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Gallot-Lavallée L, Jerlström-Hultqvist J, Zegarra-Vidarte P, Salas-Leiva DE, Stairs CW, Čepička I, Roger AJ, Archibald JM. Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes. Proc Natl Acad Sci U S A 2023; 120:e2306381120. [PMID: 38019867 DOI: 10.1073/pnas.2306381120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Inteins are self-splicing protein elements found in viruses and all three domains of life. How the DNA encoding these selfish elements spreads within and between genomes is poorly understood, particularly in eukaryotes where inteins are scarce. Here, we show that the nuclear genomes of three strains of Anaeramoeba encode between 45 and 103 inteins, in stark contrast to four found in the most intein-rich eukaryotic genome described previously. The Anaeramoeba inteins reside in a wide range of proteins, only some of which correspond to intein-containing proteins in other eukaryotes, prokaryotes, and viruses. Our data also suggest that viruses have contributed to the spread of inteins in Anaeramoeba and the colonization of new alleles. The persistence of Anaeramoeba inteins might be partly explained by intragenomic movement of intein-encoding regions from gene to gene. Our intein dataset greatly expands the spectrum of intein-containing proteins and provides insights into the evolution of inteins in eukaryotes.
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Affiliation(s)
- Lucie Gallot-Lavallée
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jon Jerlström-Hultqvist
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala 751 24, Sweden
| | - Paula Zegarra-Vidarte
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala 751 24, Sweden
| | - Dayana E Salas-Leiva
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Courtney W Stairs
- Microbiology Group, Department of Biology, Lund University, Lund 223 62, Sweden
| | - Ivan Čepička
- Department of Zoology, Charles University, Prague 128 00, Czech Republic
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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2
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Higuera A, Salas-Leiva DE, Curtis B, Patiño LH, Zhao D, Jerlström-Hultqvist J, Dlutek M, Muñoz M, Roger AJ, Ramírez JD. Draft genomes of Blastocystis subtypes from human samples of Colombia. Parasit Vectors 2023; 16:52. [PMID: 36732768 PMCID: PMC9896827 DOI: 10.1186/s13071-022-05619-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/14/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Blastocystis is one of the most common eukaryotic microorganisms colonizing the intestines of both humans and animals, but the conditions under which it may be a pathogen are unclear. METHODS To study the genomic characteristics of circulating subtypes (ST) in Colombia, we established nine xenic cultures from Blastocystis isolated from human fecal samples, we identified 10 different subtypes, since one sample had a mixed infection. Thus, the genomes of the subtypes ST1 (n = 3), ST2 (n = 1), ST3 (n = 2), ST6 (n = 1), ST7 (n = 1), and ST8 (n = 2) were sequenced using Illumina and Oxford Nanopore Technologies (ONT). RESULTS Analyses of these draft nuclear genomes indicated remarkable diversity in terms of genome size and guanine-cytosine (GC) content among the compared STs. Illumina sequencing-only draft genomes contained 824 to 2077 scaffolds, with total genome size ranging from 12 to 13.2 Mb and N50 values ranging from 10,585 to 29,404 base pairs (bp). The genome of one ST1 isolate was sequenced using ONT. This assembly was more contiguous, with a size of 20 million base pairs (Mb) spread over 116 scaffolds, and an N50 of 248,997 bp. CONCLUSION This work represents one of the few large-scale comparative genomic analyses of Blastocystis isolates, providing an additional glimpse into its genomic diversity.
