1
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Mwakibete L, Greening SS, Kalantar K, Ahyong V, Anis E, Miller EA, Needle DB, Oglesbee M, Thomas WK, Sevigny JL, Gordon LM, Nemeth NM, Ogbunugafor CB, Ayala AJ, Faith SA, Neff N, Detweiler AM, Baillargeon T, Tanguay S, Simpson SD, Murphy LA, Ellis JC, Tato CM, Gagne RB. Metagenomics for Pathogen Detection During a Mass Mortality Event in Songbirds. J Wildl Dis 2024; 60:362-374. [PMID: 38345467 DOI: 10.7589/jwd-d-23-00109] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/02/2024] [Indexed: 04/06/2024]
Abstract
Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria forming the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes, including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events.
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Affiliation(s)
| | - Sabrina S Greening
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Eman Anis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Erica A Miller
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - David B Needle
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Michael Oglesbee
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lawrence M Gordon
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Nicole M Nemeth
- Southeastern Cooperative Wildlife Disease Study and Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Georgia 30602, USA
| | - C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Andrea J Ayala
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Seth A Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | | | - Tessa Baillargeon
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stacy Tanguay
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stephen D Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lisa A Murphy
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Julie C Ellis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Cristina M Tato
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Roderick B Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
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2
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Barrera S, Vázquez-Flores S, Needle D, Rodríguez-Medina N, Iglesias D, Sevigny JL, Gordon LM, Simpson S, Thomas WK, Rodulfo H, De Donato M. Serovars, Virulence and Antimicrobial Resistance Genes of Non-Typhoidal Salmonella Strains from Dairy Systems in Mexico. Antibiotics (Basel) 2023; 12:1662. [PMID: 38136696 PMCID: PMC10740734 DOI: 10.3390/antibiotics12121662] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023] Open
Abstract
Salmonella isolated from dairy farms has a significant effect on animal health and productivity. Different serogroups of Salmonella affect both human and bovine cattle causing illness in both reservoirs. Dairy cows and calves can be silent Salmonella shedders, increasing the possibility of dispensing Salmonella within the farm. The aim of this study was to determine the genomic characteristics of Salmonella isolates from dairy farms and to detect the presence of virulence and antimicrobial resistance genes. A total of 377 samples were collected in a cross-sectional study from calves, periparturient cow feces, and maternity beds in 55 dairy farms from the states of Aguascalientes, Baja California, Chihuahua, Coahuila, Durango, Mexico, Guanajuato, Hidalgo, Jalisco, Queretaro, San Luis Potosi, Tlaxcala, and Zacatecas. Twenty Salmonella isolates were selected as representative strains for whole genome sequencing. The serological classification of the strains was able to assign groups to only 12 isolates, but with only 5 of those being consistent with the genomic serotyping. The most prevalent serovar was Salmonella Montevideo followed by Salmonella Meleagridis. All isolates presented the chromosomal aac(6')-Iaa gene that confers resistance to aminoglycosides. The antibiotic resistance genes qnrB19, qnrA1, sul2, aph(6)-Id, aph(3)-ld, dfrA1, tetA, tetC, flor2, sul1_15, mph(A), aadA2, blaCARB, and qacE were identified. Ten pathogenicity islands were identified, and the most prevalent plasmid was Col(pHAD28). The main source of Salmonella enterica is the maternity areas, where periparturient shedders are contaminants and perpetuate the pathogen within the dairy in manure, sand, and concrete surfaces. This study demonstrated the necessity of implementing One Health control actions to diminish the prevalence of antimicrobial resistant and virulent pathogens including Salmonella.
