1
|
Martínez-Domínguez L, Nicolalde-Morejón F, Vergara-Silva F, Guevara R, Gernandt DS, Stevenson DW. Species delimitation in Ceratozamia (Zamiaceae) from Southwestern Mexico, in light of reproductive and climatic diversification. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00598-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
2
|
Martínez-Domínguez L, Nicolalde-Morejón F, Lorea-Hernández FG, Vergara-Silva F, Stevenson DW. A novelty in Ceratozamia (Zamiaceae, Cycadales) from the Sierra Madre del Sur, Mexico: biogeographic and morphological patterns, DNA barcoding and phenology. PHYTOKEYS 2020; 156:1-25. [PMID: 32943975 PMCID: PMC7471474 DOI: 10.3897/phytokeys.156.53502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Ceratozamia is a genus of cycads occurring in eastern Mexico and Central America. In this study, we describe a new species from the Pacific region of Mexico in Guerrero state. This locality represents the most northwestern Mexico distribution for the genus. We focus the comparison of this species with the most geographically proximate and phenotypically relevant lineages for this taxon. We followed an integrative taxonomy approach to evaluate the classification of these species, including geographic location, morphology, DNA barcoding and phenology as primary sources of systematic data. Within the morphological dataset, reproductive structures are described in detail and new characters are proposed for microsporophylls. The comparative morphology of these structures facilitated the elucidation of differences in forms and species for identification. The two chosen DNA barcoding markers - namely, the chloroplast genome coding region matK and the nuclear ribosomal internal transcribed spacer (ITS) region - had low divergence, allowing only 61% of species identification, suggesting slow molecular evolutionary rates. Besides employing these three basic sources of evidence, we introduced phenology as additional information for species circumscription. In addition, this work includes a brief review of the genus at the species-level. This is therefore the most recent review for Ceratozamia across its full geographic range (latitudinal and elevational). Overall, this work further contributes to a comprehensive framework for systematic studies in Mexican cycads.
Collapse
Affiliation(s)
- Lilí Martínez-Domínguez
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito Exterior, Ciudad Universitaria, 04510, Coyoacán, CDMX, Mexico
- Laboratorio de Taxonomía Integrativa, Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa, 91190, Veracruz. Mexico
- Laboratorio de Sistemática Molecular (Jardín Botánico), Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito Exterior, Ciudad Universitaria, 04510, Coyoacán, CDMX. Mexico
| | - Fernando Nicolalde-Morejón
- Laboratorio de Taxonomía Integrativa, Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa, 91190, Veracruz. Mexico
| | | | - Francisco Vergara-Silva
- Laboratorio de Sistemática Molecular (Jardín Botánico), Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito Exterior, Ciudad Universitaria, 04510, Coyoacán, CDMX. Mexico
| | | |
Collapse
|
3
|
Clugston JAR, Kenicer GJ, Milne R, Overcast I, Wilson TC, Nagalingum NS. RADseq as a valuable tool for plants with large genomes—A case study in cycads. Mol Ecol Resour 2019; 19:1610-1622. [DOI: 10.1111/1755-0998.13085] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 11/26/2022]
Affiliation(s)
- James A. R. Clugston
- School of Biological Sciences The University of Edinburgh Edinburgh UK
- Royal Botanic Garden Edinburgh Edinburgh UK
| | | | - Richard Milne
- School of Biological Sciences The University of Edinburgh Edinburgh UK
| | - Isaac Overcast
- The Graduate Center of the City University of New York New York NY USA
| | | | | |
Collapse
|
4
|
Viruel J, Conejero M, Hidalgo O, Pokorny L, Powell RF, Forest F, Kantar MB, Soto Gomez M, Graham SW, Gravendeel B, Wilkin P, Leitch IJ. A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens. FRONTIERS IN PLANT SCIENCE 2019; 10:937. [PMID: 31396248 PMCID: PMC6667659 DOI: 10.3389/fpls.2019.00937] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/04/2019] [Indexed: 05/24/2023]
Abstract
Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (Dioscorea) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (Dioscorea alata, D. communis, and D. sylvatica). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.
