1
|
Newton RJ, Mackenzie BDE, Lamont BB, Gomez-Barreiro P, Cowling RM, He T. Fire-mediated germination syndromes in Leucadendron (Proteaceae) and their functional correlates. Oecologia 2021; 196:589-604. [PMID: 34159425 PMCID: PMC8241639 DOI: 10.1007/s00442-021-04947-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 05/15/2021] [Indexed: 11/29/2022]
Abstract
A mechanistic understanding of fire-driven seedling recruitment is essential for effective conservation management of fire-prone vegetation, such as South African fynbos, especially with rare and threatened taxa. The genus Leucadendron (Proteaceae) is an ideal candidate for comparative germination studies, comprising 85 species with a mixture of contrasting life-history traits (killed by fire vs able to resprout; serotinous vs geosporous) and seed morphologies (nutlets vs winged achenes). Individual and combined effects of heat and smoke on seed germination of 40 species were quantified in the laboratory, and Bayesian inference applied to distinguish biologically meaningful treatment effects from non-zero, but biologically trivial, effects. Three germination syndromes were identified based on whether germination was dependent on, enhanced by, or independent of direct fire cues (heat and smoke). Seed storage location was the most reliable predictor of germination syndromes, with soil-stored seeds c. 80% more likely to respond to direct fire cues (primarily smoke) than canopy-stored seeds. Notable exceptions were L. linifolium, with an absolute requirement for smoke to germinate (the third serotinous species so reported), and two other serotinous species with smoke-enhanced germination. Nutlet-bearing species, whether serotinous or geosporous, were c. 70% more likely to respond to fire cues than winged seeds, but there was no evidence for an effect of phylogeny or persistence strategy on germination. This comprehensive account of seed germination characteristics and identification of germination syndromes and their predictors, supports propagation, conservation and restoration initiatives in this iconic fynbos genus and other fire-prone shrubs with canopy or soil-stored seeds.
Collapse
Affiliation(s)
- Rosemary J Newton
- Conservation Science, Royal Botanic Gardens Kew, Wakehurst, Ardingly, West Sussex, RH17 6TN, UK.
| | - Berin D E Mackenzie
- Science Division, NSW Department of Planning, Industry and Environment, Locked Bag 5022, Parramatta, NSW, 2124, Australia.,Centre for Ecosystem Science, University of New South Wales, Kensington, NSW, 2052, Australia
| | - Byron B Lamont
- Ecology Section, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - Pablo Gomez-Barreiro
- Conservation Science, Royal Botanic Gardens Kew, Wakehurst, Ardingly, West Sussex, RH17 6TN, UK
| | - Richard M Cowling
- Department of Botany, Nelson Mandela Metropolitan University, PO Box 7700, Port Elizabeth, 6000, South Africa
| | - Tianhua He
- Ecology Section, School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| |
Collapse
|
2
|
An easy and robust method for isolation and validation of single-nucleotide polymorphic markers from a first Erysiphe alphitoides draft genome. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01580-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
3
|
Alonso MÁ, Vicente A, Crespo MB. Diversification of Biscutella ser. Biscutella (Brassicaceae) followed post-Miocene geologic and climatic changes in the Mediterranean basin. Mol Phylogenet Evol 2020; 142:106644. [DOI: 10.1016/j.ympev.2019.106644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 10/25/2022]
|
4
|
Identifying genetic markers for a range of phylogenetic utility-From species to family level. PLoS One 2019; 14:e0218995. [PMID: 31369563 PMCID: PMC6675087 DOI: 10.1371/journal.pone.0218995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/13/2019] [Indexed: 12/03/2022] Open
Abstract
Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.
