1
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Mechai S, Coatsworth H, Ogden NH. Possible effect of mutations on serological detection of Borrelia burgdorferi sensu stricto ospC major groups: An in-silico study. PLoS One 2023; 18:e0292741. [PMID: 37815990 PMCID: PMC10564231 DOI: 10.1371/journal.pone.0292741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
The outer surface protein C (OspC) of the agent of Lyme disease, Borrelia burgdorferi sensu stricto, is a major lipoprotein surface-expressed during early-phase human infections. Antibodies to OspC are used in serological diagnoses. This study explored the hypothesis that serological test sensitivity decreases as genetic similarity of ospC major groups (MGs) of infecting strains, and ospC A (the MG in the strain B31 used to prepare antigen for serodiagnosis assays) decreases. We used a previously published microarray dataset to compare serological reactivity to ospC A (measured as pixel intensity) versus reactivity to 22 other ospC MGs, within a population of 55 patients diagnosed by two-tier serological testing using B. burgdorferi s.s. strain B31 as antigen, in which the ospC MG is OspC A. The difference in reactivity of sera to ospC A and reactivity to each of the other 22 ospC MGs (termed 'reactivity difference') was the outcome variable in regression analysis in which genetic distance of the ospC MGs from ospC A was the explanatory variable. Genetic distance was computed for the whole ospC sequence, and 9 subsections, from Neighbour Joining phylogenetic trees of the 23 ospC MGs. Regression analysis was conducted using genetic distance for the full ospC sequence, and the subsections individually. There was a significant association between the reactivity difference and genetic distance of ospC MGs from ospC A: increased genetic distance reduced reactivity to OspC A. No single ospC subsection sequence fully explained the relationship between genetic distance and reactivity difference. An analysis of single nucleotide polymorphisms supported a biological explanation via specific amino acid modifications likely to change protein binding affinity. This adds support to the hypothesis that genetic diversity of B. burgdorferi s.s. (here specifically OspC) may impact serological diagnostic test performance. Further prospective studies are necessary to explore the clinical implications of these findings.
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Affiliation(s)
- Samir Mechai
- Public Health Risk Sciences, National Microbiology Laboratory Branch, Public Health Agency of Canada, St Hyacinthe, QC, Canada
- Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, St Hyacinthe, QC, Canada
| | - Heather Coatsworth
- One Health Division, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Nicholas H. Ogden
- Public Health Risk Sciences, National Microbiology Laboratory Branch, Public Health Agency of Canada, St Hyacinthe, QC, Canada
- Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, St Hyacinthe, QC, Canada
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2
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Grollmann MM, Jørgensen A, Møbjerg N. Actinarctus doryphorus (Tanarctidae) DNA barcodes and phylogenetic reinvestigation of Arthrotardigrada with new A. doryphorus and Echiniscoididae sequences. Zootaxa 2023; 5284:351-363. [PMID: 37518733 DOI: 10.11646/zootaxa.5284.2.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Indexed: 08/01/2023]
Abstract
Little is still known about the diversity and evolution of marine arthrotardigrades, as they are generally difficult to sample, resulting in a limited amount of molecular data for barcoding and phylogenetic studies. With the current study, we provide the first investigation into COI haplotype diversity in a marine tanarctid and at the same time readdress arthrotardigrade phylogeny. Specifically, we provide COI mtDNA, 18S and 28S rDNA sequences from a population of Actinarctus doryphorus (Tanarctidae) sampled off the coast of Roscoff, France and further provide new 18S sequences from two marine echiniscoidids. A. doryphorus COI sequences confirmed the presence of a single species and further revealed five haplotypes shared among nine sequenced individuals. Our 18S and 28S rDNA datasets were individually and combined analysed with Bayesian inference and Maximum Likelihood. Actinarctus doryphorus was placed together with Tanarctus sequences within a maximally supported Tanarctidae, confirming previous interpretations that the clade is distinct from Halechiniscidae. Although several studies in recent decades have concluded that the marine arthrotardigrades are paraphyletic, recent studies have argued that the clade may not be paraphyletic. Our phylogenetic analyses consistently inferred Arthrotardigrada as paraphyletic, as the clade includes the monophyletic Echiniscoidea. Accordingly, we propose that it is time to suppress the order Arthrotardigrada as it clearly does not reflect tardigrade phylogeny.
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Affiliation(s)
| | | | - Nadja Møbjerg
- Department of Biology; University of Copenhagen; Denmark.
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3
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DeSalle R, Narechania A, Tessler M. Multiple Outgroups Can Cause Random Rooting in Phylogenomics. Mol Phylogenet Evol 2023; 184:107806. [PMID: 37172862 DOI: 10.1016/j.ympev.2023.107806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/06/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Outgroup selection has been a major challenge since the rise of phylogenetics, and it has remained so in the phylogenomic era. Our goal here is to use large phylogenomic animal datasets to examine the impact of outgroup selection on the final topology. The results of our analyses further solidify the fact that distant outgroups can cause random rooting, and that this holds for concatenated and coalescent-based methods. The results also indicate that the standard practice of using multiple outgroups often causes random rooting. Most researchers go out of their way to get multiple outgroups, as this has been standard practice for decades. Based on our findings, this practice should stop. Instead, our results suggest that a single (most closely) related relative should be selected as the outgroup, unless all outgroups are roughly equally closely related to the ingroup.