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Affiliation(s)
- Adriana Higuera
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Dayana E. Salas-Leiva
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW United Kingdom
| | - Bruce Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Luz H. Patiño
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Dandan Zhao
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, BMC, Uppsala Universitet, Box 596, 751 24 Uppsala, Sweden
| | - Marlena Dlutek
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Marina Muñoz
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Juan David Ramírez
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia ,grid.59734.3c0000 0001 0670 2351Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY USA
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3
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González-Chávez SA, Salas-Leiva JS, Salas-Leiva DE, López-Loeza SM, Sausameda-García J, Orrantia-Borunda E, Burgos-Vargas R, Alvarado-Jáquez MF, Torres-Quintana M, Cuevas-Martínez R, Chaparro-Barrera E, Marín-Terrazas C, Espino-Solís GP, Romero-López JP, Bernal-Alferes BDJ, Pacheco-Tena C. Levofloxacin induces differential effects in the transcriptome between the gut, peripheral and axial joints in the Spondyloarthritis DBA/1 mice: Improvement of intestinal dysbiosis and the overall inflammatory process. PLoS One 2023; 18:e0281265. [PMID: 36730179 PMCID: PMC9894406 DOI: 10.1371/journal.pone.0281265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
To analyze the effect of levofloxacin-induced intestinal microbiota modifications on intestinal, joint, and systemic inflammation in the DBA/1 mice with spontaneous arthritis. The study included two groups of mice, one of which received levofloxacin. The composition and structure of the microbiota were determined in the mice's stool using 16S rRNA sequencing; the differential taxa and metabolic pathway between mice treated with levofloxacin and control mice were also defied. The effect of levofloxacin was evaluated in the intestines, hind paws, and spines of mice through DNA microarray transcriptome and histopathological analyses; systemic inflammation was measured by flow cytometry. Levofloxacin decreased the pro-inflammatory bacteria, including Prevotellaceae, Odoribacter, and Blautia, and increased the anti-inflammatory Muribaculaceae in mice's stool. Histological analysis confirmed the intestinal inflammation in control mice, while in levofloxacin-treated mice, inflammation was reduced; in the hind paws and spines, levofloxacin also decreased the inflammation. Microarray showed the downregulation of genes and signaling pathways relevant in spondyloarthritis, including several cytokines and chemokines. Levofloxacin-treated mice showed differential transcriptomic profiles between peripheral and axial joints and intestines. Levofloxacin decreased the expression of TNF-α, IL-23a, and JAK3 in the three tissues, but IL-17 behaved differently in the intestine and the joints. Serum TNF-α was also reduced in levofloxacin-treated mice. Our results suggest that the microbiota modification aimed at reducing pro-inflammatory and increasing anti-inflammatory bacteria could potentially be a coadjuvant in treating inflammatory arthropathies.
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Affiliation(s)
- Susana Aideé González-Chávez
- Facultad de Medicina y Ciencias Biomédicas, Laboratorio PABIOM, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Joan S. Salas-Leiva
- Departamento de Medio Ambiente y Energía, CONACyT-Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - Dayana E. Salas-Leiva
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry and Molecular Biology, Institute for Comparative Genomics (ICG), Dalhousie University, Halifax, NS, Canada
| | - Salma Marcela López-Loeza
- Facultad de Medicina y Ciencias Biomédicas, Laboratorio PABIOM, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Jasanai Sausameda-García
- Facultad de Medicina y Ciencias Biomédicas, Laboratorio PABIOM, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Erasmo Orrantia-Borunda
- Departamento de Medio Ambiente y Energía, CONACyT-Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - Rubén Burgos-Vargas
- Department of Rheumatology, Hospital General de México, "Dr. Eduardo Liceaga", Ciudad de México, México
| | | | - Mayra Torres-Quintana
- Facultad de Medicina y Ciencias Biomédicas, Laboratorio PABIOM, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Rubén Cuevas-Martínez
- Facultad de Medicina y Ciencias Biomédicas, Laboratorio PABIOM, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Eduardo Chaparro-Barrera
- Facultad de Medicina y Ciencias Biomédicas, Laboratorio PABIOM, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Carlos Marín-Terrazas