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Affiliation(s)
- Stephany Barrera
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Sonia Vázquez-Flores
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - David Needle
- Veterinary Diagnostic Lab, University of New Hampshire, Durham, NH 03824, USA;
| | - Nadia Rodríguez-Medina
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca 62100, MR, Mexico;
| | - Dianella Iglesias
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Joseph L. Sevigny
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Lawrence M. Gordon
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Stephen Simpson
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - W. Kelley Thomas
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Hectorina Rodulfo
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Marcos De Donato
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
- The Center for Aquaculture Technologies, San Diego, CA 92121, USA
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3
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Peterson KL, Snyder JP, Despres HW, Schmidt MM, Eckstrom KM, Unger AL, Carmolli MP, Sevigny JL, Shirley DJ, Dragon JA, Thomas WK, Bruce EA, Crothers JW. Determining the impact of vaccination on SARS-CoV-2 RT-PCR cycle threshold values and infectious viral titres. Access Microbiol 2023; 5:000597.v3. [PMID: 37970082 PMCID: PMC10634488 DOI: 10.1099/acmi.0.000597.v3] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/27/2023] [Indexed: 11/17/2023] Open
Abstract
Background As the COVID-19 pandemic continues, efforts to better understand severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral shedding and transmission in both unvaccinated and vaccinated populations remain critical to informing public health policies and vaccine development. The utility of using real time RT-PCR cycle threshold values (CT values) as a proxy for infectious viral litres from individuals infected with SARS-CoV-2 is yet to be fully understood. This retrospective observational cohort study compares quantitative infectious viral litres derived from a focus-forming viral titre assay with SARS-CoV-2 RT-PCR CT values in both unvaccinated and vaccinated individuals infected with the Delta strain. Methods Nasopharyngeal swabs positive for SARS-CoV-2 by RT-PCR with a CT value <27 collected from 26 June to 17 October 2021 at the University of Vermont Medical Center Clinical Laboratory for which vaccination records were available were included. Partially vaccinated and individuals <18 years of age were excluded. Infectious viral litres were determined using a micro-focus forming assay under BSL-3 containment. Results In total, 119 specimens from 22 unvaccinated and 97 vaccinated individuals met all inclusion criteria and had sufficient residual volume to undergo viral titring. A negative correlation between RT-PCR CT values and viral litres was observed in both unvaccinated and vaccinated groups. No difference in mean CT value or viral titre was detected between vaccinated and unvaccinated groups. Viral litres did not change as a function of time since vaccination. Conclusions Our results add to the growing body of knowledge regarding the correlation of SARS-CoV-2 RNA levels and levels of infectious virus. At similar CT values, vaccination does not appear to impact an individual's potential infectivity when infected with the Delta variant.
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Affiliation(s)
- Katherine L. Peterson
- Department of Medicine, University of Vermont Medical Center, Burlington, VT, 05405, USA
| | - Julia P. Snyder
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Hannah W. Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Madaline M. Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Korin M. Eckstrom
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Allison L. Unger
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Marya P. Carmolli
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Joseph L. Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, 03824, USA
| | - David J. Shirley
- Faraday, Inc. Data Science Department, Burlington, VT, 05405, USA
| | - Julie A. Dragon
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, 03824, USA
| | - Emily A. Bruce
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
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4
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Digirolomo MF, Sevigny JL. A palearctic bark beetle, Crypturgus hispidulus Thomson (Coleoptera: Curculionidae: Scolytinae), new to North America discovered in New England, U.S.A. Zootaxa 2023; 5325:429-435. [PMID: 38220900 DOI: 10.11646/zootaxa.5325.3.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Indexed: 01/16/2024]
Abstract
Specimens of a bark beetle, Crypturgus hispidulus Thomson, 1870, were discovered in New England, U.S.A. This is the first record of this species established in North America. Misidentified specimen records were found from multiple states in different years, confirming establishment of the species in the Northeastern United States. The morphology is presented and a modified key to Crypturgus in North America is provided to facilitate species identification.
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Affiliation(s)
- Marc F Digirolomo
- USDA Forest Service; Forest Health Protection; Durham; New Hampshire; 03824; U.S.A..
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies; University of New Hampshire; 35 Colovos Rd; Gregg Hall; Durham; NH 03824; U.S.A..
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5
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Gendron EM, Sevigny JL, Byiringiro I, Thomas WK, Powers TO, Porazinska DL. Nematode mitochondrial metagenomics: A new tool for biodiversity analysis. Mol Ecol Resour 2023. [PMID: 36727264 DOI: 10.1111/1755-0998.13761] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/03/2023]
Abstract
DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.
