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Choi TY, Lee SR. Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes. PLoS One 2024; 19:e0301346. [PMID: 38578735 PMCID: PMC10997070 DOI: 10.1371/journal.pone.0301346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, Chosun University, Gwangju, South Korea
| | - Soo-Rang Lee
- Department of Biology Education, Chosun University, Gwangju, South Korea
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Botha D, du Plessis M, Siebert F, Barnard S. Introducing an rbcL and a trnL reference library to aid in the metabarcoding analysis of foraged plants from two semi-arid eastern South African savanna bioregions. PLoS One 2023; 18:e0286144. [PMID: 37205700 DOI: 10.1371/journal.pone.0286144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna. Thereafter, rbcL and trnL sequences of species from this list were mined from GenBank and BOLD sequence databases according to specific quality criteria to ensure accurate taxonomic coverage and resolution. These were supplemented with sequences of 24 species sequenced for this study. A phylogenetic approach, employing Neighbor-Joining, was used to verify the topology of the reference libraries to known angiosperm phylogeny. The taxonomic reliability of these reference libraries was evaluated by testing for the presence of a barcode gap, identifying a data-appropriate identification threshold, and determining the identification accuracy of reference sequences via primary distance-based criteria. The final rbcL reference dataset consisted of 1238 sequences representing 318 genera and 562 species. The final trnL dataset consisted of 921 sequences representing 270 genera and 461 species. Barcode gaps were found for 76% of the taxa in the rbcL barcode reference dataset and 68% of the taxa in the trnL barcode reference dataset. The identification success rate, calculated with the k-nn criterion was 85.86% for the rbcL dataset and 73.72% for the trnL dataset. The datasets for rbcL and trnL combined during this study are not presented as complete DNA reference libraries, but rather as two datasets that should be used in unison to identify plants present in the semi-arid eastern savannas of South Africa.
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Affiliation(s)
- Danielle Botha
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mornè du Plessis
- Core Sequencing Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Frances Siebert
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Sandra Barnard
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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Mahbub S, Sawmya S, Saha A, Reaz R, Rahman MS, Bayzid MS. Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data. JOURNAL OF COMPUTATIONAL BIOLOGY : A JOURNAL OF COMPUTATIONAL MOLECULAR CELL BIOLOGY 2022; 29:1156-1172. [PMID: 36048555 DOI: 10.1089/cmb.2022.0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, for a combination of reasons (ranging from sampling biases to more biological causes, as in gene birth and loss), gene trees are often incomplete, meaning that not all species of interest have a common set of genes. Incomplete gene trees can potentially impact the accuracy of phylogenomic inference. We, for the first time, introduce the problem of imputing the quartet distribution induced by a set of incomplete gene trees, which involves adding the missing quartets back to the quartet distribution. We present Quartet based Gene tree Imputation using Deep Learning (QT-GILD), an automated and specially tailored unsupervised deep learning technique, accompanied by cues from natural language processing, which learns the quartet distribution in a given set of incomplete gene trees and generates a complete set of quartets accordingly. QT-GILD is a general-purpose technique needing no explicit modeling of the subject system or reasons for missing data or gene tree heterogeneity. Experimental studies on a collection of simulated and empirical datasets suggest that QT-GILD can effectively impute the quartet distribution, which results in a dramatic improvement in the species tree accuracy. Remarkably, QT-GILD not only imputes the missing quartets but can also account for gene tree estimation error. Therefore, QT-GILD advances the state-of-the-art in species tree estimation from gene trees in the face of missing data.
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Affiliation(s)
- Sazan Mahbub
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh.,Department of Computer Science, University of Maryland, College Park, Maryland, USA
| | - Shashata Sawmya
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Arpita Saha
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Rezwana Reaz
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - M Sohel Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
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Amiteye S. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon 2021; 7:e08093. [PMID: 34765757 PMCID: PMC8569399 DOI: 10.1016/j.heliyon.2021.e08093] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR- or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.
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Affiliation(s)
- Samuel Amiteye
- Department of Nuclear Agriculture and Radiation Processing (NARP), Graduate School of Nuclear and Allied Sciences (SNAS), College of Basic and Applied Sciences, University of Ghana, P. O. Box AE 1, Accra, Ghana
- Biotechnology Centre, Biotechnology and Nuclear Agriculture Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), P. O. Box AE 50, Accra, Ghana
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De Miranda GS, Giupponi APL, Scharff N, Prendini L. Phylogeny and biogeography of the pantropical whip spider family Charinidae (Arachnida: Amblypygi). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Abstract
The present contribution addresses the phylogeny and biogeography of the pantropical whip spider family Charinidae Quintero, 1986, the most species-rich in the arachnid order Amblypygi Thorell, 1883, based on morphology and multilocus DNA sequences, analysed simultaneously using parsimony, maximum likelihood and Bayesian inference. The morphological matrix comprises 138 characters, scored for four outgroup taxa and 103 ingroup terminals representing all genera and 64% of the species of Charinidae. The multilocus dataset comprises sequences from two nuclear and three mitochondrial gene loci for four outgroup taxa and 48 ingroup representing 30 (23%) taxa of Charinidae. Charinidae are monophyletic, with Weygoldtia Miranda et al., 2018 sister to a monophyletic group comprising Charinus Simon, 1892 and Sarax Simon, 1892, neither of which are reciprocally monophyletic. Charinidae diverged from other amblypygid families in the Late Carboniferous, c. 318 Mya, on the supercontinent Pangaea. Weygoldtia diverged from the common ancestor of Charinus and Sarax during the Late Permian, c. 257 Mya, when changes in climate reduced tropical forests. The divergence of Charinus and Sarax coincides with the fragmentation of Pangaea, c. 216 Mya. Sarax colonized South-East Asia via Australia. The charinid fauna of New Caledonia originated before the Oligocene, when the island separated from Australia, c. 80 Mya.
