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Skopalíková J, Leong-Škorničková J, Šída O, Newman M, Chumová Z, Zeisek V, Jarolímová V, Poulsen AD, Dantas-Queiroz MV, Fér T, Záveská E. Ancient hybridization in Curcuma (Zingiberaceae)-Accelerator or brake in lineage diversifications? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:773-785. [PMID: 37537754 DOI: 10.1111/tpj.16408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, more attention is focused on the role of ancient hybridization that has repeatedly been shown as triggers of evolutionary radiation, although in some cases, it can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored. Here, we present an account of several events of ancient hybridization in turmeric, the economically important plant genus Curcuma (Zingiberaceae), which harbors about 130 known species. We analyzed 1094 targeted low-copy genes and plastomes obtained by next-generation sequencing of 37 species of Curcuma, representing the known genetic diversity and spanning the geographical distribution of the genus. Using phylogenetic network analysis, we show that the entire genus Curcuma as well as its most speciose lineage arose via introgression from the genus Pyrgophyllum and one of the extinct lineages, respectively. We also document a single event of ancient hybridization, with C. vamana as a product, that represents an evolutionary dead end. We further discuss distinct circumstances of those hybridization events that deal mainly with (in)congruence in chromosome counts of the parental lineages.
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Affiliation(s)
- Jana Skopalíková
- Department of Botany, Charles University, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Jana Leong-Škorničková
- The Herbarium, Singapore Botanic Gardens, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Otakar Šída
- Department of Botany, National Museum in Prague, Prague, Czech Republic
| | - Mark Newman
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - Zuzana Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Vojtěch Zeisek
- Department of Botany, Charles University, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Vlasta Jarolímová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | | | | | - Tomáš Fér
- Department of Botany, Charles University, Prague, Czech Republic
| | - Eliška Záveská
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
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2
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Pouchon C, Boluda CG. REFMAKER: make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae. Mol Phylogenet Evol 2023:107826. [PMID: 37257798 DOI: 10.1016/j.ympev.2023.107826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10% of the produced libraries, and the low coverage associated with these libraries (< 3X) prevents the capture of nuclear sequences, which are not always available in non-model organisms or limited to the ribosomal regions. We developed REFMAKER, a user-friendly pipeline, to create specific sets of nuclear loci that can next be extracted directly from the genome skimming libraries. For this, a catalogue is built from the meta-assembly of each library contigs and cleaned by selecting the nuclear regions and removing duplicates from clustering steps. Libraries are next mapped onto this catalogue and consensus sequences are generated to produce a ready-to-use phylogenetic matrix following different filtering parameters aiming at removing putative errors and paralogous sequences. REFMAKER allowed us to infer a well resolved phylogeny in Capurodendron (Sapotaceae) on 67 nuclear loci from low-coverage libraries (<1X). The resulting phylogeny is concomitant with one previously inferred on 638 nuclear genes from target enrichment libraries. While it remains preliminary because of this low sequencing depth, REFMAKER therefore opens perspectives in phylogenomics by allowing nuclear phylogeny reconstructions with genome skimming datasets.
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Affiliation(s)
- Charles Pouchon
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland; PhyloLab, Department of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland.
| | - Carlos G Boluda
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland; PhyloLab, Department of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland
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3
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Phylogenetics and historical biogeography of Encyclia (Laeliinae: Orchidaceae) with an emphasis on the E. adenocarpos complex, a new species, and a preliminary species list for the genus. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00575-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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4
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Xiang KL, Mao W, Peng HW, Erst AS, Yang YX, He WC, Wu ZQ. Organization, Phylogenetic Marker Exploitation, and Gene Evolution in the Plastome of Thalictrum (Ranunculaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:897843. [PMID: 35668810 PMCID: PMC9166237 DOI: 10.3389/fpls.2022.897843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 05/31/2023]
Abstract
Thalictrum is a phylogenetically and economically important genus in the family Ranunculaceae, but is also regarded as one of the most challengingly difficult in plants for resolving the taxonomical and phylogenetical relationships of constituent taxa within this genus. Here, we sequenced the complete plastid genomes of two Thalictrum species using Illumina sequencing technology via de novo assembly. The two Thalictrum plastomes exhibited circular and typical quadripartite structure that was rather conserved in overall structure and the synteny of gene order. By updating the previously reported plastome annotation of other nine Thalictrum species, we found that the expansion or contraction of the inverted repeat region affect the boundary of the single-copy regions in Thalictrum plastome. We identified eight highly variable noncoding regions-infA-rps8, ccsA-ndhD, trnSUGA-psbZ, trnHGUG-psbA, rpl16-rps3, ndhG-ndhI, ndhD-psaC, and ndhJ-ndhK-that can be further used for molecular identification, phylogenetic, and phylogeographic in different species. Selective pressure and codon usage bias of all the plastid coding genes were also analyzed for the 11 species. Phylogenetic relationships showed Thalictrum is monophyly and divided into two major clades based on 11 Thalictrum plastomes. The availability of these plastomes offers valuable genetic information for accurate identification of species and taxonomy, phylogenetic resolution, and evolutionary studies of Thalictrum, and should assist with exploration and utilization of Thalictrum plants.
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Affiliation(s)
- Kun-Li Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Mao
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Huan-Wen Peng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Andrey S. Erst
- Central Siberian Botanical Garden, Russian Academy of Sciences, Novosibirsk, Russia
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, Russia
| | - Ying-Xue Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China
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5
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Debray K, Marie-Magdelaine J, Ruttink T, Clotault J, Foucher F, Malécot V. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae). BMC Evol Biol 2019; 19:152. [PMID: 31340752 PMCID: PMC6657147 DOI: 10.1186/s12862-019-1479-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. RESULTS We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. CONCLUSIONS With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks.
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Affiliation(s)
- Kevin Debray
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| | | | - Tom Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Valéry Malécot
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data. Mol Phylogenet Evol 2019; 135:98-104. [DOI: 10.1016/j.ympev.2019.02.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 12/20/2022]
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7
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Gonçalves DJP, Simpson BB, Ortiz EM, Shimizu GH, Jansen RK. Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. Mol Phylogenet Evol 2019; 138:219-232. [PMID: 31146023 DOI: 10.1016/j.ympev.2019.05.022] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 10/26/2022]
Abstract
The current classification of angiosperms is based primarily on concatenated plastid markers and maximum likelihood (ML) inference. This approach has been justified by the assumption that plastid DNA (ptDNA) is inherited as a single locus and that its individual genes produce congruent trees. However, structural and functional characteristics of ptDNA suggest that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces. To examine this idea, we produced new complete plastid genome (plastome) sequences of 27 species and combined these data with publicly available sequences to produce a final dataset that includes 78 plastid genes for 89 species of rosids and five outgroups. We used four data matrices (i.e., gene, exon, codon-aligned, and amino acid) to infer species and gene trees using ML and multispecies coalescent (MSC) methods. Rosids include about one third of all angiosperms and their two major clades, fabids and malvids, were recovered in almost all analyses. However, we detected incongruence between species trees inferred with different matrices and methods and previously published plastid and nuclear phylogenies. We visualized and tested the significance of incongruence between gene trees and species trees. We then measured the distribution of phylogenetic signal across sites and genes supporting alternative placements of five controversial nodes at different taxonomic levels. Gene trees inferred with plastid data often disagree with species trees inferred using both ML (with unpartitioned or partitioned data) and MSC. Species trees inferred with both methods produced alternative topologies for a few taxa. Our results show that, in a phylogenetic context, plastid protein-coding genes may not be fully linked and behaving as a single locus. Furthermore, concatenated matrices may produce highly supported phylogenies that are discordant with individual gene trees. We also show that phylogenies inferred with MSC are accurate. We therefore emphasize the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships. We also support the use of MSC with plastome matrices in future phylogenomic investigations.