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Affiliation(s)
- Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Apurva Narechania
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Tessler
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA; St. Francis College, Department of Biology, Brooklyn, NY 11201, USA
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4
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Asaf S, Khan AL, Jan R, Khan A, Khan A, Kim KM, Lee IJ. The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence. THE PLANT GENOME 2021; 14:e20130. [PMID: 34505399 DOI: 10.1002/tpg2.20130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 05/25/2023]
Abstract
Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present-day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales-other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time-calibrated plastid-based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, Univ. of Nizwa, Nizwa, 616, Oman
| | - Abdul Latif Khan
- Dep. of Biotechnology, College of Technology, Univ. of Houston, Houston, TX, 77204, USA
| | - Rahmatullah Jan
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord Univ., Bodø, 8049, Norway
| | - Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, 79409, USA
| | - Kyung-Min Kim
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
| | - In-Jung Lee
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life Science, Kyungpook National Univ., Daegu, 41566, Republic of Korea
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5
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Li X, St Laurent R, Earl C, Doorenweerd C, van Nieukerken EJ, Davis DR, Johns CA, Kawakita A, Kobayashi S, Zwick A, Lopez-Vaamonde C, Ohshima I, Kawahara AY. Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data. Cladistics 2021; 38:277-300. [PMID: 34710244 DOI: 10.1111/cla.12490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/27/2022] Open
Abstract
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade "LAMPO" (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade "AMO" (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the "LAMPO" clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous-Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.
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Affiliation(s)
- Xuankun Li
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chandra Earl
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Camiel Doorenweerd
- Department of Plant and Environmental Protection Services, University of Hawaii, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | | | - Donald R Davis
- Department of Entomology, NHB 105, Smithsonian Institution, Washington, DC, USA
| | - Chris A Johns
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Kawakita
- The Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, 112-0001, Japan
| | - Shigeki Kobayashi
- Entomological Laboratory, Graduate School of life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Andreas Zwick
- Australian National Insect Collection, National Research Collections Australia, CSIRO, Canberra, ACT, 2601, Australia
| | - Carlos Lopez-Vaamonde
- INRAE, URZF, Orléans, France.,IRBI, UMR 7261, CNRS-Université de Tours, Tours, France
| | - Issei Ohshima
- Department of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan.,Center for Frontier Natural History, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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6
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Zhu X, Liu M, Wu X, Ma W, Zhao X. Phylogenetic analysis of classical swine fever virus isolates from China. Arch Virol 2021; 166:2255-2261. [PMID: 34003359 DOI: 10.1007/s00705-021-05084-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 03/18/2021] [Indexed: 11/26/2022]
Abstract
Classical swine fever (CSF), caused by classical swine fever virus (CSFV), is a severe disease that causes huge economic losses in the swine industry worldwide. In China, CSF has been under control due to extensive vaccination since 1954. However, there are still sporadic CSF outbreaks in China. Here, we isolated 27 CSFV strains from three Chinese provinces (Shaanxi, Gansu, and Ningxia) from 2011 to 2018. Phylogenetic analysis based on the full-length envelope glycoprotein E2 coding region revealed that 25 out of 27 CSFV isolates clustered within subgroups 2.1 and 2.2, while two strains from Gansu belonged to subgroup 1.1. The sequence identity among these 27 isolates varied from 79.3% to 99.8% (nucleotides) and from 83.1% to 99.7% (amino acids). Further analysis based on the E2 amino acid sequences showed that these new isolates have consistent amino acid substitutions, including R31K and N34S.
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Affiliation(s)
- Xiaofu Zhu
- Key Laboratory of Animal Epidemic Disease Diagnostic Laboratory of Molecular Biology in Xianyang City, Xianyang Vocational Technical College, Xianyang, 712000, Shaanxi, China.