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Affiliation(s)
- Eli M Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Innocent Byiringiro
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
| | - W Kelley Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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6
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Ennis NJ, Dharumadurai D, Sevigny JL, Wilmot R, Alnaimat SM, Bryce JG, Thomas WK, Tisa LS. Draft Genomes Sequences of 11 Geodermatophilaceae Strains Isolated from Building Stones from New England and Indian Stone Ruins found at historic sites in Tamil Nadu, India. J Genomics 2022; 10:69-77. [PMID: 36176899 PMCID: PMC9516006 DOI: 10.7150/jgen.76121] [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] [Received: 06/14/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Metagenomic analysis of stone microbiome from samples collected in New England, USA and Tamil Nadu, India identified numerous Actinobacteria including Geodermatphilaceae. A culture-dependent approach was performed as a companion study with this culture-independent metagenomic analysis of these stone samples and resulted in the isolation of eleven Geodermatphilaceae strains (2 Geodermatophilus and 9 Blastococcus strains). The genomes of the 11 Geodermatphilaceae strains were sequenced and analyzed. The genomes for the two Geodermatophilus isolates, DF1-2 and TF2-6, were 4.45 and 4.75 Mb, respectively, while the Blastococcus genomes ranged in size from 3.98 to 5.48 Mb. Phylogenetic analysis, digital DNA:DNA hybridization (dDDH), and comparisons of the average nucleotide identities (ANI) suggest the isolates represent novel Geodermatophilus and Blastococcus species. Functional analysis of the Geodermatphilaceae genomes provides insight on the stone microbiome niche.
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Affiliation(s)
- Nathaniel J Ennis
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Present address: Seres Therapeutics, Cambridge, MA, USA
| | - Dhanasekaran Dharumadurai
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Departments of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Joseph L Sevigny
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Ryan Wilmot
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Sulaiman M Alnaimat
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Present address: Department of Medical Analysis, Al-Hussein Bin Talal University, Ma'an, Jordan
| | - Julia G Bryce
- Department of Earth Sciences, University of New Hampshire, Durham, NH, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Louis S Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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7
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Abstract
Miniaturization, which is a common feature in animals, is particularly manifest in meiofauna-animals sharing peculiar phenotypic features that evolved as adaptations to the highly specialized aquatic interstitial habitat. While revealing much about the extreme phyletic diversity of meiofauna, the genome structure of meiofaunal species could also characterize the phenotype of ancestral states as well as explain the origin and evolution of miniaturization. Here, we present a practical bioinformatics tutorial for genome assembly, genome comparison, and characterization of Hox clusters in meiofaunal species.
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Affiliation(s)
- Joseph L Sevigny
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jon L Norenburg
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Francesca Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN, USA.
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8
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Sevigny JL, Norenburg JL, Leasi F. Correction to: A Bioinformatics Tutorial for Comparative Genomics of Meiofauna. Methods Mol Biol 2021; 2219:C1. [PMID: 33405046 DOI: 10.1007/978-1-0716-0974-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Joseph L Sevigny
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jon L Norenburg
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Francesca Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN, USA.
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9
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Steinbock B, Bechtold R, Sevigny JL, Thomas D, Thomas WK, Ghosh A. Draft Genome Sequences of 10 Bacterial Strains Isolated from an Abandoned Coal Mine in Southeast Kansas. Microbiol Resour Announc 2019; 8:e01001-19. [PMID: 31624170 PMCID: PMC6797535 DOI: 10.1128/mra.01001-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/25/2019] [Indexed: 11/20/2022] Open
Abstract
Here, we report 10 bacterial strains isolated from an abandoned coal mine in southeast Kansas to determine their potential for bioremediation through comparison of the genome sizes and distribution patterns of unique metabolic genes. The selected strains belong to the genera Arthrobacter, Jeotgalibacillus, Kocuria, Microbacterium, Pantoea, Rhodococcus, Vibrio, Brevibacterium, and Paenibacillus.