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Affiliation(s)
- Deise J P Gonçalves
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA.
| | - Beryl B Simpson
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA
| | - Edgardo M Ortiz
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA; Department of Ecology & Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, Emil-Ramann Strasse 2, Freising D-85354, Germany
| | - Gustavo H Shimizu
- Department of Plant Biology, University of Campinas, 13083-970 Campinas, SP, Brazil
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA; Genomics and Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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8
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Testo WL, Sessa E, Barrington DS. The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae). THE NEW PHYTOLOGIST 2019; 222:604-613. [PMID: 30326543 DOI: 10.1111/nph.15544] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Tropical mountains are disproportionately biodiverse relative to their surface area, but the processes underlying their exceptional diversity require further study. Here, we use comparative phylogenetic methods to examine the impact of the Andean orogeny on the diversification of Neotropical Phlegmariurus, a species-rich lycophyte clade. We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus and estimated lineage diversification rates. We tested for correlations between lineage diversification rates and species range size, niche breadth, elevational range amplitude, and mean elevation of occurrence. A recently developed macroevolutionary model was used to incorporate geological data and test for an association between diversification rates and the Andean uplift. Diversification rates of Neotropical Phlegmariurus are negatively correlated with species range size and positively correlated with mean elevation of species occurrence. The rise of the Andes is strongly associated with increased rates of diversification in Neotropical Phlegmariurus during the last 10 Myr. Our study demonstrates the importance of mountain-building events and geographical isolation of alpine populations as drivers of rapid diversification, even in spore-dispersed plants. This work also highlights the usefulness of combined phylogenetic, geological and ecological datasets, and the promise of comparative environment-dependent diversification models in better understanding the evolutionary origins of biodiversity.
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Affiliation(s)
- Weston L Testo
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - David S Barrington
- Department of Plant Biology, University of Vermont, 63 Carrigan Drive, Burlington, VT, 05405, USA
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9
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Morales-Briones DF, Tank DC. Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR-based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics. AMERICAN JOURNAL OF BOTANY 2019; 106:415-437. [PMID: 30882906 DOI: 10.1002/ajb2.1253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Polyploidy has been long recognized as an important force in plant evolution. Previous studies had suggested widespread occurrence of polyploidy and the allopolyploid origin of several species in the diverse neotropical genus Lachemilla (Rosaceae). Nonetheless, this evidence has relied mostly on patterns of cytonuclear discordance, and direct evidence from nuclear allelic markers is still needed. METHODS Here we used PCR target enrichment in combination with high throughput sequencing to obtain multiple copies of the nuclear ribosomal (nr) DNA cistron and 45 regions of the plastid genome (cpDNA) from 219 accessions representing 48 species of Lachemilla and to explore the allopolyploid origin of species in this group. KEY RESULTS We were able to identify multiple nrDNA ribotypes and establish clear evidence of allopolyploidy in 33 species of Lachemilla, showing that this condition is common and widespread in the genus. Additionally, we found evidence for three autopolyploid species. We also established multiple, independent origins of several allopolyploid species. Finally, based solely on the cpDNA phylogeny, we identified that the monotypic genus Farinopsis is the sister group of Lachemilla and allied genera within subtribe Fragariinae. CONCLUSIONS Our study demonstrates the utility of the nuclear ribosomal DNA cistron to detect allopolyploidy when concerted evolution of this region is not complete. Additionally, with a robust chloroplast phylogeny in place, the direction of hybridization events can be established, and multiple, independent origins of allopolyploid species can be identified.
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Affiliation(s)
- Diego F Morales-Briones
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, ID, 83844-1133, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, ID, 83844-1133, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
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Li Y, Yang Y, Yu L, Du X, Ren G. Plastomes of nine hornbeams and phylogenetic implications. Ecol Evol 2018; 8:8770-8778. [PMID: 30271544 PMCID: PMC6157693 DOI: 10.1002/ece3.4414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 07/07/2018] [Accepted: 07/10/2018] [Indexed: 11/06/2022] Open
Abstract
Poor phylogenetic resolution and inconsistency of gene trees are major complications when attempting to construct trees of life for various groups of organisms. In this study, we addressed these issues in analyses of the genus Carpinus (hornbeams) of the Betulaceae. We assembled and annotated the chloroplast (cp) genomes (plastomes) of nine hornbeams representing main clades previously distinguished in this genus. All nine plastomes are highly conserved, with four regions, and about 158-160 kb long, including 121-123 genes. Phylogenetic analyses of whole plastome sequences, noncoding sequences, and the well-aligned coding genes resulted in high resolution of the sampled species in contrast to the failure based on a few cpDNA markers. Phylogenetic relationships in a few clades based only on the coding genes are slightly inconsistent with those based on the noncoding and total plastome datasets. Moreover, these plastome trees are highly incongruent with those based on bi-parentally inherited internal transcribed spacer (ITS) sequence variations. Such high inconsistencies suggest widespread occurrence of incomplete lineage sorting and hybrid introgression during diversification of these hornbeams.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhouGansuChina
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhouGansuChina
| | - Le Yu
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhouGansuChina
| | - Xin Du
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhouGansuChina
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhouGansuChina
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11
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Yan M, Xiong Y, Liu R, Deng M, Song J. The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks. FRONTIERS IN PLANT SCIENCE 2018; 9:569. [PMID: 29868047 PMCID: PMC5952231 DOI: 10.3389/fpls.2018.00569] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 05/10/2023]
Abstract
The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia - Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiaojiao Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shangrao Normal University, Shangrao, China
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12
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Chau JH, Rahfeldt WA, Olmstead RG. Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1032. [PMID: 29732262 PMCID: PMC5895190 DOI: 10.1002/aps3.1032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/22/2017] [Indexed: 05/21/2023]
Abstract
PREMISE OF THE STUDY Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and have orthologs in large clades of plants. METHODS We identify and compare a taxon-specific locus set and three general locus sets (conserved ortholog set [COSII], shared single-copy nuclear [APVO SSC] genes, and pentatricopeptide repeat [PPR] genes) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. RESULTS The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific data set produced the best-supported tree, but all data sets showed improved resolution over previous non-sequence capture data sets. DISCUSSION General locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.
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Affiliation(s)
- John H. Chau
- Department of Biology and Burke MuseumUniversity of WashingtonBox 351800SeattleWashington98195USA
- Centre for Ecological Genomics and Wildlife ConservationDepartment of ZoologyUniversity of JohannesburgP.O. Box 524Auckland Park2006South Africa
| | - Wolfgang A. Rahfeldt
- Department of Biology and Burke MuseumUniversity of WashingtonBox 351800SeattleWashington98195USA
| | - Richard G. Olmstead
- Department of Biology and Burke MuseumUniversity of WashingtonBox 351800SeattleWashington98195USA
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13
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Valderrama E, Richardson JE, Kidner CA, Madriñán S, Stone GN. Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae). Mol Phylogenet Evol 2018; 119:13-24. [DOI: 10.1016/j.ympev.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/17/2017] [Accepted: 10/03/2017] [Indexed: 11/25/2022]
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Abstract
Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics.