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Affiliation(s)
- Gustavo Silva De Miranda
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark (Zoological Museum), University of Copenhagen, Denmark
- Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington,DC 20560, USA
| | - Alessandro P L Giupponi
- Laboratório de Referência Nacional em Vetores das Riquetsioses, LIRN-FIOCRUZ, Rio de Janeiro,RJ, Brazil
| | - Nikolaj Scharff
- Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington,DC 20560, USA
- Zoology Section, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Lorenzo Prendini
- Division of Invertebrate Zoology, American Museum of Natural History, New York,NY 10024-5192, USA
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Pillon Y, Hopkins HCF, Maurin O, Epitawalage N, Bradford J, Rogers ZS, Baker WJ, Forest F. Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments. AMERICAN JOURNAL OF BOTANY 2021; 108:1181-1200. [PMID: 34278558 PMCID: PMC8361763 DOI: 10.1002/ajb2.1688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
PREMISE Cunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long-range disjunctions. METHODS We performed a phylogenomic study using the universal Angiosperms353 probe set for targeted sequence capture. We sampled 37 species covering all genera in the Cunoniaceae, and those in the three closely related families of the crown Oxalidales (Brunelliaceae, Cephalotaceae, and Elaeocarpaceae). We also performed analyses for molecular dating and ancestral area reconstruction. RESULTS We recovered the topology (Cunoniaceae, (Cephalotaceae, (Brunelliaceae, Elaeocarpaceae))) and a well-resolved genus-level phylogeny of Cunoniaceae with strongly supported clades corresponding to all previously recognized tribes. As previously suspected, the genera Ackama and Weinmannia were recovered as paraphyletic. Australasia was inferred as the likely ancestral area for the family. CONCLUSIONS The current distribution of Cunoniaceae is best explained by long-distance dispersal with a few possible cases of Australasian-American vicariance events. Extinctions may have been important in determining the mostly Oceanian distribution of this family while some genera in the tribe Cunonieae and in New Caledonia have undergone recent bursts of diversification. New generic diagnoses, 80 new combinations, and one new name are provided for a recircumscribed Ackama (including Spiraeopsis), a much smaller Weinmannia (mostly New World), and a resurrected Pterophylla to accommodate Old World taxa previously in Weinmannia.
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Affiliation(s)
- Yohan Pillon
- LSTMIRDINRAE, CIRADInstitut AgroUniv. MontpellierMontpellierFrance
| | | | | | | | | | - Zachary S. Rogers
- New Mexico State UniversityBox 30003MSC 3‐ILas CrucesNM88003‐8003USA
| | | | - Félix Forest
- Royal Botanic GardensKew, RichmondSurreyTW9 3AEUK
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Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea). FORESTS 2021. [DOI: 10.3390/f12070861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Abstract
Evolutionary biologists have long been fascinated with the episodes of rapid phenotypic innovation that underlie the emergence of major lineages. Although our understanding of the environmental and ecological contexts of such episodes has steadily increased, it has remained unclear how population processes contribute to emergent macroevolutionary patterns. One insight gleaned from phylogenomics is that gene-tree conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. With the understanding that phylogenomic conflict is often driven by complex population processes, we hypothesized that there may be a direct correspondence between instances of high conflict and elevated rates of phenotypic innovation if both patterns result from the same processes. We evaluated this hypothesis in six clades spanning vertebrates and plants. We found that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales. Closer examination of the biological significance of phylogenomic conflict may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.
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Li M, Hensel G, Melzer M, Junker A, Tschiersch H, Ruwe H, Arend D, Kumlehn J, Börner T, Stein N. Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley. FRONTIERS IN PLANT SCIENCE 2021; 12:732608. [PMID: 34659298 PMCID: PMC8517540 DOI: 10.3389/fpls.2021.732608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/10/2021] [Indexed: 05/12/2023]
Abstract
Gene pairs resulting from whole genome duplication (WGD), so-called ohnologous genes, are retained if at least one member of the pair undergoes neo- or sub-functionalization. Phylogenetic analyses of the ohnologous genes ALBOSTRIANS (HvAST/HvCMF7) and ALBOSTRIANS-LIKE (HvASL/HvCMF3) of barley (Hordeum vulgare) revealed them as members of a subfamily of genes coding for CCT motif (CONSTANS, CONSTANS-LIKE and TIMING OF CAB1) proteins characterized by a single CCT domain and a putative N-terminal chloroplast transit peptide. Recently, we showed that HvCMF7 is needed for chloroplast ribosome biogenesis. Here we demonstrate that mutations in HvCMF3 lead to seedlings delayed in development. They exhibit a yellowish/light green - xantha - phenotype and successively develop pale green leaves. Compared to wild type, plastids of mutant seedlings show a decreased PSII efficiency, impaired processing and reduced amounts of ribosomal RNAs; they contain less thylakoids and grana with a higher number of more loosely stacked thylakoid membranes. Site-directed mutagenesis of HvCMF3 identified a previously unknown functional domain, which is highly conserved within this subfamily of CCT domain containing proteins. HvCMF3:GFP fusion constructs were localized to plastids and nucleus. Hvcmf3Hvcmf7 double mutants exhibited a xantha-albino or albino phenotype depending on the strength of molecular lesion of the HvCMF7 allele. The chloroplast ribosome deficiency is discussed as the primary observed defect of the Hvcmf3 mutants. Based on our observations, the genes HvCMF3 and HvCMF7 have similar but not identical functions in chloroplast development of barley supporting our hypothesis of neo-/sub-functionalization between both ohnologous genes.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Michael Melzer
- Structural Cell Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Astrid Junker
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Henning Tschiersch
- Heterosis Research Group, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
| | - Daniel Arend
- Research Group Bioinformatics and Information Technology, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
- *Correspondence: Thomas Börner,
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
- Nils Stein,
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Abstract
Developing a detailed understanding of how all known forms of life are related to one another in the tree of life has been a major preoccupation of biology since the idea of tree-like evolution first took hold. Since most life is microbial, our intuitive use of morphological comparisons to infer relatedness only goes so far, and molecular sequence data, most recently from genomes and transcriptomes, has been the primary means to infer these relationships. For prokaryotes this presented new challenges, since the degree of horizontal gene transfer led some to question the tree-like depiction of evolution altogether. Most eukaryotes are also microbial, but in contrast to prokaryotic life, the application of large-scale molecular data to the tree of eukaryotes has largely been a constructive process, leading to a small number of very diverse lineages, or 'supergroups'. The tree is not completely resolved, and contentious problems remain, but many well-established supergroups now encompass much more diversity than the traditional kingdoms. Some of the most exciting recent developments come from the discovery of branches in the tree that we previously had no inkling even existed, many of which are of great ecological or evolutionary interest. These new branches highlight the need for more exploration, by high-throughput molecular surveys, but also more traditional means of observations and cultivation.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Barcaccia G, Palumbo F, Sgorbati S, Albertini E, Pupilli F. A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms. Genes (Basel) 2020; 11:E859. [PMID: 32731368 PMCID: PMC7466056 DOI: 10.3390/genes11080859] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022] Open
Abstract
Apomixis sensu stricto (agamospermy) is asexual reproduction by seed. In angiosperms it represents an easy byway of life cycle renewal through gamete-like cells that give rise to maternal embryos without ploidy reduction (meiosis) and ploidy restitution (syngamy). The origin of apomixis still represents an unsolved problem, as it may be either evolved from sex or the other way around. This review deals with a reappraisal of the origin of apomixis in order to deepen knowledge on such asexual mode of reproduction which seems mainly lacking in the most basal angiosperm orders (i.e., Amborellales, Nymphaeales and Austrobaileyales, also known as ANA-grade), while it clearly occurs in different forms and variants in many unrelated families of monocots and eudicots. Overall findings strengthen the hypothesis that apomixis as a whole may have evolved multiple times in angiosperm evolution following different developmental pathways deviating to different extents from sexuality. Recent developments on the genetic control of apomixis in model species are also presented and adequately discussed in order to shed additional light on the antagonist theories of gain- and loss-of-function over sexuality.