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Affiliation(s)
- Brady Steinbock
- Department of Biology, Pittsburg State University, Pittsburg, Kansas, USA
| | - Rachel Bechtold
- Department of Biology, Pittsburg State University, Pittsburg, Kansas, USA
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Devin Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Anuradha Ghosh
- Department of Biology, Pittsburg State University, Pittsburg, Kansas, USA
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10
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Louati M, Ennis NJ, Ghodhbane-Gtari F, Hezbri K, Sevigny JL, Fahnestock MF, Cherif-Silini H, Bryce JG, Tisa LS, Gtari M. Elucidating the ecological networks in stone-dwelling microbiomes. Environ Microbiol 2019; 22:1467-1480. [PMID: 31158316 DOI: 10.1111/1462-2920.14700] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 11/30/2022]
Abstract
Stone surfaces are extreme environments that support microbial life. This microbial growth occurs despite unfavourable conditions associated with stone including limited sources of nutrients and water, high pH and exposure to extreme variations in temperature, humidity and irradiation. These stone-dwelling microbes are often resistant to extreme environments including exposure to desiccation, heavy metals, UV and Gamma irradiation. Here, we report on the effects of climate and stone geochemistry on microbiomes of Roman stone ruins in North Africa. Stone microbiomes were dominated by Actinobacteria, Cyanobacteria and Proteobacteria but were heavily impacted by climate variables that influenced water availability. Stone geochemistry also influenced community diversity, particularly through biologically available P, Mn and Zn. Functions associated with photosynthesis and UV protection were enriched in the metagenomes, indicating the significance of these functions for community survival on stones. Core members of the stone microbial communities were also identified and included Geodermatophilaceae, Rubrobacter, Sphingomonas and others. Our research has helped to expand the understanding of stone microbial community structure and functional capacity within the context of varying climates, geochemical properties and stone conditions.
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Affiliation(s)
- Moussa Louati
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia
| | - Nathaniel J Ennis
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Faten Ghodhbane-Gtari
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia.,Laboratoire Microorganismeset Biomolécules Actives (LR03ES03), Faculté des Sciences de Tunis, Université Tunis El Manar, 2092, Tunis, Tunisia
| | - Karima Hezbri
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia
| | - Joseph L Sevigny
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Maria F Fahnestock
- Department of Earth Sciences, University of New Hampshire, Durham, NH, USA
| | - Hafsa Cherif-Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Julia G Bryce
- Department of Earth Sciences, University of New Hampshire, Durham, NH, USA
| | - Louis S Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Maher Gtari
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord, BP 676-1080, Tunis Cedex, Tunisia
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11
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Sevigny JL, Rothenheber D, Diaz KS, Zhang Y, Agustsson K, Bergeron RD, Thomas WK. Marker genes as predictors of shared genomic function. BMC Genomics 2019; 20:268. [PMID: 30947688 PMCID: PMC6449922 DOI: 10.1186/s12864-019-5641-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 07/12/2018] [Accepted: 03/24/2019] [Indexed: 12/15/2022] Open
Abstract
Background Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Here we utilize 4872 representative prokaryotic genomes from NCBI to investigate the relationship between marker gene identity and shared protein coding gene content. Results Even at 99–100% marker gene identity, genomes share on average less than 75% of their protein coding gene content. This occurs regardless of the marker gene(s) used: V4 region of the 16S rRNA, complete 16S rRNA, or single copy orthologs through a multi-locus sequence analysis. An important aspect related to this observation is the intra-organism variation of 16S copies from a single genome. Although the majority of 16S copies were found to have high sequence similarity (> 99%), several genomes contained copies that were highly diverged (< 97% identity). Conclusions This is the largest comparison between marker gene similarity and shared protein coding gene content to date. The study highlights the limitations of inferring a microbial community’s functions based on marker gene phylogeny. The data presented expands upon the results of previous studies that examined one or few bacterial species and supports the hypothesis that 16S rRNA and other marker genes cannot be directly used to fully predict the functional potential of a bacterial community. Electronic supplementary material The online version of this article (10.1186/s12864-019-5641-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA. .,Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Gregg Hall, Durham, NH, 03824, USA.