| | - Mingjie Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xujin Wu
- Key Laboratory of Animal Epidemic Disease Diagnostic Laboratory of Molecular Biology in Xianyang City, Xianyang Vocational Technical College, Xianyang, 712000, Shaanxi, China
| | - Wentao Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xuanduo Zhao
- Yangling Bodeyue Biotechnology Co., Ltd., Yangling, 712100, Shaanxi, China
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7
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Li X, Hou Z, Xu C, Shi X, Yang L, Lewis LA, Zhong B. Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae. Genome Biol Evol 2021; 13:6265471. [PMID: 33950183 PMCID: PMC8271138 DOI: 10.1093/gbe/evab101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/01/2022] Open
Abstract
The chlorophyte green algae (Chlorophyta) are species-rich ancient groups ubiquitous in various habitats with high cytological diversity, ranging from microscopic to macroscopic organisms. However, the deep phylogeny within core Chlorophyta remains unresolved, in part due to the relatively sparse taxon and gene sampling in previous studies. Here we contribute new transcriptomic data and reconstruct phylogenetic relationships of core Chlorophyta based on four large data sets up to 2,698 genes of 70 species, representing 80% of extant orders. The impacts of outgroup choice, missing data, bootstrap-support cutoffs, and model misspecification in phylogenetic inference of core Chlorophyta are examined. The species tree topologies of core Chlorophyta from different analyses are highly congruent, with strong supports at many relationships (e.g., the Bryopsidales and the Scotinosphaerales-Dasycladales clade). The monophyly of Chlorophyceae and of Trebouxiophyceae as well as the uncertain placement of Chlorodendrophyceae and Pedinophyceae corroborate results from previous studies. The reconstruction of ancestral scenarios illustrates the evolution of the freshwater-sea and microscopic–macroscopic transition in the Ulvophyceae, and the transformation of unicellular→colonial→multicellular in the chlorophyte green algae. In addition, we provided new evidence that serine is encoded by both canonical codons and noncanonical TAG code in Scotinosphaerales, and stop-to-sense codon reassignment in the Ulvophyceae has originated independently at least three times. Our robust phylogenetic framework of core Chlorophyta unveils the evolutionary history of phycoplast, cyto-morphology, and noncanonical genetic codes in chlorophyte green algae.
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Affiliation(s)
- Xi Li
- College of Life Sciences, Nanjing Normal University, China
| | - Zheng Hou
- College of Life Sciences, Nanjing Normal University, China
| | - Chenjie Xu
- College of Life Sciences, Nanjing Normal University, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, China
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, China
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8
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Lv X, Hu J, Hu Y, Li Y, Xu D, Ryder OA, Irwin DM, Yu L. Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships. Mol Phylogenet Evol 2020; 157:107065. [PMID: 33387649 DOI: 10.1016/j.ympev.2020.107065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.
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Affiliation(s)
- Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yiwen Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Yitian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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9
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Gardner EM, Johnson MG, Pereira JT, Puad ASA, Arifiani D, Sahromi , Wickett NJ, Zerega NJC. Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). Syst Biol 2020; 70:syaa073. [PMID: 32970819 PMCID: PMC8048387 DOI: 10.1093/sysbio/syaa073] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.
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Affiliation(s)
- Elliot M Gardner
- Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL 60022, USA
- Northwestern University, Plant Biology and Conservation Program, 2205 Tech Dr., Evanston, IL 60208, USA
- The Morton Arboretum, 4100 IL-53, Lisle, IL 60532, USA
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- Florida International University, Institute of Environment, 11200 SW 8th Street, OE 148 Miami, Florida 33199, USA
| | - Matthew G Johnson
- Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL 60022, USA
- Texas Tech University, Department of Biological Sciences, 2901 Main Street, Lubbock, TX 79409-3131, USA
| | - Joan T Pereira
- Forest Research Centre, Sabah Forestry Department, P.O. Box 1407, 90715 Sandakan, Sabah, Malaysia
| | - Aida Shafreena Ahmad Puad
- Faculty of Resource Science & Technology, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak 94300, Malaysia
| | - Deby Arifiani
- Herbarium Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Jawa Barat, Indonesia
| | - Sahromi
- Center for Plant Conservation Botanic Gardens, Indonesian Institute Of Sciences, Bogor, Jawa Barat, Indonesia Elliot M. Gardner and Matthew G. Johnson are co-first authors
| | - Norman J Wickett
- Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL 60022, USA
- Northwestern University, Plant Biology and Conservation Program, 2205 Tech Dr., Evanston, IL 60208, USA
| | - Nyree J C Zerega
- Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL 60022, USA
- Northwestern University, Plant Biology and Conservation Program, 2205 Tech Dr., Evanston, IL 60208, USA
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10
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Grant T. Outgroup sampling in phylogenetics: Severity of test and successive outgroup expansion. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Taran Grant
- Department of Zoology, Institute of Biosciences University of São Paulo São Paulo Brazil
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11
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Safari H, Zebarjadi A, Kahrizi D, Jafari AA. The study of inter-specific relationships of Bromus genus based on SCoT and ISSR molecular markers. Mol Biol Rep 2019; 46:5209-5223. [PMID: 31313131 DOI: 10.1007/s11033-019-04978-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
The genus of Bromus is one of the most important collection of rangeland plants, which are distributed in a wide range of natural areas of Iran. Interspecific relationships were evaluated in 90 accessions of 18 Bromus species based on 15 ISSR and 15 SCoT primers. SCoT markers separated the accessions better than ISSR marker. In addition, there was a high interspecific diversity between surveying germplasm. The sections of Bromus genus completely separated based on DNA molecular markers. SCoT markers could separate the accessions in each species. The primers of SC5 and SC35 from SCoT marker and UBC861, UBC857 and UBC844 primers from ISSR marker were identified as the best primers in revealing of genetic diversity between accessions. The sections of Ceratochloa, Genea, Pnigma and Bromus were monophyletic and were placed in one cluster. The section Bromus had a direct relationship with section Genea. In other words, section Ceratochloa has a direct relationship with Pnigma. B. tectorum and B. sericeus. B. sterilis had the most distance with other species in section Genea. B. squarrosus and B. japonicus had the most similarity and B. briziformis with B. danthoniae and B. scoparius with B. rechingeri had a moderate relationship in section Bromus. B. tomentosus and B. persicus had the highest similarity and B. riparius with B. biebersteinii and B. tomentellus with B. inermis had a moderate similarity in section Pnigma.