Collapse
|
5
|
Damerval C, Citerne H, Conde e Silva N, Deveaux Y, Delannoy E, Joets J, Simonnet F, Staedler Y, Schönenberger J, Yansouni J, Le Guilloux M, Sauquet H, Nadot S. Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:18. [PMID: 30740117 PMCID: PMC6357683 DOI: 10.3389/fpls.2019.00018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/08/2019] [Indexed: 05/30/2023]
Abstract
Proteaceae are a basal eudicot family with a highly conserved floral groundplan but which displays considerable variation in other aspects of floral and inflorescence morphology. Their morphological diversity and phylogenetic position make them good candidates for understanding the evolution of floral architecture, in particular the question of the homology of the undifferentiated perianth with the differentiated perianth of core eudicots, and the mechanisms underlying the repeated evolution of zygomorphy. In this paper, we combine a morphological approach to explore floral ontogenesis and a transcriptomic approach to access the genes involved in floral organ identity and development, focusing on Grevillea juniperina, a species from subfamily Grevilleoideae. We present developmental data for Grevillea juniperina and three additional species that differ in their floral symmetry using stereomicroscopy, SEM and High Resolution X-Ray Computed Tomography. We find that the adnation of stamens to tepals takes place at early developmental stages, and that the establishment of bilateral symmetry coincides with the asymmetrical growth of the single carpel. To set a framework for understanding the genetic basis of floral development in Proteaceae, we generated and annotated de novo a reference leaf/flower transcriptome from Grevillea juniperina. We found Grevillea homologs of all lineages of MADS-box genes involved in floral organ identity. Using Arabidopsis thaliana gene expression data as a reference, we found homologs of other genes involved in floral development in the transcriptome of G. juniperina. We also found at least 21 class I and class II TCP genes, a gene family involved in the regulation of growth processes, including floral symmetry. The expression patterns of a set of floral genes obtained from the transcriptome were characterized during floral development to assess their organ specificity and asymmetry of expression.
Collapse
Affiliation(s)
- Catherine Damerval
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hélène Citerne
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yves Deveaux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Simonnet
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Yannick Staedler
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jennifer Yansouni
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hervé Sauquet
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Sophie Nadot
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| |
Collapse
|
6
|
Yang Y, Davis TM. A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis. Genome Biol Evol 2018; 9:3433-3448. [PMID: 29045639 PMCID: PMC5751083 DOI: 10.1093/gbe/evx214] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2017] [Indexed: 12/25/2022] Open
Abstract
The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. About 24 single-copy or low-copy nuclear genes distributed across the genome were amplified and sequenced from 96 genomic DNA samples representing 16 Fragaria species from diploid (2×) to decaploid (10×), including the most extensive sampling of octoploid taxa yet reported. Individual gene trees were constructed by different tree-building methods. Mosaic genomic structures of diploid Fragaria species consisting of sequences at different phylogenetic positions were observed. Our findings support the presence in octoploid species of genetic signatures from at least five diploid ancestors (F. vesca, F. iinumae, F. bucharica, F. viridis, and at least one additional allele contributor of unknown identity), and questions the extent to which distinct subgenomes are preserved over evolutionary time in the allopolyploid Fragaria species. In addition, our data support divergence between the two wild octoploid species, F. virginiana and F. chiloensis.
Collapse
Affiliation(s)
- Yilong Yang
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire
| | - Thomas M Davis
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire
| |
Collapse
|
7
|
Tonnabel J, Schurr FM, Boucher F, Thuiller W, Renaud J, Douzery EJP, Ronce O. Life-History Traits Evolved Jointly with Climatic Niche and Disturbance Regime in the Genus Leucadendron (Proteaceae). Am Nat 2017; 191:220-234. [PMID: 29351009 DOI: 10.1086/695283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Organisms have evolved a diversity of life-history strategies to cope with variation in their environment. Persistence as adults and/or seeds across recruitment events allows species to dampen the effects of environmental fluctuations. The evolution of life cycles with overlapping generations should thus permit the colonization of environments with uncertain recruitment. We tested this hypothesis in Leucadendron (Proteaceae), a genus with high functional diversity native to fire-prone habitats in the South African fynbos. We analyzed the joint evolution of life-history traits (adult survival and seed-bank strategies) and ecological niches (climate and fire regime), using comparative methods and accounting for various sources of uncertainty. In the fynbos, species with canopy seed banks that are unable to survive fire as adults display nonoverlapping generations. In contrast, resprouters with an underground seed bank may be less threatened by extreme climatic events and fire intervals, given their iteroparity and long-lasting seed bank. Life cycles with nonoverlapping generations indeed jointly evolved with niches with less exposure to frost but not with those with less exposure to drought. Canopy seed banks jointly evolved with niches with more predictable fire return, compared to underground seed banks. The evolution of extraordinary functional diversity among fynbos plants thus reflects, at least in part, the diversity of both climates and fire regimes in this region.