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Affiliation(s)
- Gianni Barcaccia
- Department of Agronomy Food Natural Resources Animals Environment, University of Padova, Campus of Agripolis, Viale dell’Università 16, Legnaro, 35020 Padova, Italy;
| | - Fabio Palumbo
- Department of Agronomy Food Natural Resources Animals Environment, University of Padova, Campus of Agripolis, Viale dell’Università 16, Legnaro, 35020 Padova, Italy;
| | - Sergio Sgorbati
- Department of Environmental and Territory Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy;
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy;
| | - Fulvio Pupilli
- Research Division of Perugia, Institute of Biosciences and Bioresources, National Research Council (CNR), Via Madonna Alta 130, 06128 Perugia, Italy;
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Jermiin LS, Catullo RA, Holland BR. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics. NAR Genom Bioinform 2020; 2:lqaa041. [PMID: 33575594 PMCID: PMC7671319 DOI: 10.1093/nargab/lqaa041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
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Affiliation(s)
- Lars S Jermiin
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Biology & Environment Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Renee A Catullo
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Science and Health & Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
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14
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Exploring the Phytochemical Landscape of the Early-Diverging Flowering Plant Amborella trichopoda Baill. Molecules 2019; 24:molecules24213814. [PMID: 31652707 PMCID: PMC6864642 DOI: 10.3390/molecules24213814] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
Although the evolutionary significance of the early-diverging flowering plant Amborella (Amborella trichopoda Baill.) is widely recognized, its metabolic landscape, particularly specialized metabolites, is currently underexplored. In this work, we analyzed the metabolomes of Amborella tissues using liquid chromatography high-resolution electrospray ionization mass spectrometry (LC-HR-ESI-MS). By matching the mass spectra of Amborella metabolites with those of authentic phytochemical standards in the publicly accessible libraries, 63, 39, and 21 compounds were tentatively identified in leaves, stems, and roots, respectively. Free amino acids, organic acids, simple sugars, cofactors, as well as abundant glycosylated and/or methylated phenolic specialized metabolites were observed in Amborella leaves. Diverse metabolites were also detected in stems and roots, including those that were not identified in leaves. To understand the biosynthesis of specialized metabolites with glycosyl and methyl modifications, families of small molecule UDP-dependent glycosyltransferases (UGTs) and O-methyltransferases (OMTs) were identified in the Amborella genome and the InterPro database based on conserved functional domains. Of the 17 phylogenetic groups of plant UGTs (A–Q) defined to date, Amborella UGTs are absent from groups B, N, and P, but they are highly abundant in group L. Among the 25 Amborella OMTs, 7 cluster with caffeoyl-coenzyme A (CCoA) OMTs involved in lignin and phenolic metabolism, whereas 18 form a clade with plant OMTs that methylate hydroxycinnamic acids, flavonoids, or alkaloids. Overall, this first report of metabolomes and candidate metabolic genes in Amborella provides a starting point to a better understanding of specialized metabolites and biosynthetic enzymes in this basal lineage of flowering plants.
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15
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Widhelm TJ, Grewe F, Huang JP, Mercado-Díaz JA, Goffinet B, Lücking R, Moncada B, Mason-Gamer R, Lumbsch HT. Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota). Sci Rep 2019; 9:8968. [PMID: 31222061 PMCID: PMC6586878 DOI: 10.1038/s41598-019-45455-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 06/03/2019] [Indexed: 12/19/2022] Open
Abstract
In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
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Affiliation(s)
- Todd J Widhelm
- Field Museum, Science and Education, Chicago, 60605, USA.
- University of Illinois at Chicago, Biological Sciences, Chicago, 60607, USA.
| | - Felix Grewe
- Field Museum, Grainger Bioinformatics Center, Chicago, 60605, USA
| | - Jen-Pan Huang
- Field Museum, Science and Education, Chicago, 60605, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Bernard Goffinet
- University of Connecticut, Ecology and Evolutionary Biology, Storrs, 06268, USA
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Herbarium, Berlin, 14195, Germany
| | - Bibiana Moncada
- Universidad Distrital Francisco José de Caldas, Torre de Laboratorios, Herbario, Bogotá, 11021, Colombia
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16
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Li HT, Yi TS, Gao LM, Ma PF, Zhang T, Yang JB, Gitzendanner MA, Fritsch PW, Cai J, Luo Y, Wang H, van der Bank M, Zhang SD, Wang QF, Wang J, Zhang ZR, Fu CN, Yang J, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Li DZ. Origin of angiosperms and the puzzle of the Jurassic gap. NATURE PLANTS 2019; 5:461-470. [PMID: 31061536 DOI: 10.1038/s41477-019-0421-0] [Citation(s) in RCA: 348] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 04/02/2019] [Indexed: 05/19/2023]
Abstract
Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated crown age is substantially earlier than that of unequivocal angiosperm fossils, and the difference is here termed the 'Jurassic angiosperm gap'. Our time-calibrated plastid phylogenomic tree provides a highly relevant framework for future comparative studies of flowering plant evolution.