- Facultad de Medicina y Ciencias Biomédicas, Laboratorio PABIOM, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Gerardo Pável Espino-Solís
- Translational Research Laboratory and National Laboratory of Flow Cytometry, Autonomous University of Chihuahua, Circuito Universitario, Campus II, Chihuahua, Mexico
| | - José Pablo Romero-López
- Laboratorio de Inmunología Clínica 1, Instituto Politécnico Nacional de México, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Ciudad de México, México
| | - Brian de Jesús Bernal-Alferes
- Laboratorio de Inmunología Clínica 1, Instituto Politécnico Nacional de México, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Ciudad de México, México
| | - César Pacheco-Tena
- Facultad de Medicina y Ciencias Biomédicas, Laboratorio PABIOM, Universidad Autónoma de Chihuahua, Chihuahua, México
- * E-mail:
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4
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Chen Z, Li J, Salas-Leiva DE, Chen M, Chen S, Li S, Wu Y, Yi Z. Group-specific functional patterns of mitochondrion-related organelles shed light on their multiple transitions from mitochondria in ciliated protists. Mar Life Sci Technol 2022; 4:609-623. [PMID: 37078085 PMCID: PMC10077286 DOI: 10.1007/s42995-022-00147-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/23/2022] [Indexed: 05/03/2023]
Abstract
Adaptations of ciliates to hypoxic environments have arisen independently several times. Studies on mitochondrion-related organelle (MRO) metabolisms from distinct anaerobic ciliate groups provide evidence for understanding the transitions from mitochondria to MROs within eukaryotes. To deepen our knowledge about the evolutionary patterns of ciliate anaerobiosis, mass-culture and single-cell transcriptomes of two anaerobic species, Metopus laminarius (class Armophorea) and Plagiopyla cf. narasimhamurtii (class Plagiopylea), were sequenced and their MRO metabolic maps were compared. In addition, we carried out comparisons using publicly available predicted MRO proteomes from other ciliate classes (i.e., Armophorea, Litostomatea, Muranotrichea, Oligohymenophorea, Parablepharismea and Plagiopylea). We found that single-cell transcriptomes were similarly comparable to their mass-culture counterparts in predicting MRO metabolic pathways of ciliates. The patterns of the components of the MRO metabolic pathways might be divergent among anaerobic ciliates, even among closely related species. Notably, our findings indicate the existence of group-specific functional relics of electron transport chains (ETCs). Detailed group-specific ETC functional patterns are as follows: full oxidative phosphorylation in Oligohymenophorea and Muranotrichea; only electron-transfer machinery in Armophorea; either of these functional types in Parablepharismea; and ETC functional absence in Litostomatea and Plagiopylea. These findings suggest that adaptation of ciliates to anaerobic conditions is group-specific and has occurred multiple times. Our results also show the potential and the limitations of detecting ciliate MRO proteins using single-cell transcriptomes and improve the understanding of the multiple transitions from mitochondria to MROs within ciliates. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00147-w.
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Affiliation(s)
- Zhicheng Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | | | - Miaoying Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Shilong Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Senru Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Yanyan Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631 China
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5
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Gornik SG, Flores V, Reinhardt F, Erber L, Salas-Leiva DE, Douvropoulou O, Lassadi I, Einarsson E, Mörl M, Git A, Stadler PF, Pain A, Waller RF. Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes. Mol Biol Evol 2022; 39:6701636. [PMID: 36108082 PMCID: PMC9550989 DOI: 10.1093/molbev/msac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts. To determine both ancestral myzozoan and novel perkinsozoan mitochondrial genome features, we sequenced and assembled mitochondrial genomes of four Perkinsus species. These data show a simple ancestral genome with the common reduced coding capacity but disposition for rearrangement. We identified 75 frameshifts across the four species that occur as distinct types and that are highly conserved in gene location. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. The cox3 gene is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in cox1 and cob. All genes lack cysteine codons implying a reduction to 19 amino acids in these genomes. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA suggesting import into the organelle. Perkinsus demonstrates further remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.