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Affiliation(s)
- Simon Creer
- School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, United Kingdom
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15
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Kadlec M, Bellstedt DU, Le Maitre NC, Pirie MD. Targeted NGS for species level phylogenomics: "made to measure" or "one size fits all"? PeerJ 2017; 5:e3569. [PMID: 28761782 PMCID: PMC5530999 DOI: 10.7717/peerj.3569] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/22/2017] [Indexed: 12/05/2022] Open
Abstract
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for "one size fits all" universal markers, we should improve and make more accessible the tools necessary for developing "made to measure" ones.
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Affiliation(s)
- Malvina Kadlec
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk U. Bellstedt
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | | | - Michael D. Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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16
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Léveillé-Bourret É, Starr JR, Ford BA, Moriarty Lemmon E, Lemmon AR. Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics. Syst Biol 2017; 67:94-112. [DOI: 10.1093/sysbio/syx050] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/28/2017] [Indexed: 11/13/2022] Open
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17
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Kaur P, Gaikwad K. From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2017; 8:2164. [PMID: 29312405 PMCID: PMC5742236 DOI: 10.3389/fpls.2017.02164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/08/2017] [Indexed: 05/13/2023]
Abstract
Exome sequencing represents targeted capture and sequencing of 1-2% of 'high-value genomic regions' (subset of the genome) which are enriched for functional variants and harbors low level of repetitive regions. We discuss here an overview of exome sequencing, ways to approach plant exomes, and advantages and applicability of this powerful approach in deciphering functional regions of genomes. Though initially this approach was developed as an alternative to whole genome sequencing (WGS), but the multitude of benefits conferred by sequence capture via hybridization approaches created a niche for itself to solve many of biological riddles, particularly for resolving phylogenetic distances. The technique has also proved to be successful in understanding the basis of natural and induced molecular variation, marker development and developing genomic resources for complex, wild and non-model species, which are still intractable for WGS efforts. Thus, with profound applications of this powerful sequencing strategy, near future is expected to witness a collective expansion of both techniques, i.e., sequence capture via hybridization for evolutionary and ecological research and WGS approaches for its universal accessibility.
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18
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Kadlec M, Bellstedt DU, Le Maitre NC, Pirie MD. Targeted NGS for species level phylogenomics: "made to measure" or "one size fits all"? PeerJ 2017. [PMID: 28761782 DOI: 10.7717/peerj3569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for "one size fits all" universal markers, we should improve and make more accessible the tools necessary for developing "made to measure" ones.
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Affiliation(s)
- Malvina Kadlec
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | - Nicholas C Le Maitre
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
| | - Michael D Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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19
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Roy T, Catlin NS, Garner DMG, Cantino PD, Scheen AC, Lindqvist C. Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci. PeerJ 2016; 4:e2220. [PMID: 27547537 PMCID: PMC4958014 DOI: 10.7717/peerj.2220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 06/15/2016] [Indexed: 11/20/2022] Open
Abstract
The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and Synandreae include New World members. Previous studies have investigated the phylogenetic relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our results confirm previous studies based on chloroplast and nuclear ribosomal markers in supporting the monophyly of tribe Synandreae, as well as sister relationships between Brazoria and Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we observe incongruence in the relationships of Macbridea and Synandra. The placement of Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration patterns corroborates a single colonization of the New World by Synandreae during the Late Miocene/Tortonian age. This is in contrast to the only other lamioid tribe that includes New World members, Stachydeae, which colonized the New World at least twice—during the mid-Miocene and Pliocene. Edaphic conditions and intolerance of soil acidity may be factors that restricted the distribution of most genera of Synandreae to southeastern and south–central North America, whereas polyploidy could have increased the colonizing capability of the more wide-ranging genus, Physostegia.
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Affiliation(s)
- Tilottama Roy
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States; Current affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Nathan S Catlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States; Current affiliation: Department of Biology, University of Florida, Gainesville, FL, United States
| | - Drake M G Garner
- Department of Biological Sciences, University at Buffalo , Buffalo , NY , United States
| | - Philip D Cantino
- Department of Environmental and Plant Biology, Ohio University , Athens , OH , United States
| | | | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo , Buffalo , NY , United States
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20
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Customer perception of CSR initiatives: its antecedents and consequences. SOCIAL RESPONSIBILITY JOURNAL 2016. [DOI: 10.1108/srj-04-2015-0056] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Purpose
This study aims to ascertain the impact of customer perception of CSR activities (philanthropic, environmental and ethical) conducted on various consumer and corporate related dimensions including; customer loyalty, consumer attachment, corporate performance and repurchase intention. The study also adds value by taking customer perception of CSR as a mediator between green image and performance.
Design/methodology/approach
Structural equation modelling is used after using different (valid and reliable) instruments to measure latent constructs. The study has a sample size of 250 “CSR Consumers”, who had some knowledge and awareness of CSR and green image being advertised and or labelled by the company (such as printing “Recycled” or other eco-friendly images/labels on shopping bag, fliers, outlets, etc.) and are consumers/customers of such firms. The respondent’s awareness was measured by randomly asking them to recall organizations that might have eco-friendly policies.
Findings
The key findings of the study are that perceived fit of culture along with CSR capability radically influences CSR perception within consumer minds and so, subsequently, customer attachment and overall performance of the corporation. The outcomes bestow significant ramifications for marketing and advertising philosophy combined with practice.
Practical implications
Stakeholders exist in the form of consumers other than employees. So consumer satisfaction must be imparted its fair share of importance. Managers must make sure that initiatives for societal benefit are well accepted and well recognized by consumers in a positive array of light. Corporations enthusiastically involved in initiating CSR activities and forecast a positive income. The study guides managers into not falling in this misconception and by recognizing that the fact is that the company managers must only expect higher performance levels once their CSR is in synchronization with the firm’s culture.
Originality/value
A number of studies have been conducted about CSR practices in the Indian context for example (Khan and Atkinson, 1987; Krishna, 1992; Arora and Puranik, 2004; Sood and Arora, 2006; Mishra and Suar, 2010); however, there is dearth of research in its neighbouring country Pakistan about CSR practices and consumer perceptions. Therefore, this research aims to fill this gap by examining CSR practices in Pakistan which has similar historical and colonial roots with India. In doing so, this study ascertains the impact of CSR activities conducted on various consumer and corporate related dimensions that incorporate customer loyalty, consumer attachment and corporate performance.