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Affiliation(s)
- Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Michelle van der Bank
- Department of Botany & Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Qing-Feng Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Jian Wang
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Jing Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | - Mark W Chase
- Royal Botanic Gardens, Kew, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
- Biodiversity Institute, University of Florida, Gainesville, FL, USA.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
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17
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Plastid phylogenomic insights into the evolution of Caryophyllales. Mol Phylogenet Evol 2019; 134:74-86. [DOI: 10.1016/j.ympev.2018.12.023] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 11/22/2022]
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18
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Susko E, Lincker L, Roger AJ. Accelerated Estimation of Frequency Classes in Site-Heterogeneous Profile Mixture Models. Mol Biol Evol 2019; 35:1266-1283. [PMID: 29688541 DOI: 10.1093/molbev/msy026] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
As a consequence of structural and functional constraints, proteins tend to have site-specific preferences for particular amino acids. Failing to adjust for heterogeneity of frequencies over sites can lead to artifacts in phylogenetic estimation. Site-heterogeneous mixture-models have been developed to address this problem. However, due to prohibitive computational times, maximum likelihood implementations utilize fixed component frequency vectors inferred from sequences in a database that are external to the alignment under analysis. Here, we propose a composite likelihood approach to estimation of component frequencies for a mixture model that directly uses the data from the alignment of interest. In the common case that the number of taxa under study is not large, several adjustments to the default composite likelihood are shown to be necessary. In simulations, the approach is shown to provide large improvements over hierarchical clustering. For empirical data, substantial improvements in likelihoods are found over mixtures using fixed components.
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Affiliation(s)
- Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada
| | - Léa Lincker
- École Nationale Supérieure de Techniques Avancées, Palaiseau, France.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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19
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Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol 2019; 131:80-92. [DOI: 10.1016/j.ympev.2018.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
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20
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Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. AMERICAN JOURNAL OF BOTANY 2018; 105:1888-1910. [PMID: 30368769 DOI: 10.1002/ajb2.1178] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | | | - Daniel Spalink
- Department of Ecosystem Science, Texas A&M University, College Station, Texas, 77840, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Chodon Sass
- The University and Jepson Herbarium, University of California-Berkeley, Berkeley, California, 94720, USA
| | - William J D Iles
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Danilo José Lima de Sousa
- Departamento de Ciéncias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, 44036-900, Brazil
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Wendy B Zomlefer
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Maria A Gandolfo
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | | | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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21
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Herrando-Moraira S. Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae). Mol Phylogenet Evol 2018; 128:69-87. [PMID: 30036700 DOI: 10.1016/j.ympev.2018.07.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/17/2022]
Abstract
Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: Arctium, Cousinia, Saussurea, and Jurinea. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, Arctium-Cousinia and Saussurea-Jurinea, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of Arctium, Cousinia, and Saussurea are also well defined. Conversely, conflicting species relationships remain for Jurinea. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that: (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.
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Affiliation(s)
- Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s.n., 08038 Barcelona, Spain.
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22
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Hodel RG, Chandler LM, Fahrenkrog AM, Kirst M, Gitzendanner MA, Soltis DE, Soltis PS. Linking genome signatures of selection and adaptation in non-model plants: exploring potential and limitations in the angiosperm Amborella. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:81-89. [PMID: 29694936 DOI: 10.1016/j.pbi.2018.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/24/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
Selective sweeps may be caused by environmental conditions that select for a gene function or trait at one locus, causing reduced variation at neighboring sites due to linkage, with specific non-selected variants being swept along with the selected variant. For many species, genomic and environmental data are available to test hypotheses that environmental conditions are correlated with selected regions. Most genomic studies relating selection to environment use model organisms or crop species; typically, these studies have genomic data from large numbers of individuals and extensive environmental data. Here, we review studies associating selective sweeps with environment and consider the impediments to successful application of these methods to non-model species. We present an initial investigation into linking genomic regions of selection to environmental conditions in the narrowly distributed, non-model plant Amborella trichopoda (Amborellaceae), the sister species to all other living flowering plants and one of over 2500 plant species endemic to New Caledonia.
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Affiliation(s)
- Richard Gj Hodel
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Luke M Chandler
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Annette M Fahrenkrog
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA; The Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA; The Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA.
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23
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Wang HC, Minh BQ, Susko E, Roger AJ. Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation. Syst Biol 2018; 67:216-235. [PMID: 28950365 DOI: 10.1093/sysbio/syx068] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 08/02/2017] [Indexed: 11/14/2022] Open
Abstract
Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with $k$ classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately $k$/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.
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Affiliation(s)
- Huai-Chun Wang
- Department of Mathematics and Statistics, 6316 Coburg Road.,Department of Biochemistry and Molecular Biology, 5850 College Street, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna and Medical University of Vienna, Austria
| | - Edward Susko
- Department of Mathematics and Statistics, 6316 Coburg Road.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, 5850 College Street, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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24
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Nuclear, chloroplast, and mitochondrial data of a US cannabis DNA database. Int J Legal Med 2018; 132:713-725. [PMID: 29464313 DOI: 10.1007/s00414-018-1798-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
Abstract
As Cannabis sativa (marijuana) is a controlled substance in many parts of the world, the ability to track biogeographical origin of cannabis could provide law enforcement with investigative leads regarding its trade and distribution. Population substructure and inbreeding may cause cannabis plants to become more genetically related. This genetic relatedness can be helpful for intelligence purposes. Analysis of autosomal, chloroplast, and mitochondrial DNA allows for not only prediction of biogeographical origin of a plant but also discrimination between individual plants. A previously validated, 13-autosomal STR multiplex was used to genotype 510 samples. Samples were analyzed from four different sites: 21 seizures at the US-Mexico border, Northeastern Brazil, hemp seeds purchased in the US, and the Araucania area of Chile. In addition, a previously reported multi-loci system was modified and optimized to genotype five chloroplast and two mitochondrial markers. For this purpose, two methods were designed: a homopolymeric STR pentaplex and a SNP triplex with one chloroplast (Cscp001) marker shared by both methods for quality control. For successful mitochondrial and chloroplast typing, a novel real-time PCR quantitation method was developed and validated to accurately estimate the quantity of the chloroplast DNA (cpDNA) using a synthetic DNA standard. Moreover, a sequenced allelic ladder was also designed for accurate genotyping of the homopolymeric STR pentaplex. For autosomal typing, 356 unique profiles were generated from the 425 samples that yielded full STR profiles and 25 identical genotypes within seizures were observed. Phylogenetic analysis and case-to-case pairwise comparisons of 21 seizures at the US-Mexico border, using the Fixation Index (F ST ) as genetic distance, revealed the genetic association of nine seizures that formed a reference population. For mitochondrial and chloroplast typing, subsampling was performed, and 134 samples were genotyped. Complete haplotypes (STRs and SNPs) were observed for 127 samples. As expected, extensive haplotype sharing was observed; five distinguishable haplotypes were detected. In the reference population, the same haplotype was observed 39 times and two unique haplotypes were also detected. Haplotype sharing was observed between the US border seizures, Brazil, and Chile, while the hemp samples generated a distinct haplotype. Phylogenetic analysis of the four populations was performed, and results revealed that both autosomal and lineage markers could discern population substructure.