Collapse
Affiliation(s)
- Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mânoa, Honolulu, HI, United States
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Endless Forms, Leiden, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Science and Technology Faculty, University of Applied Sciences Leiden, Leiden, Netherlands
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | |
Collapse
|
5
|
Liu Y, Liu S, Yeh CF, Zhang N, Chen G, Que P, Dong L, Li SH. The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies. Sci Rep 2018; 8:15723. [PMID: 30356056 PMCID: PMC6200822 DOI: 10.1038/s41598-018-33646-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/21/2018] [Indexed: 11/24/2022] Open
Abstract
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Chia-Fen Yeh
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Guoling Chen
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Shou-Hsien Li
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China.
| |
Collapse
|
6
|
Pizarro D, Divakar PK, Grewe F, Leavitt SD, Huang JP, Dal Grande F, Schmitt I, Wedin M, Crespo A, Lumbsch HT. Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0407-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Feng X, Liu J, Chiang YC, Gong X. Investigating the Genetic Diversity, Population Differentiation and Population Dynamics of Cycas segmentifida (Cycadaceae) Endemic to Southwest China by Multiple Molecular Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:839. [PMID: 28580005 PMCID: PMC5437697 DOI: 10.3389/fpls.2017.00839] [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: 01/20/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs), three nuclear genes (nDNAs) and 12 nuclear microsatellites (SSRs), we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China. High levels of genetic diversity and genetic differentiation were revealed in C. segmentifida. Haplotypes of networks showed two evolutionary units in C. segmentifida, with the exception of the nuclear gene GTP network. Meanwhile, the UPGMA tree, structure and PCoA analyses suggested that 14 populations of C. segmentifida were divided into two clades. There was significant effect of isolation by distance (IBD) in this species. However, this species did not display a significant phylogeographic structure. The divergence time estimation suggested that its haplotypes diverged during the Middle Pleistocene. Additionally, the population dynamics inferred from different DNA sequences analyses were discordant. Bottleneck analysis showed that populations of C. segmentifida did not experience any recent bottleneck effect, but rather pointed to a contraction of its effective population size over time. Furthermore, our results suggested that the population BM which held an intact population structure and occupied undisturbed habitat was at the Hardy-Weinberg equilibrium, implying that this population is a free-mating system. These genetic features provide important information for the sustainable management of C. segmentifida.
Collapse
Affiliation(s)
- Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen UniversityKaohsiung, Taiwan
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| |
Collapse
|
9
|
Salas-Leiva DE, Meerow AW, Calonje M, Francisco-Ortega J, Griffith MP, Nakamura K, Sánchez V, Knowles L, Knowles D. Shifting Quaternary migration patterns in the Bahamian archipelago: Evidence from the Zamia pumila complex at the northern limits of the Caribbean island biodiversity hotspot. AMERICAN JOURNAL OF BOTANY 2017; 104:757-771. [PMID: 28515078 DOI: 10.3732/ajb.1700054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY The Bahamas archipelago is formed by young, tectonically stable carbonate banks that harbor direct geological evidence of global ice-volume changes. We sought to detect signatures of major changes on gene flow patterns and reconstruct the phylogeographic history of the monophyletic Zamia pumila complex across the Bahamas. METHODS Nuclear molecular markers with both high and low mutation rates were used to capture two different time scale signatures and test several gene flow and demographic hypotheses. KEY RESULTS Single-copy nuclear genes unveiled apparent ancestral admixture on Andros, suggesting a significant role of this island as main hub of diversity of the archipelago. We detected demographic and spatial expansion of the Zamia pumila complex on both paleo-provinces around the Piacenzian (Pliocene)/Gelasian (Pleistocene). Populations evidenced signatures of different migration models that have occurred at two different times. Populations on Long Island (Z. lucayana) may either represent a secondary colonization of the Bahamas by Zamia or a rapid and early-divergence event of at least one population on the Bahamas. CONCLUSIONS Despite changes in migration patterns with global climate, expected heterozygosity with both marker systems remains within the range reported for cycads, but with significant levels of increased inbreeding detected by the microsatellites. This finding is likely associated with reduced gene flow between and within paleo-provinces, accompanied by genetic drift, as rising seas enforced isolation. Our study highlights the importance of the maintenance of the predominant direction of genetic exchange and the role of overseas dispersion among the islands during climate oscillations.