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21
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Intra and interspecific sequence variation in closely related species of Cereus (CACTACEAE). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Munkert J, Costa C, Budeanu O, Petersen J, Bertolucci S, Fischer G, Müller-Uri F, Kreis W. Progesterone 5β-reductase genes of the Brassicaceae family as function-associated molecular markers. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:1113-22. [PMID: 26108256 DOI: 10.1111/plb.12361] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/22/2015] [Indexed: 05/12/2023]
Abstract
This study aimed to define progesterone 5β-reductases (P5βR, EC 1.3.99.6, enone 1,4-reductases) as function-associated molecular markers at the plant family level. Therefore cDNAs were isolated from 25 Brassicaceae species, including two species, Erysimum crepidifolium and Draba aizoides, known to produce cardiac glycosides. The sequences were used in a molecular phylogeny study. The cladogram created is congruent to the existing molecular analyses. Recombinant His-tagged forms of the P5βR cDNAs from Aethionema grandiflorum, Draba aizoides, Nasturtium officinale, Raphanus sativus and Sisymbrium officinale were expressed in E. coli. Enone 1,4-reductase activity was demonstrated in vitro using progesterone and 2-cyclohexen-1-one as substrates. Evidence is provided that functional P5βRs are ubiquitous in the Brassicaceae. The recombinant P5βR enzymes showed different substrate preferences towards progesterone and 2-cyclohexen-1-one. Sequence comparison of the catalytic pocket of the P5βR enzymes and homology modelling using Digitalis lanata P5βR (PDB ID: 2V6G) as template highlighted the importance of the hydrophobicity of the binding pocket for substrate discrimination. It is concluded that P5βR genes or P5βR proteins can be used as valuable function-associated molecular markers to infer taxonomic relationship and evolutionary diversification from a metabolic/catalytic perspective.
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Affiliation(s)
- J Munkert
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - C Costa
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - O Budeanu
- University of the Academy of Sciences of Moldova, Chisinau, Moldova Republic
| | - J Petersen
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - S Bertolucci
- Agriculture Department, Universidade Federal de Lavras, Lavras, Brazil
| | - G Fischer
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - F Müller-Uri
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - W Kreis
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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23
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Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal. Mol Phylogenet Evol 2015; 91:68-85. [DOI: 10.1016/j.ympev.2015.05.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/08/2015] [Accepted: 05/10/2015] [Indexed: 01/18/2023]
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24
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Roy T, Cole LW, Chang TH, Lindqvist C. Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae). Mol Phylogenet Evol 2015; 89:46-62. [PMID: 25888973 DOI: 10.1016/j.ympev.2015.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 03/24/2015] [Accepted: 03/26/2015] [Indexed: 02/05/2023]
Abstract
The phenomenon of polyploidy and hybridization usually results in novel genetic combinations, leading to complex, reticulate evolution and incongruence among gene trees, which in turn may show different phylogenetic histories than the inherent species tree. The largest tribe within the subfamily Lamioideae (Lamiaceae), Stachydeae, which includes the globally distributed Stachys, and one of the largest Hawaiian angiosperm radiations, the endemic mints, is a widespread and taxonomically challenging lineage displaying a wide spectrum of morphological and chromosomal diversity. Previous molecular phylogenetic studies have showed that while the Hawaiian mints group with Mexican-South American Stachys based on chloroplast DNA sequence data, nuclear ribosomal DNA (nrDNA) sequences suggest that they are most closely related to temperate North American Stachys. Here, we have utilized five independently inherited, low-copy nuclear loci, and a variety of phylogenetic methods, including multi-locus coalescence-based tree reconstructions, to provide insight into the complex origins and evolutionary relationships between the New World Stachys and the Hawaiian mints. Our results demonstrate incongruence between individual gene trees, grouping the Hawaiian mints with both temperate North American and Meso-South American Stachys clades. However, our multi-locus coalescence tree is concurrent with previous nrDNA results placing them within the temperate North American Stachys clade. Our results point toward a possible allopolyploid hybrid origin of the Hawaiian mints arising from temperate North American and Meso-South American ancestors, as well as a reticulate origin for South American Stachys. As such, our study is another significant step toward further understanding the putative parentage and the potential influence of hybridization and incomplete lineage sorting in giving rise to this insular plant lineage, which following colonization underwent rapid morphological and ecological diversification.
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Affiliation(s)
- Tilottama Roy
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
| | - Logan W Cole
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA; Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Tien-Hao Chang
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
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Sramkó G, Attila MV, Hawkins JA, Bateman RM. Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae). ANNALS OF BOTANY 2014; 114:1609-26. [PMID: 25294871 PMCID: PMC4649687 DOI: 10.1093/aob/mcu179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Lizard orchids of the genus Himantoglossum include many of Eurasia's most spectacular orchids, producing substantial spikes of showy flowers. However, until recently the genus had received only limited, and entirely traditional, systematic study. The aim of the current work was to provide a more robust molecular phylogeny in order to better understand the evolutionary relationships among species of particular conservation concern. METHODS All putative species of Himantoglossum s.l. were sampled across its geographical range. A large subsample of the 153 populations studied contributed to an initial survey of nuclear ribosomal internal transcribed spacer (nrITS) ribotypes. Smaller subsets were then sequenced for four plastid regions and the first intron of the low-copy-number nuclear gene LEAFY. Rooted using Steveniella as outgroup, phylogenetic trees were generated using parsimony and Bayesian methods from each of the three datasets, supplemented with a ribotype network. KEY RESULTS The resulting trees collectively determined the order of branching of the early divergent taxa as Himantoglossum comperianum > H. robertianum group > H. formosum, events that also involved significant morphological divergence. Relaxed molecular clock dating suggested that these divergences preceded the Pleistocene glaciations (the origin of the H. robertianum group may have coincided with the Messinian salinity crisis) and occurred in Asia Minor and/or the Caucasus. Among more controversial taxa of the H. hircinum-jankae clade, which are only subtly morphologically divergent, topological resolution was poorer and topological incongruence between datasets was consequently greater. CONCLUSIONS Plastid sequence divergence is broadly consistent with prior, morphologically circumscribed taxa and indicates a division between H. hircinum-adriaticum to the west of the Carpathians and H. jankae-caprinum (plus local endemics) to the east, a distinction also suggested by nrITS ribotypes. LEAFY phylogenies are less congruent with prior taxonomic arrangements and include one likely example of paralogy. Himantoglossum metlesicsianum fully merits its IUCN Endangered status. Potentially significant genetic variation was detected within Steveniella satyrioides, H. robertianum and H. hircinum. However, confident circumscription of the more derived species of Himantoglossum s.s., including local endemics of hybrid origin, must await future morphometric and population-genetic analyses.
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Affiliation(s)
- Gábor Sramkó
- MTA-ELTE-MTM Ecology Research Group, Pázmány P. sétány 1/C, Budapest, 1117, Hungary Department of Botany, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary
| | - Molnár V Attila
- Department of Botany, University of Debrecen, Egyetem ter 1., Debrecen, 4032, Hungary
| | - Julie A Hawkins
- School of Biological Sciences, University of Reading, Reading RG6 6AS, UK
| | - Richard M Bateman
- Jodrell Laboratory, Royal Botanical Gardens Kew, Richmond, Surrey TW9 3DS, UK
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26
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de Sousa F, Bertrand YJK, Nylinder S, Oxelman B, Eriksson JS, Pfeil BE. Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing. PLoS One 2014; 9:e109704. [PMID: 25329401 PMCID: PMC4201463 DOI: 10.1371/journal.pone.0109704] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/10/2014] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research, including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionary history of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylogenies. Identification of the processes causing this genealogical incongruence is essential for the inference of a correct species phylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtained across different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogenetic properties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-based gene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternative proves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level and allows for an increase in number and size of targeted loci. Substitution rate estimates for each of the 50 loci are provided, and an overview of the variation in substitution rates among a large number of low-copy nuclear genes in plants is presented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made available and can be used in further probe development for sequence-capture of the same markers.