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Foster CSP, Sauquet H, van der Merwe M, McPherson H, Rossetto M, Ho SYW. Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale. Syst Biol 2018; 66:338-351. [PMID: 27650175 DOI: 10.1093/sysbio/syw086] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/10/2016] [Indexed: 11/14/2022] Open
Abstract
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].
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Affiliation(s)
- Charles S P Foster
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hervê Sauquet
- Laboratoire écologie, Systématique, évolution, Université Paris-Sud, CNRS UMR 8079, bat. 360, Orsay 91405, France
| | - Marlien van der Merwe
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Hannah McPherson
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia
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26
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Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods. Mol Phylogenet Evol 2018; 118:330-342. [DOI: 10.1016/j.ympev.2017.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 12/19/2022]
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Zhong B, Betancur-R R. Expanded Taxonomic Sampling Coupled with Gene Genealogy Interrogation Provides Unambiguous Resolution for the Evolutionary Root of Angiosperms. Genome Biol Evol 2017. [PMCID: PMC5710718 DOI: 10.1093/gbe/evx233] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The branching order of major angiosperm lineages is a challenging phylogenetic question that has received substantial attention in recent years. Two main competing hypotheses place the New Caledonian Amborella as either sister to all other extant angiosperms (Amborella-sister) or to the water lilies (Amborella + Nymphaeales). Here, we revisit this question by expanding a transcriptomic data set of 310 genes previously assembled to include data from seven species comprising two major lineages of flowering plants that were poorly represented or missing from the original study. We also applied gene genealogy interrogation, a recent approach based on constrained tree searches in combination with topology tests, to account for gene tree estimation error and its downstream effects in coalescent analyses. In addition to gene genealogy interrogation, we conducted a large number of multilocus analyses, including concatenation and coalescent approaches (using both unconstrained and constrained gene trees), and based on different data sets (original and expanded) and data types (nucleotide and amino acid sequences). We show that the majority of gene trees favor Amborella-sister topology, and all multilocus analyses conducted (concatenation and coalescent) provide overwhelming support for this hypothesis regardless of data type. Beyond resolving the evolutionary root of angiosperms with confidence, our results highlight the importance of both broadening taxonomic sampling in phylogenomics and addressing the effects of gene tree error in summary coalescent inferences.
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Affiliation(s)
- Bojian Zhong
- College of Life Sciences, Nanjing Normal University, China
- Corresponding authors: E-mails: ;
| | - Ricardo Betancur-R
- Department of Biology, University of Puerto Rico – Río Piedras, San Juan, Puerto Rico
- Corresponding authors: E-mails: ;
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van Iersel L, Kelk S, Stamoulis G, Stougie L, Boes O. On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems. ALGORITHMICA 2017; 80:2993-3022. [PMID: 30956378 PMCID: PMC6428403 DOI: 10.1007/s00453-017-0366-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 08/11/2017] [Indexed: 05/04/2023]
Abstract
The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an unrooted phylogenetic network displays (i.e. embeds) an unrooted phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the tree bisection and reconnect distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.
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Affiliation(s)
- Leo van Iersel
- Delft Institute of Applied Mathematics, Delft University of Technology, Delft, The Netherlands
| | - Steven Kelk
- Department of Data Science and Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
| | - Georgios Stamoulis
- Department of Data Science and Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
| | - Leen Stougie
- CWI, INRIA-Erable and Department of Econometrics and Operations Research, Vrije Universiteit, Amsterdam, The Netherlands
| | - Olivier Boes
- Department of Data Science and Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
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29
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Yu XQ, Drew BT, Yang JB, Gao LM, Li DZ. Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny. PLoS One 2017; 12:e0178026. [PMID: 28575004 PMCID: PMC5456055 DOI: 10.1371/journal.pone.0178026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/11/2017] [Indexed: 11/19/2022] Open
Abstract
Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima.
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Affiliation(s)
- Xiang-Qin Yu
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Bryan T. Drew
- Department of Biology, University of Nebraska, Kearney, NE, United States of America
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Chen F, Liu X, Yu C, Chen Y, Tang H, Zhang L. Water lilies as emerging models for Darwin's abominable mystery. HORTICULTURE RESEARCH 2017; 4:17051. [PMID: 28979789 PMCID: PMC5626932 DOI: 10.1038/hortres.2017.51] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/30/2017] [Accepted: 07/26/2017] [Indexed: 05/02/2023]
Abstract
Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering plants. The birth and rapid radiation of flowering plants has interested many scientists and was considered 'an abominable mystery' by Charles Darwin. In searching for the angiosperm evolutionary origin and its underlying mechanisms, the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages; however, little is known regarding the genetics and genomics of another basal angiosperm lineage, namely, the water lily. In this study, we reviewed current molecular research and note that water lily research has entered the genomic era. We propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin's 'abominable mystery'. Four pantropical water lilies, especially the recently sequenced Nymphaea colorata, have characteristics such as small size, rapid growth rate and numerous seeds and can act as the best model for understanding the origin of angiosperms. The water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies.