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Affiliation(s)
| | - Victor Flores
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Franziska Reinhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Dayana E Salas-Leiva
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Olga Douvropoulou
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany,Discrete Biomathematics, Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany,Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währinger Str. 17, Alsergrund, Vienna 1090, Austria,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Arnab Pain
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,International Institute for Zoonosis Control, Hokkaido University, 001-0020 North 20, West 10 Kita-ku, Sapporo 001-0020, Japan
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6
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Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Author Correction: Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun 2021; 12:7350. [PMID: 34916502 PMCID: PMC8677737 DOI: 10.1038/s41467-021-27605-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Dayana E Salas-Leiva
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada. .,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
| | - Eelco C Tromer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Bruce A Curtis
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Jon Jerlström-Hultqvist
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Joan S Salas-Leiva
- CONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136, Chihuahua, Chihuahua, México
| | - Lucie Gallot-Lavallée
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Shelby K Williams
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute - KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - John M Archibald
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Alastair G B Simpson
- Institute for Comparative Genomics (ICG), Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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7
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Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun 2021; 12:6003. [PMID: 34650064 PMCID: PMC8516963 DOI: 10.1038/s41467-021-26077-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.
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Affiliation(s)
- Dayana E. Salas-Leiva
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada ,grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eelco C. Tromer
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom ,grid.4830.f0000 0004 0407 1981Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Bruce A. Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Martin Kolisko
- grid.418095.10000 0001 1015 3316Institute of Parasitology, Biology Centre, Czech Acad. Sci, České Budějovice, Czech Republic
| | - Zhenzhen Yi
- grid.263785.d0000 0004 0368 7397Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631 China
| | - Joan S. Salas-Leiva
- grid.466575.30000 0001 1835 194XCONACyT-Centro de Investigación en Materiales Avanzados, Departamento de medio ambiente y energía, Miguel de Cervantes 120, Complejo Industrial Chihuahua, 31136 Chihuahua, Chih. México
| | - Lucie Gallot-Lavallée
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Shelby K. Williams
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Geert J. P. L. Kops
- grid.7692.a0000000090126352Oncode Institute, Hubrecht Institute – KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - John M. Archibald
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Alastair G. B. Simpson
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
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8
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Gentekaki E, Curtis BA, Stairs CW, Klimeš V, Eliáš M, Salas-Leiva DE, Herman EK, Eme L, Arias MC, Henrissat B, Hilliou F, Klute MJ, Suga H, Malik SB, Pightling AW, Kolisko M, Rachubinski RA, Schlacht A, Soanes DM, Tsaousis AD, Archibald JM, Ball SG, Dacks JB, Clark CG, van der Giezen M, Roger AJ. Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol 2017; 15:e2003769. [PMID: 28892507 PMCID: PMC5608401 DOI: 10.1371/journal.pbio.2003769] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/21/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022] Open
Abstract
Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%-61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize α-glucans rather than β-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.
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Affiliation(s)
- Eleni Gentekaki
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Bruce A. Curtis
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Courtney W. Stairs
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Dayana E. Salas-Leiva
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Emily K. Herman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Laura Eme
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Maria C. Arias
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, Villeneuve d’Ascq Cedex, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Mary J. Klute
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Nanatsuka 562, Shobara, Hiroshima, Japan
| | - Shehre-Banoo Malik