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Affiliation(s)
- Hooshmand Safari
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran.,Faculty Member of Research Department of Forests and Rangelands, Kermanshah Agricultural and Natural Resources Research and Education Center, AREEO, Kermanshah, Iran
| | - Alireza Zebarjadi
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran.
| | - Danial Kahrizi
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran
| | - Ali Ashraf Jafari
- Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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12
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Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276-W282. [PMID: 30997504 PMCID: PMC6602446 DOI: 10.1093/nar/gkz282] [Citation(s) in RCA: 229] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/29/2019] [Accepted: 04/10/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding the evolutionary background of a bacterial isolate has applications for a wide range of research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA for species identification currently remains popular. Unfortunately, this widespread method suffers from low resolution at the species level due to high sequence conservation. Currently, there is now a wealth of genomic data that can be used to yield more accurate species designations via modern phylogenetic methods and multiple genetic loci. However, these often require extensive expertise and time. The Automated Multi-Locus Species Tree (autoMLST) was thus developed to provide a rapid 'one-click' pipeline to simplify this workflow at: https://automlst.ziemertlab.com. This server utilizes Multi-Locus Sequence Analysis (MLSA) to produce high-resolution species trees; this does not preform multi-locus sequence typing (MLST), a related classification method. The resulting phylogenetic tree also includes helpful annotations, such as species clade designations and secondary metabolite counts to aid natural product prospecting. Distinct from currently available web-interfaces, autoMLST can automate selection of reference genomes and out-group organisms based on one or more query genomes. This enables a wide range of researchers to perform rigorous phylogenetic analyses more rapidly compared to manual MLSA workflows.
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Affiliation(s)
- Mohammad Alanjary
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Katharina Steinke
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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13
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Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections. Mol Phylogenet Evol 2018; 122:59-79. [DOI: 10.1016/j.ympev.2018.01.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/08/2018] [Accepted: 01/18/2018] [Indexed: 11/18/2022]
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14
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Saarela JM, Burke SV, Wysocki WP, Barrett MD, Clark LG, Craine JM, Peterson PM, Soreng RJ, Vorontsova MS, Duvall MR. A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions. PeerJ 2018; 6:e4299. [PMID: 29416954 PMCID: PMC5798404 DOI: 10.7717/peerj.4299] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
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Affiliation(s)
- Jeffery M. Saarela
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Sean V. Burke
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - William P. Wysocki
- Center for Data Intensive Sciences, University of Chicago, Chicago, IL, USA
| | - Matthew D. Barrett
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, West Perth, WA, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lynn G. Clark
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Paul M. Peterson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Robert J. Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Maria S. Vorontsova
- Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Melvin R. Duvall
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA
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15
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Li Z, De La Torre AR, Sterck L, Cánovas FM, Avila C, Merino I, Cabezas JA, Cervera MT, Ingvarsson PK, Van de Peer Y. Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants. Genome Biol Evol 2017; 9:1130-1147. [PMID: 28460034 PMCID: PMC5414570 DOI: 10.1093/gbe/evx070] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2017] [Indexed: 01/02/2023] Open
Abstract
Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.
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Affiliation(s)
- Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium
| | - Amanda R De La Torre
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Sciences, University of California-Davis, Davis, CA
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, Málaga, Spain
| | - Concepción Avila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos s/n, Málaga, Spain
| | - Irene Merino
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | | | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent, Belgium.,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, South Africa
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16
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Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E. Evidence for an ancient whole genome duplication in the cycad lineage. PLoS One 2017; 12:e0184454. [PMID: 28886111 PMCID: PMC5590961 DOI: 10.1371/journal.pone.0184454] [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: 03/09/2017] [Accepted: 08/24/2017] [Indexed: 11/26/2022] Open
Abstract
Contrary to the many whole genome duplication events recorded for angiosperms (flowering plants), whole genome duplications in gymnosperms (non-flowering seed plants) seem to be much rarer. Although ancient whole genome duplications have been reported for most gymnosperm lineages as well, some are still contested and need to be confirmed. For instance, data for ginkgo, but particularly cycads have remained inconclusive so far, likely due to the quality of the data available and flaws in the analysis. We extracted and sequenced RNA from both the cycad Encephalartos natalensis and Ginkgo biloba. This was followed by transcriptome assembly, after which these data were used to build paralog age distributions. Based on these distributions, we identified remnants of an ancient whole genome duplication in both cycads and ginkgo. The most parsimonious explanation would be that this whole genome duplication event was shared between both species and had occurred prior to their divergence, about 300 million years ago.
