerance, which are characteristics seen across the vast majority of derived and ecologically dominant angiosperms today.
Collapse
Affiliation(s)
- T S Feild
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37919 USA
| | | | | |
Collapse
|