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Affiliation(s)
- Fei Chen
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Liu
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuiwei Yu
- Zhejiang Humanities Landscape Co., LTD, Hangzhou 310030, China
| | - Yuchu Chen
- Zhejiang Humanities Landscape Co., LTD, Hangzhou 310030, China
| | - Haibao Tang
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
- )
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31
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Simmons MP. Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella
is supported as sister and Observed Variability is biased. Cladistics 2016; 33:488-512. [DOI: 10.1111/cla.12177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2016] [Indexed: 01/16/2023] Open
Affiliation(s)
- Mark P. Simmons
- Department of Biology; Colorado State University; Fort Collins CO 80523-1878 USA
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32
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Simmons MP, Gatesy J. Biases of tree-independent-character-subsampling methods. Mol Phylogenet Evol 2016; 100:424-443. [DOI: 10.1016/j.ympev.2016.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022]
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Givnish TJ, Zuluaga A, Marques I, Lam VKY, Gomez MS, Iles WJD, Ames M, Spalink D, Moeller JR, Briggs BG, Lyon SP, Stevenson DW, Zomlefer W, Graham SW. Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica. Cladistics 2016; 32:581-605. [DOI: 10.1111/cla.12153] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- Thomas J. Givnish
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Alejandro Zuluaga
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
- Departamento de Biología; Universidad del Valle; Cali Colombia
| | - Isabel Marques
- Department of Botany; University of British Columbia; Vancouver Canada V6T 1Z4
- Department of Agriculture (Botany); High Polytechnic School of Huesca; University of Zaragoza; Carretera de Cuarte Km 1 Huesca E22071 Spain
| | - Vivienne K. Y. Lam
- Department of Botany; University of British Columbia; Vancouver Canada V6T 1Z4
| | - Marybel Soto Gomez
- Department of Botany; University of British Columbia; Vancouver Canada V6T 1Z4
| | - William J. D. Iles
- University and Jepson Herbaria; University of California-Berkeley; Berkeley CA 94720 USA
| | - Mercedes Ames
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Daniel Spalink
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Jackson R. Moeller
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | | | - Stephanie P. Lyon
- Department of Botany; University of Wisconsin-Madison; Madison WI 53706 USA
| | | | - Wendy Zomlefer
- Department of Plant Biology; University of Georgia; Athens GA 30602 USA
| | - Sean W. Graham
- Department of Botany; University of British Columbia; Vancouver Canada V6T 1Z4
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34
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Kusch S, Pesch L, Panstruga R. Comprehensive Phylogenetic Analysis Sheds Light on the Diversity and Origin of the MLO Family of Integral Membrane Proteins. Genome Biol Evol 2016; 8:878-95. [PMID: 26893454 PMCID: PMC4824068 DOI: 10.1093/gbe/evw036] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2016] [Indexed: 12/11/2022] Open
Abstract
Mildew resistanceLocusO(MLO) proteins are polytopic integral membrane proteins that have long been considered as plant-specific and being primarily involved in plant-powdery mildew interactions. However, research in the past decade has revealed that MLO proteins diverged into a family with several clades whose members are associated with different physiological processes. We provide a largely increased dataset of MLO amino acid sequences, comprising nearly all major land plant lineages. Based on this comprehensive dataset, we defined seven phylogenetic clades and reconstructed the likely evolution of the MLO family in embryophytes. We further identified several MLO peptide motifs that are either conserved in all MLO proteins or confined to one or several clades, supporting the notion that clade-specific diversification of MLO functions is associated with particular sequence motifs. In baker's yeast, some of these motifs are functionally linked to transmembrane (TM) transport of organic molecules and ions. In addition, we attempted to define the evolutionary origin of the MLO family and found that MLO-like proteins with highly diverse membrane topologies are present in green algae, but also in the distinctly related red algae (Rhodophyta), Amoebozoa, and Chromalveolata. Finally, we discovered several instances of putative fusion events between MLO proteins and different kinds of proteins. Such Rosetta stone-type hybrid proteins might be instructive for future analysis of potential MLO functions. Our findings suggest that MLO is an ancient protein that possibly evolved in unicellular photosynthetic eukaryotes, and consolidated in land plants with a conserved topology, comprising seven TM domains and an intrinsically unstructured C-terminus.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
| | - Lina Pesch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
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35
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Simmons MP, Sloan DB, Gatesy J. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Mol Phylogenet Evol 2016; 97:76-89. [PMID: 26768112 DOI: 10.1016/j.ympev.2015.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/03/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
Abstract
Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic inference. We sampled eight empirical studies of ancient lineages with diverse numbers of taxa and genes for which the original authors applied one or more coalescent methods. We found that the average pairwise congruence among gene trees varied greatly both between studies and also often within a study. We recommend that presenting plots of pairwise congruence among gene trees in a dataset be treated as a standard practice for empirical coalescent studies so that readers can readily assess the extent and distribution of incongruence among gene trees. ASTRAL-based coalescent analyses generally outperformed MP-EST and STAR with respect to both internal consistency (congruence between analyses of subsamples of genes with the complete dataset of all genes) and congruence with the concatenation-based topology. We evaluated the approach of subsampling gene trees that are, on average, more congruent with other gene trees as a method to reduce artifacts caused by gene-tree-estimation errors on coalescent analyses. We suggest that this method is well suited to testing whether gene-tree-estimation error is a primary cause of incongruence between concatenation- and coalescent-based results, to reconciling conflicting phylogenetic results based on different coalescent methods, and to identifying genes affected by artifacts that may then be targeted for reciprocal illumination. We provide scripts that automate the process of calculating pairwise gene-tree incongruence and subsampling trees while accounting for differential taxon sampling among genes. Finally, we assert that multiple tree-search replicates should be implemented as a standard practice for empirical coalescent studies that apply MP-EST.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
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36
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Taylor ZN, Rice DW, Palmer JD. The Complete Moss Mitochondrial Genome in the Angiosperm Amborella Is a Chimera Derived from Two Moss Whole-Genome Transfers. PLoS One 2015; 10:e0137532. [PMID: 26618775 PMCID: PMC4664403 DOI: 10.1371/journal.pone.0137532] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 08/19/2015] [Indexed: 11/18/2022] Open
Abstract
Sequencing of the 4-Mb mitochondrial genome of the angiosperm Amborella trichopoda has shown that it contains unprecedented amounts of foreign mitochondrial DNA, including four blocks of sequences that together correspond almost perfectly to one entire moss mitochondrial genome. This implies whole-genome transfer from a single moss donor but conflicts with phylogenetic results from an earlier, PCR-based study that suggested three different moss donors to Amborella. To resolve this conflict, we conducted an expanded set of phylogenetic analyses with respect to both moss lineages and mitochondrial loci. The moss DNA in Amborella was consistently placed in either of two positions, depending on the locus analyzed, as sister to the Ptychomniales or within the Hookeriales. This agrees with two of the three previously suggested donors, whereas the third is no longer supported. These results, combined with synteny analyses and other considerations, lead us to favor a model involving two successive moss-to-Amborella whole-genome transfers, followed by recombination that produced a single intact and chimeric moss mitochondrial genome integrated in the Amborella mitochondrial genome. Eight subsequent recombination events account for the state of fragmentation, rearrangement, duplication, and deletion of this chimeric moss mitochondrial genome as it currently exists in Amborella. Five of these events are associated with short-to-intermediate sized repeats. Two of the five probably occurred by reciprocal homologous recombination, whereas the other three probably occurred in a non-reciprocal manner via microhomology-mediated break-induced replication (MMBIR). These findings reinforce and extend recent evidence for an important role of MMBIR in plant mitochondrial DNA evolution.
