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Patterson QM, Kraberger S, Martin DP, Shero MR, Beltran RS, Kirkham AL, Aleamotu'a M, Ainley DG, Kim S, Burns JM, Varsani A. Circoviruses and cycloviruses identified in Weddell seal fecal samples from McMurdo Sound, Antarctica. Infect Genet Evol 2021; 95:105070. [PMID: 34481994 DOI: 10.1016/j.meegid.2021.105070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/19/2022]
Abstract
Circoviridae is a family of circular single-stranded DNA viruses whose members infect a wide variety of hosts. While well characterized in avian and mammalian hosts, little is known about circoviruses associated with Antarctic animals. From 48 Weddell seal (Leptonychotes weddellii) fecal samples collected on the sea ice in McMurdo between Nov 2014 and Dec 2014, we identified and determined the genomes of novel viruses that fall within two genera of the family Circoviridae, i.e. Circovirus (n = 7) and Cyclovirus (n = 45). We named these viruses as werosea circovirus (WerCV) and werosea cyclovirus (WerCyV). The genomes of WerCV and WerCyV share ~63-64% genome-wide pairwise identity with classified circoviruses and cycloviruses, respectively. Based on the species demarcation threshold of 80% for members of the Circoviridae, the genomes of WerCV and WerCyV represent new species in their respective genera. Evidence indicated recombination in five of the 45 WerCyV genomes identified in this study. These are the first circoviruses found associated with Antarctic pinnipeds, adding to those recently identified associated with Adélie (Pygoscelis adeliae) and chinstrap penguins (P. antarcticus).
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Affiliation(s)
- Quinn M Patterson
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 7925, South Africa
| | - Michelle R Shero
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Roxanne S Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Amy L Kirkham
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK 99801, USA
| | - Maketalena Aleamotu'a
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | | | - Stacy Kim
- Moss Landing Marine Laboratories, Moss Landing, CA 95039, USA
| | - Jennifer M Burns
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925 Cape Town, South Africa.
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Fontenele RS, Roumagnac P, Richet C, Kraberger S, Stainton D, Aleamotu'a M, Filloux D, Bernardo P, Harkins GW, McCarthy J, Charles LS, Lamas NS, Abreu EFM, Abreu RA, Batista GB, Lacerda ALM, Salywon A, Wojciechowski MF, Majure LC, Martin DP, Ribeiro SG, Lefeuvre P, Varsani A. Diverse genomoviruses representing twenty-nine species identified associated with plants. Arch Virol 2020; 165:2891-2901. [PMID: 32893316 DOI: 10.1007/s00705-020-04801-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/09/2020] [Indexed: 02/06/2023]
Abstract
Genomoviruses (family Genomoviridae) are circular single-stranded DNA viruses that have been mainly identified through metagenomics studies in a wide variety of samples from various environments. Here, we describe 98 genomes of genomoviruses found associated with members of 19 plant families from Australia, Brazil, France, South Africa and the USA. These 98 genomoviruses represent 29 species, 26 of which are new, in the genera Gemykolovirus (n = 37), Gemyduguivirus (n = 9), Gemygorvirus (n = 8), Gemykroznavirus (n = 6), Gemycircularvirus (n = 21) and Gemykibivirus (n = 17).