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Affiliation(s)
- Danielle Roodt
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Riaan L. Swanepoel
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
| | - Yves Van de Peer
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, South Africa
- * E-mail:
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17
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Fogliani B, Gâteblé G, Villegente M, Fabre I, Klein N, Anger N, Baskin CC, Scutt CP. The morphophysiological dormancy in Amborella trichopoda seeds is a pleisiomorphic trait in angiosperms. ANNALS OF BOTANY 2017; 119:581-590. [PMID: 28087660 PMCID: PMC5379585 DOI: 10.1093/aob/mcw244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/05/2016] [Accepted: 10/05/2016] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Recent parsimony-based reconstructions suggest that seeds of early angiosperms had either morphophysiological or physiological dormancy, with the former considered as more probable. The aim of this study was to determine the class of seed dormancy present in Amborella trichopoda , the sole living representative of the most basal angiosperm lineage Amborellales, with a view to resolving fully the class of dormancy present at the base of the angiosperm clade. METHODS Drupes of A. trichopoda without fleshy parts were germinated and dissected to observe their structure and embryo growth. Pre-treatments including acid scarification, gibberellin treatment and seed excision were tested to determine their influence on dormancy breakage and germination. Character-state mapping by maximum parsimony, incorporating data from the present work and published sources, was then used to determine the likely class of dormancy present in early angiosperms. KEY RESULTS Germination in A. trichopoda requires a warm stratification period of at least approx. 90 d, which is followed by endosperm swelling, causing the water-permeable pericarp-mesocarp envelope to split open. The embryo then grows rapidly within the seed, to radicle emergence some 17 d later and cotyledon emergence after an additional 24 d. Gibberellin treatment, acid scarification and excision of seeds from the surrounding drupe tissues all promoted germination by shortening the initial phase of dormancy, prior to embryo growth. CONCLUSIONS Seeds of A. trichopoda have non-deep simple morphophysiological dormancy, in which mechanical resistance of the pericarp-mesocarp envelope plays a key role in the initial physiological phase. Maximum parsimony analyses, including data obtained in the present work, indicate that morphophysiological dormancy is likely to be a pleisiomorphic trait in flowering plants. The significance of this conclusion for studies of early angiosperm evolution is discussed.
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Affiliation(s)
- Bruno Fogliani
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
- Laboratoire Insulaire du Vivant et de l’Environnement (LIVE)–EA 4243, University of New Caledonia (UNC), BP R4, 98851 Noumea, New Caledonia
| | - Gildas Gâteblé
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
| | - Matthieu Villegente
- Laboratoire Insulaire du Vivant et de l’Environnement (LIVE)–EA 4243, University of New Caledonia (UNC), BP R4, 98851 Noumea, New Caledonia
| | - Isabelle Fabre
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
| | - Nicolas Klein
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
- Laboratoire Insulaire du Vivant et de l’Environnement (LIVE)–EA 4243, University of New Caledonia (UNC), BP R4, 98851 Noumea, New Caledonia
| | - Nicolas Anger
- Institut Agronomique néo-Calédonien (IAC), BP 73 Port Laguerre, 98890 Païta, New Caledonia
| | - Carol C Baskin
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Charlie P Scutt
- Reproduction et Développement des Plantes (RDP; UMR5667, CNRS-INRA-Université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
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18
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He D, Sierra R, Pawlowski J, Baldauf SL. Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria. Mol Phylogenet Evol 2016; 101:1-7. [DOI: 10.1016/j.ympev.2016.04.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/23/2016] [Accepted: 04/26/2016] [Indexed: 12/22/2022]
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19
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Xi Z, Liu L, Davis CC. The Impact of Missing Data on Species Tree Estimation. Mol Biol Evol 2015; 33:838-60. [DOI: 10.1093/molbev/msv266] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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20
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Wang YC, Wang JD, Chen CH, Chen YW, Li C. A novel BLAST-Based Relative Distance (BBRD) method can effectively group members of protein arginine methyltransferases and suggest their evolutionary relationship. Mol Phylogenet Evol 2015; 84:101-11. [PMID: 25576770 DOI: 10.1016/j.ympev.2014.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/24/2014] [Accepted: 12/05/2014] [Indexed: 01/06/2023]
Abstract
We developed a novel BLAST-Based Relative Distance (BBRD) method by Pearson's correlation coefficient to avoid the problems of tedious multiple sequence alignment and complicated outgroup selection. We showed its application on reconstructing reliable phylogeny for nucleotide and protein sequences as exemplified by the fmr-1 gene and dihydrolipoamide dehydrogenase, respectively. We then used BBRD to resolve 124 protein arginine methyltransferases (PRMTs) that are homologues of nine mammalian PRMTs. The tree placed the uncharacterized PRMT9 with PRMT7 in the same clade, outside of all the Type I PRMTs including PRMT1 and its vertebrate paralogue PRMT8, PRMT3, PRMT6, PRMT2 and PRMT4. The PRMT7/9 branch then connects with the type II PRMT5. Some non-vertebrates contain different PRMTs without high sequence homology with the mammalian PRMTs. For example, in the case of Drosophila arginine methyltransferase (DART) and Trypanosoma brucei methyltransferases (TbPRMTs) in the analyses, the BBRD program grouped them with specific clades and thus suggested their evolutionary relationships. The BBRD method thus provided a great tool to construct a reliable tree for members of protein families through evolution.