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Affiliation(s)
- Z. Nathan Taylor
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Danny W. Rice
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Jeffrey D. Palmer
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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37
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Mirarab S, Warnow T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 2015; 31:i44-52. [PMID: 26072508 PMCID: PMC4765870 DOI: 10.1093/bioinformatics/btv234] [Citation(s) in RCA: 578] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Motivation: The estimation of species phylogenies requires multiple loci, since different loci can have different trees due to incomplete lineage sorting, modeled by the multi-species coalescent model. We recently developed a coalescent-based method, ASTRAL, which is statistically consistent under the multi-species coalescent model and which is more accurate than other coalescent-based methods on the datasets we examined. ASTRAL runs in polynomial time, by constraining the search space using a set of allowed ‘bipartitions’. Despite the limitation to allowed bipartitions, ASTRAL is statistically consistent. Results: We present a new version of ASTRAL, which we call ASTRAL-II. We show that ASTRAL-II has substantial advantages over ASTRAL: it is faster, can analyze much larger datasets (up to 1000 species and 1000 genes) and has substantially better accuracy under some conditions. ASTRAL’s running time is O(n2k|X|2), and ASTRAL-II’s running time is O(nk|X|2), where n is the number of species, k is the number of loci and X is the set of allowed bipartitions for the search space. Availability and implementation: ASTRAL-II is available in open source at https://github.com/smirarab/ASTRAL and datasets used are available at http://www.cs.utexas.edu/~phylo/datasets/astral2/. Contact:smirarab@gmail.com Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Siavash Mirarab
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA and Departments of Computer Science and Bioengineering, The University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Tandy Warnow
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA and Departments of Computer Science and Bioengineering, The University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
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38
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Taylor ML, Cooper RL, Schneider EL, Osborn JM. Pollen structure and development in Nymphaeales: insights into character evolution in an ancient angiosperm lineage. AMERICAN JOURNAL OF BOTANY 2015; 102:1685-1702. [PMID: 26419810 DOI: 10.3732/ajb.1500249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY A knowledge of pollen characters in early-diverging angiosperm lineages is essential for understanding pollen evolution and the role of pollen in angiosperm diversification. In this paper, we report and synthesize data on mature pollen and pollen ontogeny from all genera of Nymphaeales within a comparative, phylogenetic context and consider pollen evolution in this early-diverging angiosperm lineage. We describe mature pollen characters for Euryale, Barclaya, and Nymphaea ondinea, taxa for which little to no structural data exist. METHODS We studied mature pollen for all nymphaealean genera using light, scanning electron, and transmission electron microscopy. We reviewed published reports of nymphaealean pollen to provide a comprehensive discussion of pollen characters in water lilies. KEY RESULTS Nymphaeales exhibit diversity in key pollen characters, including dispersal unit size, ornamentation, aperture morphology, and tapetum type. All Nymphaeales pollen are tectate-columellate, exhibiting one of two distinct patterns of infratectal ultrastructure-a thick infratectal space with robust columellae or a thin infratectal space with thin columellae. All genera have pollen with a lamellate endexine that becomes compressed in the proximal, but not distal wall. This endexine ultrastructure supports the operculate hypothesis for aperture origin. Nymphaeaceae pollen exhibit a membranous granular layer, which is a synapomorphy of the family. CONCLUSIONS Variation in pollen characters indicates that significant potential for lability in pollen development was present in Nymphaeales at the time of its divergence from the rest of angiosperms. Structural and ontogenetic data are essential for interpreting pollen characters, such as infratectum and endexine ultrastructure in Nymphaeales.
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Affiliation(s)
- Mackenzie L Taylor
- Department of Biology, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178-0324 USA
| | - Ranessa L Cooper
- Biology Department, Hillsdale College, 33 East College Street, Hillsdale, Michigan 49242 USA
| | - Edward L Schneider
- The University of Minnesota Landscape Arboretum, 3675 Arboretum Drive, Chaska, Minnesota 55318 USA
| | - Jeffrey M Osborn
- School of Science, The College of New Jersey, P.O. Box 7718, 2000 Pennington Road, Ewing, New Jersey 08628-0718 USA
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Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol Phylogenet Evol 2015; 91:98-122. [DOI: 10.1016/j.ympev.2015.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/01/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022]
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Goremykin VV, Nikiforova SV, Cavalieri D, Pindo M, Lockhart P. The Root of Flowering Plants and Total Evidence. Syst Biol 2015; 64:879-91. [DOI: 10.1093/sysbio/syv028] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
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Su Z, Townsend JP. Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects. BMC Evol Biol 2015; 15:86. [PMID: 25968460 PMCID: PMC4429678 DOI: 10.1186/s12862-015-0364-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/29/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The detection and avoidance of "long-branch effects" in phylogenetic inference represents a longstanding challenge for molecular phylogenetic investigations. A consequence of parallelism and convergence, long-branch effects arise in phylogenetic inference when there is unequal molecular divergence among lineages, and they can positively mislead inference based on parsimony especially, but also inference based on maximum likelihood and Bayesian approaches. Long-branch effects have been exhaustively examined by simulation studies that have compared the performance of different inference methods in specific model trees and branch length spaces. RESULTS In this paper, by generalizing the phylogenetic signal and noise analysis to quartets with uneven subtending branches, we quantify the utility of molecular characters for resolution of quartet phylogenies via parsimony. Our quantification incorporates contributions toward the correct tree from either signal or homoplasy (i.e. "the right result for either the right reason or the wrong reason"). We also characterize a highly conservative lower bound of utility that incorporates contributions to the correct tree only when they correspond to true, unobscured parsimony-informative sites (i.e. "the right result for the right reason"). We apply the generalized signal and noise analysis to classic quartet phylogenies in which long-branch effects can arise due to unequal rates of evolution or an asymmetrical topology. Application of the analysis leads to identification of branch length conditions in which inference will be inconsistent and reveals insights regarding how to improve sampling of molecular loci and taxa in order to correctly resolve phylogenies in which long-branch effects are hypothesized to exist. CONCLUSIONS The generalized signal and noise analysis provides analytical prediction of utility of characters evolving at diverse rates of evolution to resolve quartet phylogenies with unequal branch lengths. The analysis can be applied to identifying characters evolving at appropriate rates to resolve phylogenies in which long-branch effects are hypothesized to occur.