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics and Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-5001, USA.,School of Life sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Philippe Roumagnac
- CIRAD, BGPI, 34398, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34398, Montpellier, France
| | - Cécile Richet
- CIRAD, BGPI, 34398, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34398, Montpellier, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics and Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, 72701, USA
| | - Maketalena Aleamotu'a
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Denis Filloux
- CIRAD, BGPI, 34398, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34398, Montpellier, France
| | - Pauline Bernardo
- CIRAD, BGPI, 34398, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, 34398, Montpellier, France.,Enza Zaden, Haling 1-E, 1602 DB, Enkhuizen, The Netherlands
| | - Gordon W Harkins
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - James McCarthy
- Manaaki Whenua, Landcare Research, Lincoln, 7640, New Zealand
| | - Lachlan S Charles
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Natalia S Lamas
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | | | - Rayane A Abreu
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.,PPG Ciências Naturais e Biotecnologia, Universidade Federal de Campina Grande, Cuité, PB, Brazil
| | - Graciete B Batista
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.,PPG Ciências Naturais e Biotecnologia, Universidade Federal de Campina Grande, Cuité, PB, Brazil
| | - Ana L M Lacerda
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | | | | | - Lucas C Majure
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 7925, South Africa
| | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.,PPG Ciências Naturais e Biotecnologia, Universidade Federal de Campina Grande, Cuité, PB, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics and Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-5001, USA. .,School of Life sciences, Arizona State University, Tempe, AZ, 85287-5001, USA. .,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7925, Cape Town, South Africa.
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Aleamotu'a M, McCurdy DW, Collings DA. Phi thickenings in roots: novel secondary wall structures responsive to biotic and abiotic stresses. J Exp Bot 2019; 70:4631-4642. [PMID: 31106830 DOI: 10.1093/jxb/erz240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 12/12/2018] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Phi thickenings are specialized secondary walls found in root cortical cells. Despite their widespread occurrence throughout the plant kingdom, these specialized thickenings remain poorly understood. First identified by Van Tieghem in 1871, phi thickenings are a lignified and thickened cell wall band that is deposited inside the primary wall, as a ring around the cells' radial walls. Phi thickenings can, however, display structural variations including a fine, reticulate network of wall thickenings extending laterally from the central lignified band. While phi thickenings have been proposed to mechanically strengthen roots, act as a permeability barrier to modulate solute movement, and regulate fungal interactions, these possibilities remain to be experimentally confirmed. Furthermore, since temporal and spatial development of phi thickenings varies widely between species, thickenings may perform diverse roles in different species. Phi thickenings can be induced by abiotic stresses in different species; they can, for example, be induced by heavy metals in the Zn/Cd hyperaccumulator Thlaspi caerulescens, and in a cultivar-specific manner by water stress in Brassica. This latter observation provides an experimental platform to probe phi thickening function, and to identify genetic pathways responsible for their formation. These pathways might be expected to differ from those involved in secondary wall formation in xylem, since phi thickening deposition in not linked to programmed cell death.
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Affiliation(s)
- Maketalena Aleamotu'a
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan NSW, Australia
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Aleamotu'a M, Tai YT, McCurdy DW, Collings DA. Developmental Biology and Induction of Phi Thickenings by Abiotic Stress in Roots of the Brassicaceae. Plants (Basel) 2018; 7:E47. [PMID: 29921823 PMCID: PMC6027303 DOI: 10.3390/plants7020047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/14/2018] [Accepted: 06/17/2018] [Indexed: 01/13/2023]
Abstract
Phi thickenings are specialized bands of secondary wall deposited around radial walls of root cortical cells. These structures have been reported in various species from the Brassicaceae, including Brassica oleracea, where previous reports using hydroponics indicated that they can be induced by exposure to salt. Using roots grown on agar plates, we show that both salt and sucrose can induce the formation of phi thickenings in a diverse range of species within the Brassicaceae. Within the genus Brassica, both B. oleracea and B. napus demonstrated the formation of phi thickenings, but in a strongly cultivar-specific manner. Confocal microscopy of phi thickenings showed that they form a complex network of reinforcement surrounding the inner root cortex, and that a delicate, reticulate network of secondary wall deposition can also variously form on the inner face of the cortical cell layer with phi thickenings adjacent to the endodermal layer. Results presented here indicate that phi thickenings can be induced in response to salt and water stress and that wide variation occurs in these responses even within the same species.
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Affiliation(s)
- Maketalena Aleamotu'a
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Yu-Ting Tai
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - David W McCurdy
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - David A Collings
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
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