Collapse
|
8
|
Chery JG, Sass C, Specht CD. Development of single-copy nuclear intron markers for species-level phylogenetics: Case study with Paullinieae (Sapindaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1700051. [PMID: 28989824 PMCID: PMC5628028 DOI: 10.3732/apps.1700051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY We developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted introns of single-copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline. METHODS AND RESULTS Transcriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single-nucleotide polymorphisms are called, generating a "pseudoreference" closer to the lineage of interest. Several filters are applied to meet the criteria of single-copy nuclear loci with introns of a desired size. Primers are designed in conserved coding sequences flanking introns. Using this pipeline, we developed nine single-copy nuclear intron markers for Paullinieae. CONCLUSIONS This pipeline is highly flexible and can be used for any group with available genomic and transcriptomic resources. This pipeline led to the development of nine variable markers for phylogenetic study without generating sequence data de novo.
Collapse
Affiliation(s)
- Joyce G. Chery
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, California 94720 USA
- University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, California 94720 USA
| | - Chodon Sass
- University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, California 94720 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, California 94720 USA
| | - Chelsea D. Specht
- School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| |
Collapse
|
9
|
Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae). Mol Phylogenet Evol 2017; 107:345-355. [DOI: 10.1016/j.ympev.2016.11.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 11/19/2016] [Accepted: 11/27/2016] [Indexed: 11/17/2022]
|
10
|
Mitchell N, Lewis PO, Lemmon EM, Lemmon AR, Holsinger KE. Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L. AMERICAN JOURNAL OF BOTANY 2017; 104:102-115. [PMID: 28104589 DOI: 10.3732/ajb.1600227] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/30/2016] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree-species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization. KEY RESULTS Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches. CONCLUSIONS Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.
Collapse
Affiliation(s)
- Nora Mitchell
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States
| | - Paul O Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306 United States
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306 United States
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 United States
| |
Collapse
|
11
|
Huang J, Zeng SY, Zhao JH, Han K, Li J, Li Z, Liu ZL. Genetic variation and phylogenetic relationships among Rehmannia (Scrophulariaceae) species as revealed by a novel set of single-copy nuclear gene markers. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
12
|
Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SCK, Cronn RC, Dreyer LL, Suda J. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae). Mol Ecol Resour 2015; 16:1124-35. [DOI: 10.1111/1755-0998.12487] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/06/2015] [Accepted: 11/05/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Roswitha Schmickl
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
| | - Aaron Liston
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Vojtěch Zeisek
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
| | - Kenneth Oberlander
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Kevin Weitemier
- Department of Botany and Plant Pathology; Oregon State University; 2082 Cordley Hall Corvallis OR 97331 USA
| | - Shannon C. K. Straub
- Department of Biology; Hobart and William Smith Colleges; 213 Eaton Hall Geneva NY 14456 USA
| | - Richard C. Cronn
- USDA Forest Service; Pacific Northwest Research Station; 3200 SW Jefferson Way Corvallis OR 97331 USA
| | - Léanne L. Dreyer
- Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Jan Suda
- Institute of Botany; The Czech Academy of Sciences; Zámek 1 252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 128 01 Prague Czech Republic
| |
Collapse
|
13
|
Granados Mendoza C, Naumann J, Samain MS, Goetghebeur P, De Smet Y, Wanke S. A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea. BMC Evol Biol 2015; 15:132. [PMID: 26141718 PMCID: PMC4491267 DOI: 10.1186/s12862-015-0416-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/09/2015] [Indexed: 12/21/2022] Open
Abstract
Background Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other “fast” evolving plastid markers. Results Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae). Conclusions While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0416-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Carolina Granados Mendoza
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium. .,Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510, Coyoacán, Distrito Federal, Mexico.
| | - Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany.
| | - Marie-Stéphanie Samain
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium. .,Instituto de Ecología, A.C., Centro Regional del Bajío, Avenida Lázaro Cárdenas 253, 61600, Pátzcuaro, Michoacán, Mexico.
| | - Paul Goetghebeur
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Yannick De Smet
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany.
| |
Collapse
|
14
|
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
|
15
|
Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, Barbazuk WB, Soltis DE, Soltis PS. MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1400115. [PMID: 25909041 PMCID: PMC4406834 DOI: 10.3732/apps.1400115] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/25/2015] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. METHODS AND RESULTS We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. CONCLUSIONS MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.
Collapse
Affiliation(s)
- Srikar Chamala
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Author for correspondence:
| | - Nicolás García
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Grant T. Godden
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Rancho Santa Ana Botanic Garden, Claremont, California, USA
| | | | - Ingrid E. Jordon-Thaden
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
- Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA
| | - Riet De Smet
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
16
|
Tonnabel J, Mignot A, Douzery EJP, Rebelo AG, Schurr FM, Midgley J, Illing N, Justy F, Orcel D, Olivieri I. CONVERGENT AND CORRELATED EVOLUTION OF MAJOR LIFE-HISTORY TRAITS IN THE ANGIOSPERM GENUSLEUCADENDRON(PROTEACEAE). Evolution 2014; 68:2775-92. [DOI: 10.1111/evo.12480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 02/25/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Jeanne Tonnabel
- Institut des Sciences de l’Évolution de Montpellier; CNRS (UMR 5554); Place Eugène Bataillon 34095 Montpellier cedex 05 France
| | - Agnès Mignot
- Institut des Sciences de l’Évolution de Montpellier; CNRS (UMR 5554); Place Eugène Bataillon 34095 Montpellier cedex 05 France
| | - Emmanuel J. P. Douzery
- Institut des Sciences de l’Évolution de Montpellier; CNRS (UMR 5554); Place Eugène Bataillon 34095 Montpellier cedex 05 France
| | - Anthony G. Rebelo
- Threatened Species Research Unit; South African National Biodiversity Institute; Private Bag X7 Kirstenbosch 7735 South Africa
| | - Frank M. Schurr
- Institut des Sciences de l’Évolution de Montpellier; CNRS (UMR 5554); Place Eugène Bataillon 34095 Montpellier cedex 05 France
- Institute of Landscape and Plant Ecology; University of Hohenheim; 70593 Stuttgart Germany
| | - Jeremy Midgley
- Department of Biological Sciences; University of Cape Town; Private Bag; Rondebosch 7701 South Africa
| | - Nicola Illing
- Department of Molecular and Cell Biology; University of Cape Town; Rondebosch 7701 South Africa
| | - Fabienne Justy
- Institut des Sciences de l’Évolution de Montpellier; CNRS (UMR 5554); Place Eugène Bataillon 34095 Montpellier cedex 05 France
| | - Denis Orcel
- Institut des Sciences de l’Évolution de Montpellier; CNRS (UMR 5554); Place Eugène Bataillon 34095 Montpellier cedex 05 France
| | - Isabelle Olivieri
- Institut des Sciences de l’Évolution de Montpellier; CNRS (UMR 5554); Place Eugène Bataillon 34095 Montpellier cedex 05 France
| |
Collapse
|
17
|
Salas-Leiva DE, Meerow AW, Francisco-Ortega J, Calonje M, Griffith MP, Stevenson DW, Nakamura K. Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads. Mol Ecol Resour 2014; 14:831-45. [PMID: 24444413 DOI: 10.1111/1755-0998.12228] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 01/28/2023]
Abstract
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
Collapse
Affiliation(s)
- Dayana E Salas-Leiva
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA; USDA-ARS-SHRS, National Germplasm Repository, Miami, FL, 33158, USA; Montgomery Botanical Center, Miami, FL, 33156, USA
| | | | | | | | | | | | | |
Collapse
|