1
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Kobayashi G, Abe H. Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing. Mol Biol Rep 2024; 51:887. [PMID: 39105821 DOI: 10.1007/s11033-024-09811-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND The marine environment harbors high biodiversity; however, it is poorly understood. Nucleotide sequence data of all marine organisms should be accumulated before natural and/or anthropogenic environmental changes jeopardize the marine environment. In this study, we report a cost-effective and easy DNA barcoding method. This method can be readily adopted without using library preparation kits. It includes multiplex PCR of short targets, indexing PCR, and outsourcing to a sequencing service using the NovaSeq system. METHODS AND RESULTS We targeted four mitochondrial genes [cytochrome c oxidase subunit I (COI), COIII, 16S rRNA (16S), and 12S rRNA (12S)] and three nuclear genes [18S rRNA (18S), 28S rRNA (28S), internal transcribed spacer 2 (ITS2)] in 95 marine invertebrate specimens, which were primarily annelids. The primers, including adapters and indices for NovaSeq sequencing, were newly designed. Two PCR runs were conducted. The 1st PCR amplified specific loci with universal primers and the 2nd added sequencing adapters and indices to the 1st PCR products. The gene sequences obtained from the FASTQ files were subjected to BLAST search and phylogenetic analyses. One run using 95 specimens yielded sequences averaging 2816 bp per specimen for a total length of six loci. Nuclear genes were more successfully assembled compared with mitochondrial genes. A weak but significantly negative correlation was observed between the average length of each locus and success rate of the assembly. Some of the sequences were almost identical to the sequences obtained from specimens collected far from Japan, indicating the presence of potentially invasive species identified for the first time. CONCLUSIONS We obtained gene sequences efficiently using next-generation sequencing rather than Sanger sequencing. Although this method requires further optimization to increase the success rate for some loci, it is used as a first step to select specimens for further analyses by determining the specific loci of the targets.
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Affiliation(s)
- Genki Kobayashi
- Research Center for Creative Partnerships, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan.
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan.
| | - Hirokazu Abe
- Faculty of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
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2
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Kurata S, Mano S, Nakahama N, Hirota SK, Suyama Y, Ito M. Development of mitochondrial DNA cytochrome c oxidase subunit I primer sets to construct DNA barcoding library using next-generation sequencing. Biodivers Data J 2024; 12:e117014. [PMID: 38933488 PMCID: PMC11199957 DOI: 10.3897/bdj.12.e117014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.
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Affiliation(s)
- Seikan Kurata
- Tomakomai Experimental Forest, Hokkaido University, Tomakomai, JapanTomakomai Experimental Forest, Hokkaido UniversityTomakomaiJapan
| | - Shota Mano
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, JapanFaculty of Bioresource Sciences, Akita Prefectural UniversityAkitaJapan
| | - Naoyuki Nakahama
- Institute of Natural and Environmental Sciences, University of Hyogo, hyogo, JapanInstitute of Natural and Environmental Sciences, University of HyogohyogoJapan
| | - Shun K Hirota
- Botanical Gardens, Osaka Metropolitan University, Osaka, JapanBotanical Gardens, Osaka Metropolitan UniversityOsakaJapan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, JapanGraduate School of Agricultural Science, Tohoku UniversityMiyagiJapan
| | - Motomi Ito
- Komaba museum, University of Tokyo, Tokyo, JapanKomaba museum, University of TokyoTokyoJapan
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3
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Iqbal Z, Azad R, Chen XS, Lin XL, Zhou Z, Wang XM, Nie RE. A New Species of Scymnus (Coleoptera, Coccinellidae) from Pakistan with Mitochondrial Genome and Its Phylogenetic Implications. INSECTS 2024; 15:371. [PMID: 38786927 PMCID: PMC11122443 DOI: 10.3390/insects15050371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
In this study, a new species of the subgenus Pullus belonging to the Scymnus genus from Pakistan, Scymnus (Pullus) cardi sp. nov., was described and illustrated, with information on its distribution, host plants, and prey. Additionally, the completed mitochondrial genome (mitogenome) of the new species using high-throughput sequencing technology was obtained. The genome contains the typical 37 genes (13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs) and a non-coding control region, and is arranged in the same order as that of the putative ancestor of beetles. The AT content of the mitogenome is approximately 85.1%, with AT skew and GC skew of 0.05 and -0.43, respectively. The calculated values of relative synonymous codon usage (RSCU) determine that the codon UUA (L) has the highest frequency. Furthermore, we explored the phylogenetic relationship among 59 representatives of the Coccinellidae using Bayesian inference and maximum likelihood methods, the results of which strongly support the monophyly of Coccinellinae. The phylogenetic results positioned Scymnus (Pullus) cardi in a well-supported clade with Scymnus (Pullus) loewii and Scymnus (Pullus) rubricaudus within the genus Scymnus and the tribe Scymnini. The mitochondrial sequence of S. (P.) cardi will contribute to the mitochondrial genome database and provide helpful information for the identification and phylogeny of Coccinellidae.