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Affiliation(s)
- Yi-Chun Wang
- Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan.
| | - Jing-Doo Wang
- Department of Computer Science and Information Engineering, Asia University, No. 500, Lioufeng Rd., Wufeng District, Taichung 41354, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chin-Han Chen
- Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan
| | - Yi-Wen Chen
- Department of Life Science, Tunghai University, No. 1727, Sec. 4, Taiwan Boulevard, Xitun District, Taichung 40704, Taiwan
| | - Chuan Li
- Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., Taichung 40201, Taiwan.
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21
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Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GKS, Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A 2014; 111:E4859-68. [PMID: 25355905 PMCID: PMC4234587 DOI: 10.1073/pnas.1323926111] [Citation(s) in RCA: 749] [Impact Index Per Article: 74.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
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Affiliation(s)
- Norman J Wickett
- Chicago Botanic Garden, Glencoe, IL 60022; Program in Biological Sciences, Northwestern University, Evanston, IL 60208;
| | - Siavash Mirarab
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Nam Nguyen
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Tandy Warnow
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Naim Matasci
- iPlant Collaborative, Tucson, AZ 85721; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Matthew A Gitzendanner
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611
| | - Brad R Ruhfel
- Department of Biology and Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475; Florida Museum of Natural History, Gainesville, FL 32611
| | - Eric Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | - Joshua P Der
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | | | - Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, MA 02138
| | | | - Douglas E Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | - Pamela S Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | | | - Carl J Rothfels
- Department of Biology, Duke University, Durham, NC 27708; Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Lisa Pokorny
- Department of Biology, Duke University, Durham, NC 27708; Department of Biodiversity and Conservation, Real Jardín Botánico-Consejo Superior de Investigaciones Cientificas, 28014 Madrid, Spain
| | | | | | | | - Barbara Surek
- Botanical Institute, Universität zu Köln, Cologne D-50674, Germany
| | - Juan Carlos Villarreal
- Department fur Biologie, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universitat, 80638 Munich, Germany
| | - Béatrice Roure
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7
| | - Hervé Philippe
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7; CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | | | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
| | - Toni M Kutchan
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | | | - Jun Wang
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Yong Zhang
- CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | - Zhijian Tian
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Zhixiang Yan
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiaolei Wu
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiao Sun
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9; BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1
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Jiang W, Chen SY, Wang H, Li DZ, Wiens JJ. Should genes with missing data be excluded from phylogenetic analyses? Mol Phylogenet Evol 2014; 80:308-18. [DOI: 10.1016/j.ympev.2014.08.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 07/15/2014] [Accepted: 08/03/2014] [Indexed: 10/24/2022]
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Evolution and biogeography of gymnosperms. Mol Phylogenet Evol 2014; 75:24-40. [DOI: 10.1016/j.ympev.2014.02.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022]
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Xi Z, Rest JS, Davis CC. Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS One 2013; 8:e80870. [PMID: 24278335 PMCID: PMC3836751 DOI: 10.1371/journal.pone.0080870] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 10/15/2013] [Indexed: 12/29/2022] Open
Abstract
The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant gymnosperms (i.e., conifers, cycads, Ginkgo, and gnetophytes) are monophyletic, ii) gnetophytes exhibit discordant placements within conifers between their nuclear and plastid genomes, and iii) cycads plus Ginkgo form a clade that is sister to all remaining extant gymnosperms. We additionally observe that the placement of Ginkgo inferred from coalescent analyses is congruent across different nucleotide rate partitions. In contrast, the standard concatenation method produces strongly supported, but incongruent placements of Ginkgo between slow- and fast-evolving sites. Specifically, fast-evolving sites yield relationships in conflict with coalescent analyses. We hypothesize that this incongruence may be related to the way in which concatenation methods treat sites with elevated nucleotide substitution rates. More empirical and simulation investigations are needed to understand this potential weakness of concatenation methods.
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Affiliation(s)
- Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Joshua S. Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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Zhao L, Zhang N, Ma PF, Liu Q, Li DZ, Guo ZH. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae. PLoS One 2013; 8:e64642. [PMID: 23734211 PMCID: PMC3667173 DOI: 10.1371/journal.pone.0064642] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/16/2013] [Indexed: 11/23/2022] Open
Abstract
BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.