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arthur W. Pightling
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Martin Kolisko
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Alexander Schlacht
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Darren M. Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Anastasios D. Tsaousis
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M. Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity, Toronto, Canada
| | - Steven G. Ball
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, Villeneuve d’Ascq Cedex, France
| | - Joel B. Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - C. Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Andrew J. Roger
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity, Toronto, Canada
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9
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Salas-Leiva DE, Meerow AW, Calonje M, Francisco-Ortega J, Griffith MP, Nakamura K, Sánchez V, Knowles L, Knowles D. Shifting Quaternary migration patterns in the Bahamian archipelago: Evidence from the Zamia pumila complex at the northern limits of the Caribbean island biodiversity hotspot. Am J Bot 2017; 104:757-771. [PMID: 28515078 DOI: 10.3732/ajb.1700054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY The Bahamas archipelago is formed by young, tectonically stable carbonate banks that harbor direct geological evidence of global ice-volume changes. We sought to detect signatures of major changes on gene flow patterns and reconstruct the phylogeographic history of the monophyletic Zamia pumila complex across the Bahamas. METHODS Nuclear molecular markers with both high and low mutation rates were used to capture two different time scale signatures and test several gene flow and demographic hypotheses. KEY RESULTS Single-copy nuclear genes unveiled apparent ancestral admixture on Andros, suggesting a significant role of this island as main hub of diversity of the archipelago. We detected demographic and spatial expansion of the Zamia pumila complex on both paleo-provinces around the Piacenzian (Pliocene)/Gelasian (Pleistocene). Populations evidenced signatures of different migration models that have occurred at two different times. Populations on Long Island (Z. lucayana) may either represent a secondary colonization of the Bahamas by Zamia or a rapid and early-divergence event of at least one population on the Bahamas. CONCLUSIONS Despite changes in migration patterns with global climate, expected heterozygosity with both marker systems remains within the range reported for cycads, but with significant levels of increased inbreeding detected by the microsatellites. This finding is likely associated with reduced gene flow between and within paleo-provinces, accompanied by genetic drift, as rising seas enforced isolation. Our study highlights the importance of the maintenance of the predominant direction of genetic exchange and the role of overseas dispersion among the islands during climate oscillations.
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Affiliation(s)
- Dayana E Salas-Leiva
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Alan W Meerow
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Michael Calonje
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Javier Francisco-Ortega
- International Center for Tropical Botany, Department of Biological Sciences, 11200 S.W. 8th Street, Florida International University, Miami, Florida 33199 USA
- Kushlan Tropical Science Institute, 11935 Old Cutler Road, Fairchild Tropical Botanic Garden, Coral Gables, Florida 33156 USA
| | - M Patrick Griffith
- Montgomery Botanical Center, 11901 Old Cutler Road, Coral Gables, Florida 33156 USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Vanessa Sánchez
- USDA-ARS-SHRS, 13601 Old Cutler Road, Miami, Florida 33158 USA
| | - Lindy Knowles
- Bahamas National Trust, P. O. Box N-4105, Bay Street Business Centre, Bay Street, Nassau
| | - David Knowles
- The Bahamas, Bahamas National Trust, Abaco National Park, P.O. Box AB-20953, Marsh Harbour, Abaco, The Bahamas
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Cerón-Souza I, Gonzalez EG, Schwarzbach AE, Salas-Leiva DE, Rivera-Ocasio E, Toro-Perea N, Bermingham E, McMillan WO. Contrasting demographic history and gene flow patterns of two mangrove species on either side of the Central American Isthmus. Ecol Evol 2015; 5:3486-99. [PMID: 26380680 PMCID: PMC4569042 DOI: 10.1002/ece3.1569] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/12/2015] [Indexed: 11/18/2022] Open
Abstract
Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day marine currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life-history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major marine (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid-Pleistocene and early Holocene, (3) asymmetric historical migration with higher gene flow from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary gene flow between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life-history traits of mangrove species, which should have had a strong influence on seed dispersal capability and, thus, population connectivity, we found that vicariant events, climate fluctuations and marine currents have shaped the distribution of genetic diversity in strikingly similar ways.