Collapse
Affiliation(s)
- Dayana E Salas-Leiva
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Alan W Meerow
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Michael Calonje
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Javier Francisco-Ortega
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- Kushlan Tropical Science Institute, 11935 Old Cutler Road, Fairchild Tropical Botanic Garden, Coral Gables, Florida 33156 USA
| | - M Patrick Griffith
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Vanessa Sánchez
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Lindy Knowles
- Bahamas National Trust, P. O. Box N-4105, Bay Street Business Centre, Bay Street, Nassau
| | - David Knowles
- The Bahamas, Bahamas National Trust, Abaco National Park, P.O. Box AB-20953, Marsh Harbour, Abaco, The Bahamas
| |
Collapse
|
10
|
García N, Folk RA, Meerow AW, Chamala S, Gitzendanner MA, Oliveira RSD, Soltis DE, Soltis PS. Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Mol Phylogenet Evol 2017; 111:231-247. [PMID: 28390909 DOI: 10.1016/j.ympev.2017.04.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 12/23/2022]
Abstract
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: (1) Tocantinia and Hippeastrum with 2n=22, and (2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n=12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.
Collapse
Affiliation(s)
- Nicolás García
- Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Av. Santa Rosa 11315, La Pintana, Santiago, Chile; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
| | - Ryan A Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
| | - Alan W Meerow
- USDA-ARS-SHRS-National Germplasm Repository, 13601 Old Cutler Road, Miami, FL 33158, USA.
| | - Srikar Chamala
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA.
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Renata Souza de Oliveira
- GaTE Laboratory, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, IBUSP, Rua do Matão 277, CEP: 05508-090 São Paulo, SP, Brazil.
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| |
Collapse
|
11
|
Zheng Y, Liu J, Gong X. Tectonic and climatic impacts on the biota within the Red River Fault, evidence from phylogeography of Cycas dolichophylla (Cycadaceae). Sci Rep 2016; 6:33540. [PMID: 27629063 PMCID: PMC5024324 DOI: 10.1038/srep33540] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/30/2016] [Indexed: 11/22/2022] Open
Abstract
Dramatic crustal deformation and river incision in Southwest China induced by the Indo-Asian collision have long been argued to contribute to the complicated landscapes, heterogeneous environment and abundant biodiversity in this region. However, biological impacts in promoting intraspecific phylogeographical subdivision and divergence along the Red River Fault zone (RRF) remain poorly understood. To investigate the possible biological effects of tectonic movements and environment variations within the RRF, the phylogeography of Cycas dolichophylla-an endemic but widely distributed Cycas in Southwest China and North Vietnam along the RRF were carried out based on four chloroplast DNA intergenic spacers (cpDNA), three nuclear DNA sequences (nDNA) and 16 simple sequence repeat variations (SSR). Two different phylogeographical patterns were detected: a Southwest-Northeast break across the RRF disclosed by chlorotypes and a China-Vietnam separation revealed by SSR. A Bayesian skyline plot from cpDNA data demonstrated a historical increasing, but a recent declining, dynamic in population size during the Pleistocene. Consequently, we infer it is the local environmental variation during Cenozoic that contributed to the complex landscape and microclimate mosaics, facilitating speciation and divergence of C. dolichophylla. Subsequently, the Quaternary climatic fluctuations coupled with human activities profoundly influenced the genetic structure and demographic history of this species.
Collapse
Affiliation(s)
- Ying Zheng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| |
Collapse
|
12
|
Middle-Upper Pleistocene climate changes shaped the divergence and demography of Cycas guizhouensis (Cycadaceae): Evidence from DNA sequences and microsatellite markers. Sci Rep 2016; 6:27368. [PMID: 27270859 PMCID: PMC4895228 DOI: 10.1038/srep27368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 05/16/2016] [Indexed: 11/24/2022] Open
Abstract
Climatic oscillations in the Pleistocene have had profound effects on the demography and genetic diversity of many extant species. Cycas guizhouensis Lan & R.F. Zou is an endemic and endangered species in Southwest China that is primarily distributed along the valleys of the Nanpan River. In this study, we used four chloroplast DNAs (cpDNA), three nuclear genes (nDNA) and 13 microsatellite (SSR) loci to investigate the genetic structure, divergence time and demographic history of 11 populations of C. guizhouensis. High genetic diversity and high levels of genetic differentiation among the populations were observed. Two evolutionary units were revealed based on network and Structure analysis. The divergence time estimations suggested that haplotypes of C. guizhouensis were diverged during the Middle-Upper Pleistocene. Additionally, the demographic histories deduced from different DNA sequences were discordant, but overall indicated that C. guizhouensis had experienced a recent population expansion during the post-glacial period. Microsatellite data revealed that there was a contraction in effective population size in the past. These genetic features allow conservation measures to be taken to ensure the protection of this endangered species from extinction.