| | - Derek Rothenheber
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA
| | - Krystalle Sharlyn Diaz
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA.,Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Gregg Hall, Durham, NH, 03824, USA
| | - Ying Zhang
- Department of Computer Science, University of New Hampshire, 33 Academic Way, Kingsbury Hall, Durham, NH, 0324, USA
| | - Kristin Agustsson
- Department of Computer Science, University of New Hampshire, 33 Academic Way, Kingsbury Hall, Durham, NH, 0324, USA
| | - R Daniel Bergeron
- Department of Computer Science, University of New Hampshire, 33 Academic Way, Kingsbury Hall, Durham, NH, 0324, USA
| | - W Kelley Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA.,Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Gregg Hall, Durham, NH, 03824, USA
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12
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Leasi F, Sevigny JL, Laflamme EM, Artois T, Curini-Galletti M, de Jesus Navarrete A, Di Domenico M, Goetz F, Hall JA, Hochberg R, Jörger KM, Jondelius U, Todaro MA, Wirshing HH, Norenburg JL, Thomas WK. Erratum: Author Correction: Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach. Commun Biol 2018; 1:237. [PMID: 30588516 PMCID: PMC6301964 DOI: 10.1038/s42003-018-0249-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
[This corrects the article DOI: 10.1038/s42003-018-0119-2.].
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Affiliation(s)
- Francesca Leasi
- 1Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Avenue, 37403 Chattanooga, TN USA.,2Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, 03824 Durham, NH USA
| | - Joseph L Sevigny
- 2Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, 03824 Durham, NH USA
| | - Eric M Laflamme
- 3Department of Mathematics, Plymouth State University, MSC29, 17 High Street, 03264 Plymouth, NH USA
| | - Tom Artois
- 4Centre for Environmental Sciences, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Marco Curini-Galletti
- 5Dipartimento di Medicina Veterinaria, University of Sassari, via Muroni 25, 07100 Sassari, Italy
| | - Alberto de Jesus Navarrete
- Departmento de Sistemática y Ecología Acuática, El Colegio de la Frontera Sur, Unidad Chetumal, Av. Centenario Km. 5.5 Chetumal Quintana Roo, 77014 Chetumal, Mexico
| | - Maikon Di Domenico
- 7Centro de Estudos do Mar, Universidade Federal do Paraná, Av. Beira-Mar, s/n, Pontal do Sul, PO Box 61, 83255-976 Pontal do Paraná, PR Brazil
| | - Freya Goetz
- 8Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, 20560 Washington, DC, USA
| | - Jeffrey A Hall
- 2Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, 03824 Durham, NH USA
| | - Rick Hochberg
- 9Department of Biological Science, University of Massachusetts Lowell, Olsen Hall 414, 198 Riverside St., 01854 Lowell, MA USA
| | - Katharina M Jörger
- 10Department of Biology, Ludwig-Maximilians-University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Munich Germany
| | - Ulf Jondelius
- 11Swedish Museum of Natural History, POB 5007, SE-104 05 Stockholm, Sweden
| | - M Antonio Todaro
- 12Department of Life Sciences, University of Modena & Reggio Emilia, Via G. Campi 213/d, 41125 Modena, Italy
| | - Herman H Wirshing
- 8Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, 20560 Washington, DC, USA
| | - Jon L Norenburg
- 8Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, 20560 Washington, DC, USA
| | - W Kelley Thomas
- 2Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, 03824 Durham, NH USA
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13
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Sevigny JL, LaJoie J, Shehata S, Christensen E, Cornfield S, Koziol L. Whole-Genome Sequences of Two Pseudomonas fluorescens Strains Isolated from Roots of Tomato and Cucumber Plants. Microbiol Resour Announc 2018; 7:e00974-18. [PMID: 30533937 PMCID: PMC6256529 DOI: 10.1128/mra.00974-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/08/2018] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas fluorescens strain EC1 was isolated from Cucumis sativus (cucumber) roots, and P. fluorescens SC1 was isolated from Solanum lycopersicum (tomato) roots. The P. fluorescens SC1 genome has a total sequence length of 6,157,842 bp, and the P. fluorescens EC1 genome has a total sequence length of 6,125,428 bp.