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Affiliation(s)
- Ivania Cerón-Souza
- Smithsonian Tropical Research Institute Apartado, 0843-03092, Panama ; University of Puerto Rico - Rio Piedras Campus PO BOX 23360, San Juan, Puerto Rico, 00931-3360
| | - Elena G Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Andrea E Schwarzbach
- Department of Biomedicine, University of Texas One West University Blvd., Brownsville, Texas, 78520
| | - Dayana E Salas-Leiva
- Department of Biological Sciences, Florida International University Miami, Florida, 33199 ; USDA-ARS-SHRS, National Germplasm Repository Miami, Florida, 33158
| | - Elsie Rivera-Ocasio
- Department of Biology, University of Puerto Rico-Bayamon Parque Industrial Minillas Carr 174, Bayamón, Puerto Rico, 00959-1911
| | - Nelson Toro-Perea
- Departamento de Biología, Sección de Genética, Universidad del Valle AA 25360, Cali, Colombia
| | - Eldredge Bermingham
- Patricia and Phillip Frost Museum of Science, 3280 South Miami Avenue Miami, Florida
| | - W Owen McMillan
- Smithsonian Tropical Research Institute Apartado, 0843-03092, Panama
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11
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Meerow AW, Noblick L, Salas-Leiva DE, Sanchez V, Francisco-Ortega J, Jestrow B, Nakamura K. Phylogeny and historical biogeography of the cocosoid palms (Arecaceae, Arecoideae, Cocoseae) inferred from sequences of six WRKY gene family loci. Cladistics 2014; 31:509-534. [DOI: 10.1111/cla.12100] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Alan W. Meerow
- USDA-ARS-SHRS-National Germplasm Repository; 13601 Old Cutler Rd. Miami FL 33158 USA
| | - Larry Noblick
- Montgomery Botanical Center; 11901 Old Cutler Rd. Coral Gables FL 33156 USA
| | - Dayana E. Salas-Leiva
- USDA-ARS-SHRS-National Germplasm Repository; 13601 Old Cutler Rd. Miami FL 33158 USA
- Montgomery Botanical Center; 11901 Old Cutler Rd. Coral Gables FL 33156 USA
- Department of Biological Sciences; Florida International University; 11200 SW 8th St. Miami FL 33199 USA
| | - Vanessa Sanchez
- USDA-ARS-SHRS-National Germplasm Repository; 13601 Old Cutler Rd. Miami FL 33158 USA
| | - Javier Francisco-Ortega
- Department of Biological Sciences; Florida International University; 11200 SW 8th St. Miami FL 33199 USA
- Kushlan Tropical Science Institute; Fairchild Tropical Botanical Garden; 10901 Old Cutler Rd. Miami FL 33156 USA
| | - Brett Jestrow
- Kushlan Tropical Science Institute; Fairchild Tropical Botanical Garden; 10901 Old Cutler Rd. Miami FL 33156 USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS-National Germplasm Repository; 13601 Old Cutler Rd. Miami FL 33158 USA
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12
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Salas-Leiva DE, Meerow AW, Francisco-Ortega J, Calonje M, Griffith MP, Stevenson DW, Nakamura K. Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads. Mol Ecol Resour 2014; 14:831-45. [PMID: 24444413 DOI: 10.1111/1755-0998.12228] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 01/28/2023]
Abstract
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
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Affiliation(s)
- Dayana E Salas-Leiva
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA; USDA-ARS-SHRS, National Germplasm Repository, Miami, FL, 33158, USA; Montgomery Botanical Center, Miami, FL, 33156, USA
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13
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Salas-Leiva DE, Meerow AW, Calonje M, Griffith MP, Francisco-Ortega J, Nakamura K, Stevenson DW, Lewis CE, Namoff S. Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods. Ann Bot 2013; 112:1263-78. [PMID: 23997230 PMCID: PMC3806525 DOI: 10.1093/aob/mct192] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/15/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene tree-species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera. METHODS DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree-species tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted. KEY RESULTS Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (Macrozamia-Lepidozamia-Encephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia. CONCLUSIONS A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae.
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Affiliation(s)
- Dayana E. Salas-Leiva
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- USDA-ARS-SHRS, National Germplasm Repository, Miami, FL 33158, USA
| | - Alan W. Meerow
- USDA-ARS-SHRS, National Germplasm Repository, Miami, FL 33158, USA
| | - Michael Calonje
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Montgomery Botanical Center, Miami, FL 33156, USA
| | | | - Javier Francisco-Ortega
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Fairchild Tropical Botanic Garden, Coral Gables, FL 33156, USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS, National Germplasm Repository, Miami, FL 33158, USA
| | | | | | - Sandra Namoff
- Rancho Santa Ana Botanic Garden and Claremont Graduate University, Claremont, CA 91711, USA
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