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Affiliation(s)
- Zafar Iqbal
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
| | - Rashid Azad
- Department of Entomology, The University of Haripur, Haripur 22620, Pakistan;
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China
| | - Xiao-Sheng Chen
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, China;
- Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Ling Lin
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
| | - Zichen Zhou
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2BX, UK;
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Xing-Min Wang
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China
- Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, Guangzhou 510640, China
| | - Rui-E Nie
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
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4
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Ferreira S, Corley MFV, Nunes J, Rosete J, Vasconcelos S, Mata VA, Veríssimo J, Silva TL, Sousa P, Andrade R, Grosso-Silva JM, Pinho CJ, Chaves C, Martins FMS, Pinto J, Puppo P, Muñoz-Mérida A, Archer J, Pauperio J, Beja P. The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths. Biodivers Data J 2024; 12:e117169. [PMID: 38903959 PMCID: PMC11188589 DOI: 10.3897/bdj.12.e117169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/19/2024] [Indexed: 06/22/2024] Open
Abstract
Background The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens of moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All specimens have been morphologically identified to species or subspecies level and represent 1158 species in total. The species of this dataset correspond to about 42% of mainland Portuguese Lepidoptera species. All specimens were collected in mainland Portugal between 2001 and 2022. All DNA extracts and over 96% of the specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. New information The authors enabled "The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths" in order to release the majority of data of DNA barcodes of Portuguese moths within the InBIO Barcoding Initiative. This dataset increases the knowledge on the DNA barcodes of 1158 species from Portugal belonging to 51 families. There is an increase in DNA barcodes of 205% in Portuguese specimens publicly available. The dataset includes 61 new Barcode Index Numbers. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF).
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Affiliation(s)
- Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões,
Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
| | - Martin F. V. Corley
- Pucketty Farm Cottage, Faringdon, Oxfordshire SN7 8JP,
U.K, Oxfordshire, United KingdomPucketty Farm Cottage, Faringdon, Oxfordshire SN7 8JP, U.KOxfordshireUnited Kingdom
| | - João Nunes
- Rua Eduardo Joaquim Reis Figueira, 1104 RC AR, 4440-647,
Valongo, PortugalRua Eduardo Joaquim Reis Figueira, 1104 RC AR, 4440-647ValongoPortugal
| | - Jorge Rosete
- Urbanização Lourisol, Rua Manuel Cerqueira Nobrega, Lote
16, 2. frente, P-3105-165 Louriçal, Pombal, PortugalUrbanização Lourisol, Rua Manuel Cerqueira Nobrega, Lote 16, 2. frente,
P-3105-165 LouriçalPombalPortugal
| | - Sasha Vasconcelos
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia,
Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Instituto Superior de Agronomia, Universidade de
LisboaLisboaPortugal
- Department of Ecology, Swedish University of Agricultural
Sciences, PO Box 7044, 750 07, Uppsala, SwedenDepartment of Ecology, Swedish University of Agricultural Sciences, PO Box
7044, 750 07UppsalaSweden
| | - Vanessa A. Mata
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências,
Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto,
4169-007PortoPortugal
| | - Teresa L Silva
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Pedro Sousa
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- International Union for Conservation of Nature (IUCN),
Species Survival Commission (SSC), Spider and Scorpion Specialist Group, Gland,
SwitzerlandInternational Union for Conservation of Nature (IUCN), Species Survival
Commission (SSC), Spider and Scorpion Specialist GroupGlandSwitzerland
| | - Rui Andrade
- Rua Calouste Gulbenkian 237 4H3, 4050-145, Porto,
PortugalRua Calouste Gulbenkian 237 4H3, 4050-145PortoPortugal
| | - José Manuel Grosso-Silva
- Museu de História Natural e da Ciência da Universidade do
Porto, Porto, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Catarina J. Pinho
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências,
Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto,
4169-007PortoPortugal
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Filipa MS Martins
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Pamela Puppo
- Marshall University, Department of Biological Sciences,
Huntington, West Virginia, United States of AmericaMarshall University, Department of Biological SciencesHuntington, West VirginiaUnited States of America
| | - Antonio Muñoz-Mérida
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - John Archer
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
| | - Joana Pauperio
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto,,
4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairão, Universidade do Porto,4485–661 Vairão, Vila do CondePortugal
- European Molecular Biology Laboratory, European
Bioinformatics Institute, Hinxton, Cambridge, United KingdomEuropean Molecular Biology Laboratory, European Bioinformatics