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Affiliation(s)
- Lei Zhao
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ning Zhang
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Peng-Fei Ma
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qi Liu
- Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - De-Zhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhen-Hua Guo
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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26
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Wu CS, Chaw SM, Huang YY. Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads. Genome Biol Evol 2013; 5:243-54. [PMID: 23315384 PMCID: PMC3595029 DOI: 10.1093/gbe/evt001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2013] [Indexed: 12/23/2022] Open
Abstract
Molecular phylogenetic studies have not yet reached a consensus on the placement of Ginkgoales, which is represented by the only living species, Ginkgo biloba (common name: ginkgo). At least six discrepant placements of ginkgo have been proposed. This study aimed to use the chloroplast phylogenomic approach to examine possible factors that lead to such disagreeing placements. We found the sequence types used in the analyses as the most critical factor in the conflicting placements of ginkgo. In addition, the placement of ginkgo varied in the trees inferred from nucleotide (NU) sequences, which notably depended on breadth of taxon sampling, tree-building methods, codon positions, positions of Gnetopsida (common name: gnetophytes), and including or excluding gnetophytes in data sets. In contrast, the trees inferred from amino acid (AA) sequences congruently supported the monophyly of a ginkgo and Cycadales (common name: cycads) clade, regardless of which factors were examined. Our site-stripping analysis further revealed that the high substitution saturation of NU sequences mainly derived from the third codon positions and contributed to the variable placements of ginkgo. In summary, the factors we surveyed did not affect results inferred from analyses of AA sequences. Congruent topologies in our AA trees give more confidence in supporting the ginkgo-cycad sister-group hypothesis.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Yi Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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27
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Ammerman LK, Lee DN, Tipps TM. First molecular phylogenetic insights into the evolution of free-tailed bats in the subfamily Molossinae (Molossidae, Chiroptera). J Mammal 2012. [DOI: 10.1644/11-mamm-a-103.1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Torruella G, Derelle R, Paps J, Lang BF, Roger AJ, Shalchian-Tabrizi K, Ruiz-Trillo I. Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol Biol Evol 2012; 29:531-44. [PMID: 21771718 PMCID: PMC3350318 DOI: 10.1093/molbev/msr185] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dynamics (i.e., gene duplications and losses) and incorrect orthology assignments are always appropriately taken into account. In this paper, we present an innovative strategy for overcoming orthology assignment problems. Rather than identifying and eliminating genes with paralogy problems, we have constructed a data set comprised exclusively of conserved single-copy protein domains that, unlike most of the commonly used phylogenomic data sets, should be less confounded by orthology miss-assignments. To evaluate the power of this approach, we performed maximum likelihood and Bayesian analyses to infer the evolutionary relationships within the opisthokonts (which includes Metazoa, Fungi, and related unicellular lineages). We used this approach to test 1) whether Filasterea and Ichthyosporea form a clade, 2) the interrelationships of early-branching metazoans, and 3) the relationships among early-branching fungi. We also assessed the impact of some methods that are known to minimize systematic error, including reducing the distance between the outgroup and ingroup taxa or using the CAT evolutionary model. Overall, our analyses support the Filozoa hypothesis in which Ichthyosporea are the first holozoan lineage to emerge followed by Filasterea, Choanoflagellata, and Metazoa. Blastocladiomycota appears as a lineage separate from Chytridiomycota, although this result is not strongly supported. These results represent independent tests of previous phylogenetic hypotheses, highlighting the importance of sophisticated approaches for orthology assignment in phylogenomic analyses.
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Affiliation(s)
- Guifré Torruella
- Departament de Genètica and Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
| | - Romain Derelle
- Departament de Genètica and Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
- Present address: Centre de regulació genòmica (CRG), Parc de recerca biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Jordi Paps
- Departament de Genètica and Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
- Present address: Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - B. Franz Lang
- Département de Biochimie, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | | | - Iñaki Ruiz-Trillo
- Departament de Genètica and Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
- Institució Catalana per a la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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McCouch SR, McNally KL, Wang W, Sackville Hamilton R. Genomics of gene banks: A case study in rice. AMERICAN JOURNAL OF BOTANY 2012; 99:407-23. [PMID: 22314574 DOI: 10.3732/ajb.1100385] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Only a small fraction of the naturally occurring genetic diversity available in the world's germplasm repositories has been explored to date, but this is expected to change with the advent of affordable, high-throughput genotyping and sequencing technology. It is now possible to examine genome-wide patterns of natural variation and link sequence polymorphisms with downstream phenotypic consequences. In this paper, we discuss how dramatic changes in the cost and efficiency of sequencing and genotyping are revolutionizing the way gene bank scientists approach the responsibilities of their job. Sequencing technology provides a set of tools that can be used to enhance the quality, efficiency, and cost-effectiveness of gene bank operations, the depth of scientific knowledge of gene bank holdings, and the level of public interest in natural variation. As a result, gene banks have the chance to take on new life. Previously seen as "warehouses" where seeds were diligently maintained, but evolutionarily frozen in time, gene banks could transform into vibrant research centers that actively investigate the genetic potential of their holdings. In this paper, we will discuss how genotyping and sequencing can be integrated into the activities of a modern gene bank to revolutionize the way scientists document the genetic identity of their accessions; track seed lots, varieties, and alleles; identify duplicates; and rationalize active collections, and how the availability of genomics data are likely to motivate innovative collaborations with the larger research and breeding communities to engage in systematic and rigorous phenotyping and multilocation evaluation of the genetic resources in gene banks around the world. The objective is to understand and eventually predict how variation at the DNA level helps determine the phenotypic potential of an individual or population. Leadership and vision are needed to coordinate the characterization of collections and to integrate genotypic and phenotypic information in ways that will illuminate the value of these resources. Genotyping of collections represents a powerful starting point that will enable gene banks to become more effective as stewards of crop biodiversity.