Collapse
|
13
|
Huang J, Gao Y, Jia H, Zhang Z. Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication. Mol Ecol Resour 2016; 16:1465-1477. [DOI: 10.1111/1755-0998.12526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Huang
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Youjun Gao
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Haitao Jia
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
- College of Life Science; Huanggang Normal University; Huanggang 438000 China
| |
Collapse
|
14
|
Feng X, Liu J, Gong X. Species Delimitation of the Cycas segmentifida Complex (Cycadaceae) Resolved by Phylogenetic and Distance Analyses of Molecular Data. FRONTIERS IN PLANT SCIENCE 2016; 7:134. [PMID: 26913044 PMCID: PMC4753401 DOI: 10.3389/fpls.2016.00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/25/2016] [Indexed: 06/02/2023]
Abstract
The Cycas segmentifida complex consists of eight species whose distributions overlap in a narrow region in Southwest China. These eight taxa are also morphologically similar and are difficult to be distinguished. Consequently, their taxonomic status has been a matter of discussion in recent years. To study this species complex, we sequenced four plastid intergenic spacers (cpDNA), three nuclear genes and genotyped 12 microsatellites for the eight taxa from 19 different localities. DNA sequences were analyzed using Maximum Likelihood (ML) method and Bayesian Inference (BI), and microsatellites were analyzed using the Neighbor-joining (NJ) and structure inference methods. Results of cpDNA, nuclear gene GTP and microsatellites all rejected the hypotheses that this complex consisted of eight taxa or one distinct lineage (species) but two previously described species were adopted: Cycas guizhouensis K. M. Lan et R. F. Zou and Cycas segmentifida D. Y. Wang et C. Y. Deng. Cycas longlinensis H. T. Chang et Y. C. Zhong was included in C. guizhouensis and the other five taxa were included in C. segmentifida. Our species delimitation inferred from molecular data largely corresponds to morphological differentiation. However, the other two nuclear genes were unable to resolve species boundaries for this complex independently. This study offered evidences from different genomes for dealing with the species boundaries and taxonomical treatment of the C. segmentifida complex in an integrated perspective.
Collapse
Affiliation(s)
- Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| |
Collapse
|
15
|
Zhou T, Chen C, Wei Y, Chang Y, Bai G, Li Z, Kanwal N, Zhao G. Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species. FRONTIERS IN PLANT SCIENCE 2016; 7:1512. [PMID: 27790228 PMCID: PMC5061820 DOI: 10.3389/fpls.2016.01512] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/23/2016] [Indexed: 05/21/2023]
Abstract
Dipteronia (order Sapindales) is an endangered genus endemic to China and has two living species, D.sinensis and D. dyeriana. The plants are closely related to the genus Acer, which is also classified in the order Sapindales. Evolutionary studies on Dipteronia have been hindered by the paucity of information on their genomes and plastids. Here, we used next generation sequencing to characterize the transcriptomes and complete chloroplast genomes of both Dipteronia species. A comparison of the transcriptomes of both species identified a total of 7814 orthologs. Estimation of selection pressures using Ka/Ks ratios showed that only 30 of 5435 orthologous pairs had a ratio significantly >1, i.e., showing positive selection. However, 4041 orthologs had a Ka/Ks < 0.5 (p < 0.05), suggesting that most genes had likely undergone purifying selection. Based on orthologous unigenes, 314 single copy nuclear genes (SCNGs) were identified. Through a combination of de novo and reference guided assembly, plastid genomes were obtained; that of D. sinensis was 157,080 bp and that of D. dyeriana was 157,071 bp. Both plastid genomes encoded 87 protein coding genes, 40 tRNAs, and 8 rRNAs; no significant differences were detected in the size, gene content, and organization of the two plastomes. We used the whole chloroplast genomes to determine the phylogeny of D. sinensis and D. dyeriana and confirmed that the two species were highly divergent. Overall, our study provides comprehensive transcriptomic and chloroplast genomic resources, which will be valuable for future evolutionary studies of Dipteronia.