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Affiliation(s)
- Joseph L. Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Jessica LaJoie
- Department of Biology, New England College, Henniker, New Hampshire, USA
| | - Shania Shehata
- Department of Biology, New England College, Henniker, New Hampshire, USA
| | - Elijah Christensen
- Department of Biology, New England College, Henniker, New Hampshire, USA
| | - Scott Cornfield
- Department of Biology, New England College, Henniker, New Hampshire, USA
| | - Lori Koziol
- Department of Biology, New England College, Henniker, New Hampshire, USA
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14
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Leasi F, Sevigny JL, Laflamme EM, Artois T, Curini-Galletti M, de Jesus Navarrete A, Di Domenico M, Goetz F, Hall JA, Hochberg R, Jörger KM, Jondelius U, Todaro MA, Wirshing HH, Norenburg JL, Thomas WK. Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach. Commun Biol 2018; 1:112. [PMID: 30271992 PMCID: PMC6123632 DOI: 10.1038/s42003-018-0119-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/24/2018] [Indexed: 01/05/2023] Open
Abstract
Accurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and time-effective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates.
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Affiliation(s)
- Francesca Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Avenue, Chattanooga, TN, 37403, USA.
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA.
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
| | - Eric M Laflamme
- Department of Mathematics, Plymouth State University, MSC29, 17 High Street, Plymouth, NH, 03264, USA
| | - Tom Artois
- Centre for Environmental Sciences, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium
| | - Marco Curini-Galletti
- Dipartimento di Medicina Veterinaria, University of Sassari, via Muroni 25, 07100, Sassari, Italy
| | - Alberto de Jesus Navarrete
- Departmento de Sistemática y Ecología Acuática, El Colegio de la Frontera Sur, Unidad Chetumal, Av. Centenario Km. 5.5 Chetumal Quintana Roo, 77014, Chetumal, Mexico
| | - Maikon Di Domenico
- Centro de Estudos do Mar, Universidade Federal do Paraná, Av. Beira-Mar, s/n, Pontal do Sul, PO Box 61, 83255-976, Pontal do Paraná, PR, Brazil
| | - Freya Goetz
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - Jeffrey A Hall
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
| | - Rick Hochberg
- Department of Biological Science, University of Massachusetts Lowell, Olsen Hall 414, 198 Riverside St., Lowell, MA, 01854, USA
| | - Katharina M Jörger
- Department of Biology, Ludwig-Maximilians-University of Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Munich, Germany
| | - Ulf Jondelius
- Swedish Museum of Natural History, POB 5007, SE-104 05, Stockholm, Sweden
| | - M Antonio Todaro
- Department of Life Sciences, University of Modena & Reggio Emilia, Via G. Campi 213/d, 41125, Modena, Italy
| | - Herman H Wirshing
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - Jon L Norenburg
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave NW, Washington, DC, 20560, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
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15
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Sevigny JL, Kirouac LE, Thomas WK, Ramsdell JS, Lawlor KE, Sharifi O, Grewal S, Baysdorfer C, Curr K, Naimie AA, Okamoto K, Murray JA, Newcomb JM. The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny. PLoS One 2015; 10:e0127519. [PMID: 25996944 PMCID: PMC4440745 DOI: 10.1371/journal.pone.0127519] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 01/28/2015] [Accepted: 04/15/2015] [Indexed: 01/28/2023] Open
Abstract
The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group.
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Affiliation(s)
- Joseph L. Sevigny
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Lauren E. Kirouac
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - William Kelley Thomas
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Jordan S. Ramsdell
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Kayla E. Lawlor
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Osman Sharifi
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Simarvir Grewal
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Christopher Baysdorfer
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Kenneth Curr
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Amanda A. Naimie
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Kazufusa Okamoto
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - James A. Murray
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - James M. Newcomb
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
- * E-mail:
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