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Affiliation(s)
- Zhuo Su
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
| | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
- Department of Biostatistics, Yale University, New Haven, CT, 06520, USA.
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
- Department of Biostatistics, Yale School of Public Health, 135 College St #222., New Haven, CT, 06511, United States of America.
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Tang L, Zou XH, Zhang LB, Ge S. Multilocus species tree analyses resolve the ancient radiation of the subtribe Zizaniinae (Poaceae). Mol Phylogenet Evol 2015; 84:232-9. [DOI: 10.1016/j.ympev.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 01/06/2015] [Accepted: 01/24/2015] [Indexed: 10/24/2022]
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Wheeler GL, Dorman HE, Buchanan A, Challagundla L, Wallace LE. A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps.1400059. [PMID: 25506520 PMCID: PMC4259455 DOI: 10.3732/apps.1400059] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/06/2014] [Indexed: 05/02/2023]
Abstract
Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995-2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology.
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Affiliation(s)
- Gregory L. Wheeler
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Hanna E. Dorman
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Alenda Buchanan
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Lavanya Challagundla
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Lisa E. Wallace
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
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Wu Z, Gui S, Quan Z, Pan L, Wang S, Ke W, Liang D, Ding Y. A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots. BMC PLANT BIOLOGY 2014; 14:289. [PMID: 25407166 PMCID: PMC4245832 DOI: 10.1186/s12870-014-0289-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 10/15/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The chloroplast genome is important for plant development and plant evolution. Nelumbo nucifera is one member of relict plants surviving from the late Cretaceous. Recently, a new sequencing platform PacBio RS II, known as 'SMRT (Single Molecule, Real-Time) sequencing', has been developed. Using the SMRT sequencing to investigate the chloroplast genome of N. nucifera will help to elucidate the plastid evolution of basal eudicots. RESULTS The sizes of the de novo assembled complete chloroplast genome of N. nucifera were 163,307 bp, 163,747 bp and 163,600 bp with average depths of coverage of 7×, 712× and 105× sequenced by Sanger, Illumina MiSeq and PacBio RS II, respectively. The precise chloroplast genome of N. nucifera was obtained from PacBio RS II data proofread by Illumina MiSeq reads, with a quadripartite structure containing a large single copy region (91,846 bp) and a small single copy region (19,626 bp) separated by two inverted repeat regions (26,064 bp). The genome contains 113 different genes, including four distinct rRNAs, 30 distinct tRNAs and 79 distinct peptide-coding genes. A phylogenetic analysis of 133 taxa from 56 orders indicated that Nelumbo with an age of 177 million years is a sister clade to Platanus, which belongs to the basal eudicots. Basal eudicots began to emerge during the early Jurassic with estimated divergence times at 197 million years using MCMCTree. IR expansions/contractions within the basal eudicots seem to have occurred independently. CONCLUSIONS Because of long reads and lack of bias in coverage of AT-rich regions, PacBio RS II showed a great promise for highly accurate 'finished' genomes, especially for a de novo assembly of genomes. N. nucifera is one member of basal eudicots, however, evolutionary analyses of IR structural variations of N. nucifera and other basal eudicots suggested that IR expansions/contractions occurred independently in these basal eudicots or were caused by independent insertions and deletions. The precise chloroplast genome of N. nucifera will present new information for structural variation of chloroplast genomes and provide new insight into the evolution of basal eudicots at the primary sequence and structural level.
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Affiliation(s)
- Zhihua Wu
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| | - Songtao Gui
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| | | | - Lei Pan
- />College of Life Sciences, Jianghan University, Wuhan, 430056 China
| | - Shuzhen Wang
- />College of Life Sciences, Huanggang Normal University, Huanggang, 438000 Hubei China
| | - Weidong Ke
- />Wuhan Vegetable Scientific Research Institute, Wuhan National Field Observation & Research Station for Aquatic Vegetables, Wuhan, 430065 China
| | - Dequan Liang
- />Nextomics Biosciences Co., Ltd., Wuhan, 430075 China
| | - Yi Ding
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
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Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae. Mol Phylogenet Evol 2014; 80:169-85. [PMID: 25109653 DOI: 10.1016/j.ympev.2014.07.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 11/21/2022]
Abstract
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value.
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Xi Z, Liu L, Rest JS, Davis CC. Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies. Syst Biol 2014; 63:919-32. [DOI: 10.1093/sysbio/syu055] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; 2Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 3Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liang Liu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; 2Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 3Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Joshua S. Rest
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; 2Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 3Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; 2Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; 3Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
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Reconstructing the age and historical biogeography of the ancient flowering-plant family Hydatellaceae (Nymphaeales). BMC Evol Biol 2014; 14:102. [PMID: 24884487 PMCID: PMC4030046 DOI: 10.1186/1471-2148-14-102] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/01/2014] [Indexed: 12/26/2022] Open
Abstract
Background The aquatic flowering-plant family Hydatellaceae has a classic Gondwanan distribution, as it is found in Australia, India and New Zealand. To shed light on the biogeographic history of this apparently ancient branch of angiosperm phylogeny, we dated the family in the context of other seed-plant divergences, and evaluated its biogeography using parsimony and likelihood methods. We also explicitly tested the effect of different extinction rates on biogeographic inferences. Results We infer that the stem lineage of Hydatellaceae originated in the Lower Cretaceous; in contrast, its crown originated much more recently, in the early Miocene, with the bulk of its diversification after the onset of the Pliocene. Biogeographic reconstructions predict a mix of dispersal and vicariance events, but considerations of geological history preclude most vicariance events, besides a split at the root of the family between southern and northern clades. High extinction rates are plausible in the family, and when these are taken into account there is greater uncertainty in biogeographic inferences. Conclusions A stem origin for Hydatellaceae in the Lower Cretaceous is consistent with the initial appearance of fossils attributed to its sister clade, the water lilies. In contrast, the crown clade is young, indicating that vicariant explanations for species outside Australia are improbable. Although long-distance dispersal is likely the primary driver of biogeographic distribution in Hydatellaceae, we infer that the recent drying out of central Australia divided the family into tropical vs. subtropical/temperate clades around the beginning of the Miocene.
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