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Affiliation(s)
- Filipe de Sousa
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Yann J. K. Bertrand
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Stephan Nylinder
- Department of Botany, Swedish Museum of Natural History, Stockholm, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jonna S. Eriksson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bernard E. Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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27
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Evolution of stamen number in Ptychospermatinae (Arecaceae): Insights from a new molecular phylogeny of the subtribe. Mol Phylogenet Evol 2014; 76:227-40. [DOI: 10.1016/j.ympev.2014.02.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/19/2014] [Accepted: 02/28/2014] [Indexed: 11/20/2022]
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28
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Sun C, Yu G, Bao M, Zheng B, Ning G. Biological pattern and transcriptomic exploration and phylogenetic analysis in the odd floral architecture tree: Helwingia willd. BMC Res Notes 2014; 7:402. [PMID: 24969969 PMCID: PMC4083144 DOI: 10.1186/1756-0500-7-402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Odd traits in few of plant species usually implicate potential biology significances in plant evolutions. The genus Helwingia Willd, a dioecious medical shrub in Aquifoliales order, has an odd floral architecture-epiphyllous inflorescence. The potential significances and possible evolutionary origin of this specie are not well understood due to poorly available data of biological and genetic studies. In addition, the advent of genomics-based technologies has widely revolutionized plant species with unknown genomic information. RESULTS Morphological and biological pattern were detailed via anatomical and pollination analyses. An RNA sequencing based transcriptomic analysis were undertaken and a high-resolution phylogenetic analysis was conducted based on single-copy genes in more than 80 species of seed plants, including H. japonica. It is verified that a potential fusion of rachis to the leaf midvein facilitates insect pollination. RNA sequencing yielded a total of 111450 unigenes; half of them had significant similarity with proteins in the public database, and 20281 unigenes were mapped to 119 pathways. Deduced from the phylogenetic analysis based on single-copy genes, the group of Helwingia is closer with Euasterids II and rather than Euasterids, congruent with previous reports using plastid sequences. CONCLUSIONS The odd flower architecture make H. Willd adapt to insect pollination by hosting those insects larger than the flower in size via leave, which has little common character that other insect pollination plants hold. Further the present transcriptome greatly riches genomics information of Helwingia species and nucleus genes based phylogenetic analysis also greatly improve the resolution and robustness of phylogenetic reconstruction in H. japonica.
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Affiliation(s)
| | | | | | | | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, P, R, China.
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Griffin PC, Hoffmann AA. Limited genetic divergence among Australian alpine Poa tussock grasses coupled with regional structuring points to ongoing gene flow and taxonomic challenges. ANNALS OF BOTANY 2014; 113:953-65. [PMID: 24607721 PMCID: PMC3997636 DOI: 10.1093/aob/mcu017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/27/2014] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS While molecular approaches can often accurately reconstruct species relationships, taxa that are incompletely differentiated pose a challenge even with extensive data. Such taxa are functionally differentiated, but may be genetically differentiated only at small and/or patchy regions of the genome. This issue is considered here in Poa tussock grass species that dominate grassland and herbfields in the Australian alpine zone. METHODS Previously reported tetraploidy was confirmed in all species by sequencing seven nuclear regions and five microsatellite markers. A Bayesian approach was used to co-estimate nuclear and chloroplast gene trees with an overall dated species tree. The resulting species tree was used to examine species structure and recent hybridization, and intertaxon fertility was tested by experimental crosses. KEY RESULTS Species tree estimation revealed Poa gunnii, a Tasmanian endemic species, as sister to the rest of the Australian alpine Poa. The taxa have radiated in the last 0·5-1·2 million years and the non-gunnii taxa are not supported as genetically distinct. Recent hybridization following past species divergence was also not supported. Ongoing gene flow is suggested, with some broad-scale geographic structure within the group. CONCLUSIONS The Australian alpine Poa species are not genetically distinct despite being distinguishable phenotypically, suggesting recent adaptive divergence with ongoing intertaxon gene flow. This highlights challenges in using conventional molecular taxonomy to infer species relationships in recent, rapid radiations.
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Affiliation(s)
- Philippa C. Griffin
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Ary A. Hoffmann
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
- Pest and Environmental Adaptation Research Group, Department of Zoology, University of Melbourne, Parkville 3010, Victoria, Australia
- Long Term Ecological Research Network, http://www.ltern.org.au/
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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.
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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
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The origin of the early differentiation of Ivies (Hedera L.) and the radiation of the Asian Palmate group (Araliaceae). Mol Phylogenet Evol 2014; 70:492-503. [DOI: 10.1016/j.ympev.2013.10.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 11/22/2022]
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Shahin A, Smulders MJM, van Tuyl JM, Arens P, Bakker FT. Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars. FRONTIERS IN PLANT SCIENCE 2014; 5:567. [PMID: 25368628 PMCID: PMC4202788 DOI: 10.3389/fpls.2014.00567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/01/2014] [Indexed: 05/19/2023]
Abstract
Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium.
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Affiliation(s)
- Arwa Shahin
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marinus J. M. Smulders
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Jaap M. van Tuyl
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Paul Arens
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Freek T. Bakker
- Biosystematics Group, Wageningen UniversityWageningen, Netherlands
- *Correspondence: Freek T. Bakker, Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6700 AP Wageningen, Netherlands e-mail:
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Novel nuclear markers inform the systematics and the evolution of serpentine use in Streptanthus and allies (Thelypodieae, Brassicaceae). Mol Phylogenet Evol 2013; 72:71-81. [PMID: 24333439 DOI: 10.1016/j.ympev.2013.11.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 11/13/2013] [Accepted: 11/28/2013] [Indexed: 11/22/2022]
Abstract
Streptanthus is a genus of ca. 35 species in the tribe Thelypodieae (Brassicaceae) that has remarkable morphological and ecological diversity, a large number of species in the group being edaphic specialists endemic to unusual soils such as serpentine. While ecological research has shed some light on adaptation to serpentine in Streptanthus, there have been few insights on the origins and evolution of serpentine tolerance in this group, largely due to limited success in resolving the phylogenetic relationships among Streptanthus and allied genera of the Thelypodieae (Streptanthoid complex). We present a well-resolved phylogenetic hypothesis for the Streptanthoid complex, based on three newly identified and highly variable single copy nuclear regions (AT4G34700, AT1G61620, and AT1G56590, and three others that are widely used (ITS, phyA, and PEPC). We also include data for two chloroplast regions (trnL and trnH-psbA). Collectively, our new markers provide 75% of the nuclear parsimony informative characters in our data. Taxonomically, our sampling is the most inclusive of any study of the Streptanthoid Complex to date, including 46 out of the 53 species of Streptanthus and Caulanthus, as well as representatives of several closely allied genera in the Thelypodieae. Our results reveal that Streptanthus, Caulanthus, and Thelypodium are not reciprocally monophyletic as currently defined. The species of Streptanthus form two rather distantly related clades. One clade (SC-I) is comprised of species with bilateral flowers and urn-shaped calyces that occur mainly within the California Floristic Province (CFP) hotspot; the other clade (SC-II) is composed of species with extant ranges mainly outside the CFP. Our data indicate that serpentine tolerance has evolved between eight and ten times in this group, of which between four and five have resulted in endemism. While serpentine endemism has been rarely lost, large and diverse clades composed mainly of serpentine endemics indicate that serpentine endemics in this group are more than mere 'dead-ends'.