Collapse
Affiliation(s)
- Tao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Chen Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Yue Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Yongxia Chang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Guoqing Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi ProvinceXi'an, China
| | - Zhonghu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Nazish Kanwal
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
- *Correspondence: Guifang Zhao
| |
Collapse
|
16
|
Stockenhuber R, Zoller S, Shimizu-Inatsugi R, Gugerli F, Shimizu KK, Widmer A, Fischer MC. Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing. PLoS One 2015; 10:e0128181. [PMID: 26061739 PMCID: PMC4465667 DOI: 10.1371/journal.pone.0128181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/24/2015] [Indexed: 11/19/2022] Open
Abstract
The lack of DNA sequence information for most non-model organisms impairs the design of primers that are universally applicable for the study of molecular polymorphisms in nuclear markers. Next-generation sequencing (NGS) techniques nowadays provide a powerful approach to overcome this limitation. We present a flexible and inexpensive method to identify large numbers of nuclear primer pairs that amplify in most Brassicaceae species. We first obtained and mapped NGS transcriptome sequencing reads from two of the distantly related Brassicaceae species, Cardamine hirsuta and Arabis alpina, onto the Arabidopsis thaliana reference genome, and then identified short conserved sequence motifs among the three species bioinformatically. From these, primer pairs to amplify coding regions (nuclear protein coding loci, NPCL) and exon-primed intron-crossing sequences (EPIC) were developed. We identified 2,334 universally applicable primer pairs, targeting 1,164 genes, which provide a large pool of markers as readily usable genomic resource that will help addressing novel questions in the Brassicaceae family. Testing a subset of the newly designed nuclear primer pairs revealed that a great majority yielded a single amplicon in all of the 30 investigated Brassicaceae taxa. Sequence analysis and phylogenetic reconstruction with a subset of these markers on different levels of phylogenetic divergence in the mustard family were compared with previous studies. The results corroborate the usefulness of the newly developed primer pairs, e.g., for phylogenetic analyses or population genetic studies. Thus, our method provides a cost-effective approach for designing nuclear loci across a broad range of taxa and is compatible with current NGS technologies.
Collapse
Affiliation(s)
- Reinhold Stockenhuber
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre, ETH Zurich, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | | |
Collapse
|
17
|
Mao Y, Zhang Y, Xu C, Qiu Y. Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae. Mol Ecol Resour 2015; 16:228-41. [PMID: 25879377 DOI: 10.1111/1755-0998.12415] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/09/2015] [Accepted: 04/14/2015] [Indexed: 12/13/2022]
Abstract
Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53,929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.
Collapse
Affiliation(s)
- Yunrui Mao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yonghua Zhang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuan Xu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yingxiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
18
|
Ai B, Gao Y, Zhang X, Tao J, Kang M, Huang H. Comparative transcriptome resources of eleven Primulina species, a group of 'stone plants' from a biodiversity hot spot. Mol Ecol Resour 2014; 15:619-32. [PMID: 25243665 DOI: 10.1111/1755-0998.12333] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 11/28/2022]
Abstract
The genus Primulina is an emerging model system in studying the drivers and mechanisms of species diversification, for its high species richness and endemism, together with high degree of habitat specialization. In this study, we sequenced transcriptomes for eleven Primulina species across the phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of 336 million clean reads were processed into 355 573 unigenes with a mean length of 1336 bp and an N50 value of 2191 bp after pooling and reassembling twelve individual pre-assembled unigene sets. Of these unigenes, 249 973 (70%) were successfully annotated and 256 601 (72%) were identified as coding sequences (CDSs). We identified a total of 38 279 simple sequence repeats (SSRs) and 367 123 single nucleotide polymorphisms (SNPs). Marker validation assay revealed that 354 (27.3%) of the 1296 SSR and 795 (39.6%) of the 2008 SNP loci showed successful genotyping performance and exhibited expected polymorphism profiles. We screened 834 putative single-copy nuclear genes and proved their high effectiveness in phylogeny construction and estimation of ancestral population parameters. We identified a total of 85 candidate orthologs under positive selection for 46 of the 66 species pairs. This study provided an efficient application of RNA-seq in development of genomic resources for a group of 'stone plants' from south China Karst regions, a biodiversity hot spot of the World. The assembled unigenes with annotations and the massive gene-associated molecular markers would help guide further molecular systematic, population genetic and ecological genomics studies in Primulina and its relatives.
Collapse
Affiliation(s)
- Bin Ai
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | | | | | | | | |
Collapse
|