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Affiliation(s)
- Susan R McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NewYork 14853-1901, USA.
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30
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Nabhan AR, Sarkar IN. The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy. Brief Bioinform 2012; 13:122-34. [PMID: 21436145 PMCID: PMC3251835 DOI: 10.1093/bib/bbr014] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 02/25/2011] [Indexed: 11/13/2022] Open
Abstract
Over the past two decades, there has been a long-standing debate about the impact of taxon sampling on phylogenetic inference. Studies have been based on both real and simulated data sets, within actual and theoretical contexts, and using different inference methods, to study the impact of taxon sampling. In some cases, conflicting conclusions have been drawn for the same data set. The main questions explored in studies to date have been about the effects of using sparse data, adding new taxa, including more characters from genome sequences and using different (or concatenated) locus regions. These questions can be reduced to more fundamental ones about the assessment of data quality and the design guidelines of taxon sampling in phylogenetic inference experiments. This review summarizes progress to date in understanding the impact of taxon sampling on the accuracy of phylogenetic analysis.
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Affiliation(s)
- Ahmed Ragab Nabhan
- Center for Clinical and Translational Science, 89 Beaumont Avenue, Given Courtyard N309, Burlington, VT 05405, USA
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31
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Wu CS, Wang YN, Hsu CY, Lin CP, Chaw SM. Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny. Genome Biol Evol 2011; 3:1284-95. [PMID: 21933779 PMCID: PMC3219958 DOI: 10.1093/gbe/evr095] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2011] [Indexed: 12/13/2022] Open
Abstract
The relationships among the extant five gymnosperm groups--gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads--remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the "gnepines" hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Nan Wang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Chi-Yao Hsu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Ping Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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32
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Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ. Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol 2011; 60:117-25. [PMID: 21186249 PMCID: PMC3038350 DOI: 10.1093/sysbio/syq072] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 07/03/2009] [Accepted: 08/17/2010] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.
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Affiliation(s)
- J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL 32609, USA.
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33
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Chang WC, Burleigh GJ, Fernández-Baca DF, Eulenstein O. An ILP solution for the gene duplication problem. BMC Bioinformatics 2011; 12 Suppl 1:S14. [PMID: 21342543 PMCID: PMC3044268 DOI: 10.1186/1471-2105-12-s1-s14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Background The gene duplication (GD) problem seeks a species tree that implies the fewest gene duplication events across a given collection of gene trees. Solving this problem makes it possible to use large gene families with complex histories of duplication and loss to infer phylogenetic trees. However, the GD problem is NP-hard, and therefore, most analyses use heuristics that lack any performance guarantee. Results We describe the first integer linear programming (ILP) formulation to solve instances of the gene duplication problem exactly. With simulations, we demonstrate that the ILP solution can solve problem instances with up to 14 taxa. Furthermore, we apply the new ILP solution to solve the gene duplication problem for the seed plant phylogeny using a 12-taxon, 6, 084-gene data set. The unique, optimal solution, which places Gnetales sister to the conifers, represents a new, large-scale genomic perspective on one of the most puzzling questions in plant systematics. Conclusions Although the GD problem is NP-hard, our novel ILP solution for it can solve instances with data sets consisting of as many as 14 taxa and 1, 000 genes in a few hours. These are the largest instances that have been solved to optimally to date. Thus, this work can provide large-scale genomic perspectives on phylogenetic questions that previously could only be addressed by heuristic estimates.
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Affiliation(s)
- Wen-Chieh Chang
- Department of Computer Science, Iowa State University, Ames 50011, USA.
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34
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Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci U S A 2010; 107:16196-200. [PMID: 20798348 DOI: 10.1073/pnas.1006538107] [Citation(s) in RCA: 353] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being applied to organisms based on their interesting ecological, physiological, developmental, or evolutionary properties and not on the depth of genetic information available for them. Here, we illustrate this point using a low-cost, efficient technique to determine the fine-scale phylogenetic relationships among recently diverged populations in a species. This application of restriction site-associated DNA tags (RAD tags) reveals previously unresolved genetic structure and direction of evolution in the pitcher plant mosquito, Wyeomyia smithii, from a southern Appalachian Mountain refugium following recession of the Laurentide Ice Sheet at 22,000-19,000 B.P. The RAD tag method can be used to identify detailed patterns of phylogeography in any organism regardless of existing genomic data, and, more broadly, to identify incipient speciation and genome-wide variation in natural populations in general.
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35
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Cibrián-Jaramillo A, De la Torre-Bárcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol 2010; 2:225-39. [PMID: 20624728 PMCID: PMC2997538 DOI: 10.1093/gbe/evq012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2010] [Indexed: 01/01/2023] Open
Abstract
We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.
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Affiliation(s)
- Angélica Cibrián-Jaramillo
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA.
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