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Särkinen T, George M. Predicting plastid marker variation: can complete plastid genomes from closely related species help? PLoS One 2013; 8:e82266. [PMID: 24312409 PMCID: PMC3843732 DOI: 10.1371/journal.pone.0082266] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 11/01/2013] [Indexed: 11/19/2022] Open
Abstract
Rapidly evolving non-coding plastid regions (NCPs) are currently widely used in evolutionary biology especially in plant systematic studies where NCPs have become one of the most commonly used tools in clarifying species relationships. Currently, the generally small amount of sequence variation provided by NCPs compared to nuclear regions makes plastid phylogeny reconstruction challenging at the species-level, especially so in species rich clades such as Solanum with c. 1,200 species. Previous studies have established that the set of most highly variable NCPs vary between major plant families, and here we explore whether this variation extends beyond family level to genera and major clades within genera. Using full plastome data, we identify the most highly variable plastid markers in the Potato clade of Solanum. We then compare sequence variation between the Potato and the closely related Morelloid clade. Results show that whilst a narrow set of NCPs show consistently high variation, levels of sequence variation in most NCPs differ greatly between the two closely related clades. The high variation detected between closely related groups implies that repeated screening studies will be needed for individual projects despite the potential availability of results from closely related taxa, and indicates a narrower applicability of family-specific screening studies than previously thought.
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Affiliation(s)
- Tiina Särkinen
- Life Sciences Department, The Natural History Museum, London, United Kingdom
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Morvah George
- Millenium Seed Bank, Royal Botanic Gardens, Kew, United Kingdom
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Pillon Y, Johansen JB, Sakishima T, Roalson EH, Price DK, Stacy EA. Gene discordance in phylogenomics of recent plant radiations, an example from Hawaiian Cyrtandra (Gesneriaceae). Mol Phylogenet Evol 2013; 69:293-8. [PMID: 23685062 DOI: 10.1016/j.ympev.2013.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 05/04/2013] [Accepted: 05/06/2013] [Indexed: 12/11/2022]
Abstract
Resolving species relationships within recent radiations requires analysis at the interface of phylogenetics and population genetics, where coalescence and hybridization may confound our understanding of relationships. We developed 18 new primer pairs for nuclear loci in Cyrtandra (Gesneriaceae), one of the largest plant radiations in the Pacific Islands, and tested the concordance of 14 loci in establishing the phylogenetic relationships of a small number of Hawaiian species. Four genes yielded tree topologies conflicting with the primary concordance tree, suggesting plastid capture and horizontal transfer via hybridization. Combining all concordant genes yielded a tree with stronger support and a different topology from the total-evidence tree. We conclude that a small number of genes may be insufficient for accurate reconstruction of the phylogenetic relationships among closely related species. Further, the combination of genes for phylogenetic analysis without preliminary concordance tests can yield an erroneous tree topology. It seems that the number of genes needed for phylogenetic analysis of closely related species is significantly greater than the small numbers commonly used, which fail to isolate coalescence, introgression and hybridization.
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Affiliation(s)
- Yohan Pillon
- Tropical Conservation Biology and Environmental Science Program, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, HI 96720, USA.
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Zimmer EA, Wen J. Reprint of: using nuclear gene data for plant phylogenetics: progress and prospects. Mol Phylogenet Evol 2013; 66:539-50. [PMID: 23375140 DOI: 10.1016/j.ympev.2013.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022]
Abstract
The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.
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Affiliation(s)
- Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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Hong-Wa C, Besnard G. Intricate patterns of phylogenetic relationships in the olive family as inferred from multi-locus plastid and nuclear DNA sequence analyses: a close-up on Chionanthus and Noronhia (Oleaceae). Mol Phylogenet Evol 2013; 67:367-78. [PMID: 23415987 DOI: 10.1016/j.ympev.2013.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 10/19/2012] [Accepted: 02/04/2013] [Indexed: 12/28/2022]
Abstract
Noronhia represents the most successful radiation of the olive family (Oleaceae) in Madagascar with more than 40 named endemic species distributed in all ecoregions from sea level to high mountains. Its position within the subtribe Oleinae has, however, been largely unresolved and its evolutionary history has remained unexplored. In this study, we generated a dataset of plastid (trnL-F, trnT-L, trnS-G, trnK-matK) and nuclear (internal transcribed spacer [ITS]) DNA sequences to infer phylogenetic relationships within Oleinae and to examine evolutionary patterns within Noronhia. Our sample included most species of Noronhia and representatives of the ten other extant genera within the subtribe with an emphasis on Chionanthus. Bayesian inferences and maximum likelihood analyses of plastid and nuclear data indicated several instances of paraphyly and polyphyly within Oleinae, with some geographic signal. Both plastid and ITS data showed a polyphyletic Noronhia that included Indian Ocean species of Chionanthus. They also found close relationships between Noronhia and African Chionanthus. However, the plastid data showed little clear differentiation between Noronhia and the African Chionanthus whereas relationships suggested by the nuclear ITS data were more consistent with taxonomy and geography. We used molecular dating to discriminate between hybridization and lineage sorting/gene duplication as alternative explanations for these topological discordances and to infer the biogeographic history of Noronhia. Hybridization between African Chionanthus and Noronhia could not be ruled out. However, Noronhia has long been established in Madagascar after a likely Cenozoic dispersal from Africa, suggesting any hybridization between representatives of African and Malagasy taxa was ancient. In any case, the African and Indian Ocean Chionanthus and Noronhia together formed a strongly supported monophyletic clade distinct and distant from other Chionanthus, which calls for a revised and more conservative taxonomy for this group.
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Affiliation(s)
- Cynthia Hong-Wa
- Department of Biology, University of Missouri - St. Louis, One University Blvd., St. Louis, MO 63121-4000, USA.
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Cardoso D, Paganucci de Queiroz L, Cavalcante de Lima H, Suganuma E, van den Berg C, Lavin M. A molecular phylogeny of the vataireoid legumes underscores floral evolvability that is general to many early-branching papilionoid lineages. AMERICAN JOURNAL OF BOTANY 2013; 100:403-421. [PMID: 23378491 DOI: 10.3732/ajb.1200276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF STUDY Flowering traits can sometimes be overemphasized in taxonomic classifications. The fused and completely differentiated papilionate floral organs in the neotropical legume trees Vatairea and Vataireopsis were traditionally used in part to ascribe these genera to the tribe Dalbergieae. In contrast, the free and mostly undifferentiated floral parts of Luetzelburgia and Sweetia fit the circumscription of the "primitive" Sophoreae. Such divergent floral morphologies thought to divide deep phylogenetic lineages indeed may be prone to episodic transformation among close papilionoid relatives. METHODS We sampled 26 of 27 known species of Luetzelburgia, Sweetia, Vatairea, and Vataireopsis in parsimony and Bayesian phylogenetic analyses of nuclear ribosomal ITS/5.8S and six plastid (matK, 3'-trnK, psbA-trnH, trnL intron, rps16 intron, and trnD-T) DNA sequence loci. KEY RESULTS The analyses of individual and combined data sets strongly resolved the monophyly of each of Luetzelburgia, Sweetia, Vatairea, and Vataireopsis. Vataireopsis was resolved as sister to the rest and the morphologically divergent Luetzelburgia and Vatairea were strongly resolved as sister clades. Floral morphology was generally not a good predictor of phylogenetic relatedness. CONCLUSIONS Luetzelburgia, Sweetia, Vatairea, and Vataireopsis are unequivocally resolved as the "vataireoid" clade. Fruit and vegetative traits are found to be more phylogenetically conserved than many floral traits. This explains why the identity of the vataireoids has been overlooked or confused. The evolvability of floral traits may also be a general condition among many of the early-branching papilionoid lineages.
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Affiliation(s)
- Domingos Cardoso
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900, Feira de Santana, Bahia, Brazil.
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Liu PL, Wan Q, Guo YP, Yang J, Rao GY. Phylogeny of the genus Chrysanthemum L.: evidence from single-copy nuclear gene and chloroplast DNA sequences. PLoS One 2012; 7:e48970. [PMID: 23133665 PMCID: PMC3486802 DOI: 10.1371/journal.pone.0048970] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 10/03/2012] [Indexed: 02/07/2023] Open
Abstract
Chrysanthemum L. (Asteraceae-Anthemideae) is a genus with rapid speciation. It comprises about 40 species, most of which are distributed in East Asia. Many of these are narrowly distributed and habitat-specific. Considerable variations in morphology and ploidy are found in this genus. Some species have been the subjects of many studies, but the relationships between Chrysanthemum and its allies and the phylogeny of this genus remain poorly understood. In the present study, 32 species/varieties from Chrysanthemum and 11 from the allied genera were analyzed using DNA sequences of the single-copy nuclear CDS gene and seven cpDNA loci (psbA-trnH, trnC-ycf6, ycf6-psbM, trnY-rpoB, rpS4-trnT, trnL-F, and rpL16). The cpDNA and nuclear CDS gene trees both suggest that 1) Chrysanthemum is not a monophyletic taxon, and the affinity between Chrysanthemum and Ajania is so close that these two genera should be incorporated taxonomically; 2) Phaeostigma is more closely related to the Chrysanthemum+Ajania than other generic allies. According to pollen morphology and to the present cpDNA and CDS data, Ajania purpurea is a member of Phaeostigma. Species differentiation in Chrysanthemum appears to be correlated with geographic and environmental conditions. The Chinese Chrysanthemum species can be divided into two groups, the C. zawadskii group and the C. indicum group. The former is distributed in northern China and the latter in southern China. Many polyploid species, such as C. argyrophyllum, may have originated from allopolyploidization involving divergent progenitors. Considering all the evidence from present and previous studies, we conclude that geographic and ecological factors as well as hybridization and polyploidy play important roles in the divergence and speciation of the genus Chrysanthemum.
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Affiliation(s)
- Ping-Li Liu
- College of Life Sciences, Peking University, Beijing, China
| | - Qian Wan
- College of Life Sciences, Peking University, Beijing, China
| | - Yan-Ping Guo
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ji Yang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Guang-Yuan Rao
- College of Life Sciences, Peking University, Beijing, China
- * E-mail:
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Zimmer EA, Wen J. Using nuclear gene data for plant phylogenetics: Progress and prospects. Mol Phylogenet Evol 2012; 65:774-85. [DOI: 10.1016/j.ympev.2012.07.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 10/28/2022]
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Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species. Mol Phylogenet Evol 2012; 65:23-34. [DOI: 10.1016/j.ympev.2012.05.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 11/21/2022]
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42
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Moody ML, Rieseberg LH. Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus). Mol Phylogenet Evol 2012; 64:145-55. [PMID: 22724134 DOI: 10.1016/j.ympev.2012.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.
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Affiliation(s)
- Michael L Moody
- School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia.
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43
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Zarrei M, Wilkin P, Ingrouille MJ, Leitch IJ, Buerki S, Fay MF, Chase MW. Speciation and evolution in the Gagea reticulata species complex (Tulipeae; Liliaceae). Mol Phylogenet Evol 2012; 62:624-39. [DOI: 10.1016/j.ympev.2011.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 10/29/2011] [Accepted: 11/04/2011] [Indexed: 10/15/2022]
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Grover CE, Salmon A, Wendel JF. Targeted sequence capture as a powerful tool for evolutionary analysis. AMERICAN JOURNAL OF BOTANY 2012; 99:312-9. [PMID: 22268225 DOI: 10.3732/ajb.1100323] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Next-generation sequencing technologies (NGS) have revolutionized biological research by significantly increasing data generation while simultaneously decreasing the time to data output. For many ecologists and evolutionary biologists, the research opportunities afforded by NGS are substantial; even for taxa lacking genomic resources, large-scale genome-level questions can now be addressed, opening up many new avenues of research. While rapid and massive sequencing afforded by NGS increases the scope and scale of many research objectives, whole genome sequencing is often unwarranted and unnecessarily complex for specific research questions. Recently developed targeted sequence enrichment, coupled with NGS, represents a beneficial strategy for enhancing data generation to answer questions in ecology and evolutionary biology. This marriage of technologies offers researchers a simple method to isolate and analyze a few to hundreds, or even thousands, of genes or genomic regions from few to many samples in a relatively efficient and effective manner. These strategies can be applied to questions at both the infra- and interspecific levels, including those involving parentage, gene flow, divergence, phylogenetics, reticulate evolution, and many more. Here we provide a brief overview of targeted sequence enrichment, and emphasize the power of this technology to increase our ability to address a wide range of questions of interest to ecologists and evolutionary biologists, particularly for those working with taxa for which few genomic resources are available.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, Iowa 50011, USA.
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Soza VL, Brunet J, Liston A, Smith PS, Di Stilio VS. Phylogenetic insights into the correlates of dioecy in meadow-rues (Thalictrum, Ranunculaceae). Mol Phylogenet Evol 2012; 63:180-92. [PMID: 22289865 DOI: 10.1016/j.ympev.2012.01.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 11/19/2011] [Accepted: 01/08/2012] [Indexed: 11/25/2022]
Abstract
Numerous studies have examined the evolution of sexual systems in angiosperms, but few explore the interaction between these and the evolution of pollination mode. Wind pollination is often associated with unisexual flowers, but which evolved first and played a causative role in the evolution of the other is unclear. Thalictrum, meadow-rues (Ranunculaceae), provides a unique opportunity to study the evolution of these traits because it contains insect and wind pollination and four sexual systems. We used a phylogenetic approach to reconstruct ancestral states for sexual system, pollination mode, and geographic distribution in Thalictrum, and tested for correlations to uncover the factors involved in the evolution of unisexuality and wind pollination. Our results show that dioecy, andro- and gynomonoecy evolved at least twice from hermaphroditism. Wind pollination, unisexual flowers, and New World distribution were all significantly correlated. Wind pollination may have evolved early in the genus, followed by multiple losses and gains, and likely preceded the origin of unisexual flowers in several cases; we found no evidence for unisexual flowers evolving prior to wind pollination. Given a broad scale study showing the evolution of dioecy before wind pollination, our results from a finer scale analysis highlight that different evolutionary pathways are likely to occur throughout angiosperms.
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Affiliation(s)
- Valerie L Soza
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
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Bartholmes C, Hidalgo O, Gleissberg S. Evolution of the YABBY gene family with emphasis on the basal eudicot Eschscholzia californica (Papaveraceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:11-23. [PMID: 21974722 DOI: 10.1111/j.1438-8677.2011.00486.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
YABBY genes are seed plant-specific transcriptional regulators that are involved in diverse aspects of leaf, shoot and flower development. A series of duplications gave rise to five gene groups found throughout flowering plants. In Arabidopsis and other species, expression of two gene groups, CRABS CLAW and INNER NO OUTER, is restricted to floral organs. In contrast, members of the FILAMENTOUS FLOWER, YABBY2 and YABBY5 gene groups are also expressed in leaves and have been termed 'vegetative YABBYs'. How the five paralogue groups evolved and how their expression and function diversified have remained largely unresolved, precluding a reconstruction of the natural history of this gene family. Here, we report new genes from Eschscholzia californica (Ranunculales, Papaveraceae) that we use together with currently available database sequences in a comprehensive phylogenetic re-evaluation of the YABBY gene family. Multilayered Bayesian analysis covering seed plants allowed us to locate Eschscholzia YABBY sequences within the gene family phylogeny. We established that vegetative YABBYs do not form a monophyletic clade, and that CRABS CLAW and FILAMENTOUS FLOWER arose from a common ancestor gene. INNER NO OUTER genes are sister to that ancestral gene. We identified several conserved motifs outside of known amino acid domains that define all five angiosperm YABBY gene clades. Further, we inferred the evolution of gene expression and provide evidence for release of purifying constraint in certain branches of the gene family tree. Finally, we report expression patterns for five Eschscholzia YABBY genes consistent with functional conservation between early-diverged and core eudicots.
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Affiliation(s)
- C Bartholmes
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
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Naumann J, Symmank L, Samain MS, Müller KF, Neinhuis C, dePamphilis CW, Wanke S. Chasing the hare - evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae). BMC Evol Biol 2011; 11:357. [PMID: 22151585 PMCID: PMC3252395 DOI: 10.1186/1471-2148-11-357] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 12/12/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and identified a set of nuclear genes that occur in single copy in multiple sequenced angiosperms. The present study is the first to apply genomic sequence of one of these low copy genes, agt1, as a phylogenetic marker for species-level phylogenetics. Its utility is compared to the performance of several coding and non-coding chloroplast loci that have been suggested as most applicable for this taxonomic level. As a model group, we chose Tildenia, a subgenus of Peperomia (Piperaceae), one of the largest plant genera. Relationships are particularly difficult to resolve within these species rich groups due to low levels of polymorphisms and fast or recent radiation. Therefore, Tildenia is a perfect test case for applying new phylogenetic tools. RESULTS We show that the nuclear marker agt1, and in particular the agt1 introns, provide a significantly increased phylogenetic signal compared to chloroplast markers commonly used for low level phylogenetics. 25% of aligned characters from agt1 intron sequence are parsimony informative. In comparison, the introns and spacer of several common chloroplast markers (trnK intron, trnK-psbA spacer, ndhF-rpl32 spacer, rpl32-trnL spacer, psbA-trnH spacer) provide less than 10% parsimony informative characters. The agt1 dataset provides a deeper resolution than the chloroplast markers in Tildenia. CONCLUSIONS Single (or very low) copy nuclear genes are of immense value in plant phylogenetics. Compared to other nuclear genes that are members of gene families of all sizes, lab effort, such as cloning, can be kept to a minimum. They also provide regions with different phylogenetic content deriving from coding and non-coding parts of different length. Thus, they can be applied to a wide range of taxonomic levels from family down to population level. As more plant genomes are sequenced, we will obtain increasingly precise information about which genes return to single copy most rapidly following gene duplication and may be most useful across a wide range of plant groups.
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Affiliation(s)
- Julia Naumann
- Technische Universität Dresden, Institut für Botanik, D-01062 Dresden, Germany.
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Delgado-Salinas A, Thulin M, Pasquet R, Weeden N, Lavin M. Vigna (Leguminosae) sensu lato: the names and identities of the American segregate genera. AMERICAN JOURNAL OF BOTANY 2011; 98:1694-715. [PMID: 21980163 DOI: 10.3732/ajb.1100069] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF STUDY The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology. METHODS The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives. KEY RESULTS The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna. CONCLUSIONS American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6-7 million yr, which belies much greater floral variation in the Americas.
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Affiliation(s)
- Alfonso Delgado-Salinas
- Universidad Nacional Autónoma de México, Instituto de Biología, Departamento de Botánica, México, Distrito Federal, Mexico.
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Neves SS, Forrest LL. Plant DNA sequencing for phylogenetic analyses: from plants to sequences. Methods Mol Biol 2011; 781:183-235. [PMID: 21877283 DOI: 10.1007/978-1-61779-276-2_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA sequences are important sources of data for phylogenetic analysis. Nowadays, DNA sequencing is a routine technique in molecular biology laboratories. However, there are specific questions associated with project design and sequencing of plant samples for phylogenetic analysis, which may not be familiar to researchers starting in the field. This chapter gives an overview of methods and protocols involved in the sequencing of plant samples, including general recommendations on the selection of species/taxa and DNA regions to be sequenced, and field collection of plant samples. Protocols of plant sample preparation, DNA extraction, PCR and cloning, which are critical to the success of molecular phylogenetic projects, are described in detail. Common problems of sequencing (using the Sanger method) are also addressed. Possible applications of second-generation sequencing techniques in plant phylogenetics are briefly discussed. Finally, orientation on the preparation of sequence data for phylogenetic analyses and submission to public databases is also given.
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Affiliation(s)
- Susana S Neves
- Plant Cell Biotechnology Laboratory, ITQB Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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Brokaw JM, Hufford L. Origins and introgression of polyploid species in Mentzelia section Trachyphytum (Loasaceae). AMERICAN JOURNAL OF BOTANY 2010; 97:1457-1473. [PMID: 21616900 DOI: 10.3732/ajb.0900388] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Polyploid speciation has been important in plant evolution. However, the conditions that favor the origination and persistence of polyploids are still not well understood. Here, we examine origins of 16 polyploid species in Mentzelia section Trachyphytum. • METHODS We used phylogeny reconstructions based on DNA sequences from plastid regions and the nuclear gene isocitrate dehydrogenase (idh) to construct hypotheses of introgression and polyploidization. • KEY RESULTS Molecular data suggest that homoploid hybridization has been surprisingly common in Trachyphytum. Diploid species had unequal involvement in polyploid origins, but most polyploid taxa had allopolyploid origins from extant progenitors. A few polyploids with extreme phenotypes did not appear to have extant progenitors. We infer that the progenitors of these species were derived from extinct diploid lineages or ancestral lineages of multiple extant diploids. In agreement with other recent studies, we recovered molecular evidence of multiple phylogenetically distinct origins for several polyploid taxa, including the widespread octoploid M. albicaulis. • CONCLUSIONS Evidence of high levels of introgression and allopolyploidy suggests that hybridization has played an important role in the evolution of Trachyphytum. Although idh sequences exhibited complicated evolution, including gene duplication, deletion, and recombination, they provided a higher percentage of informative characters for phylogeny reconstruction than the most variable plastid regions, allowing tests of hypotheses regarding polyploid origins. Given the necessity for rapidly evolving low-copy nuclear genes, researchers studying hybridization and polyploidy may increasingly turn to complex sequence data.
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Affiliation(s)
- Joshua M Brokaw
- School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236 USA
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