InstituteHinxton, CambridgeUnited Kingdom
| | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto,
4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661
VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land
Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de
Vairao, 4485-661 VairaoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e
Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia,
Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO
Laboratório Associado, Instituto Superior de Agronomia, Universidade de
LisboaLisboaPortugal
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5
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Pina S, Pauperio J, Barros F, Chaves C, Martins FMS, Pinto J, Veríssimo J, Mata VA, Beja P, Ferreira S. The InBIO Barcoding Initiative Database: DNA barcodes of Orthoptera from Portugal. Biodivers Data J 2024; 12:e118010. [PMID: 38784157 PMCID: PMC11112160 DOI: 10.3897/bdj.12.e118010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/24/2024] [Indexed: 05/25/2024] Open
Abstract
Background The InBIO Barcoding Initiative (IBI) Orthoptera dataset contains records of 420 specimens covering all the eleven Orthoptera families occurring in Portugal. Specimens were collected in continental Portugal from 2005 to 2021 and were morphologically identified to species level by taxonomists. A total of 119 species were identified corresponding to about 77% of all the orthopteran species known from continental Portugal. New information DNA barcodes of 54 taxa were made public for the first time at the Barcode of Life Data System (BOLD). Furthermore, the submitted sequences were found to cluster in 129 BINs (Barcode Index Numbers), 35 of which were new additions to the Barcode of Life Data System (BOLD). All specimens have their DNA barcodes publicly accessible through BOLD online database. Stenobothruslineatus is recorded for the first time for continental Portugal. This dataset greatly increases the knowledge on the DNA barcodes and distribution of Orthoptera from Portugal. All DNA extractions and most specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.
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Affiliation(s)
- Sílvia Pina
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Joana Pauperio
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United KingdomEuropean Molecular Biology Laboratory, European Bioinformatics InstituteWellcome Genome Campus, Hinxton, CambridgeUnited Kingdom
| | - Francisco Barros
- Rua da Eira 3, S. Salvador, 2550-251, Cercal, PortugalRua da Eira 3, S. Salvador, 2550-251CercalPortugal
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 VairãoVila do CondePortugal
| | - Filipa MS Martins
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 VairãoVila do CondePortugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 VairãoVila do CondePortugal
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 VairãoVila do CondePortugal
| | - Vanessa A Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 VairãoVila do CondePortugal
| | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485–661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 VairãoVila do CondePortugal
- EBM, Estação Biológica de Mertola, Praça Luis de Camoes, Mertola, Mertola, PortugalEBM, Estação Biológica de Mertola, Praça Luis de Camoes, MertolaMertolaPortugal
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6
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Shon J, Han Y, Song S, Kwon SY, Na K, Lindroth AM, Park YJ. Anti-obesity effect of butyrate links to modulation of gut microbiome and epigenetic regulation of muscular circadian clock. J Nutr Biochem 2024; 127:109590. [PMID: 38311045 DOI: 10.1016/j.jnutbio.2024.109590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/31/2023] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
The role of the muscle circadian clock in regulating oxidative metabolism exerts a significant influence on whole-body energy metabolism; however, research on the connection between the muscle circadian clock and obesity is limited. Moreover, there is a lack of studies demonstrating the regulatory effects of dietary butyrate on muscle circadian clock and the resulting antiobesity effects. This study aimed to investigate the impacts of dietary butyrate on metabolic and microbiome alterations and muscle circadian clock in a diet-induced obesity model. Male Sprague-Dawley rats were fed a high-fat diet with or without butyrate. Gut microbiota and serum metabolome were analyzed, and molecular changes were examined using tissues and a cell line. Further correlation analysis was performed on butyrate-induced results. Butyrate supplementation reduced weight gain, even with increased food intake. Gut microbiome analysis revealed an increased abundance of Firmicutes in butyrate group. Serum metabolite profile in butyrate group exhibited reduced amino acid and increased fatty acid content. Muscle circadian clock genes were upregulated, resulting in increased transcription of fatty acid oxidation-related genes. In myoblast cells, butyrate also enhanced pan-histone acetylation via histone deacetylase inhibition, particularly modulating acetylation at the promoter of circadian clock genes. Correlation analysis revealed potential links between Firmicutes phylum, including certain genera within it, and butyrate-induced molecular changes in muscle as well as phenotypic alterations. The butyrate-driven effects on diet-induced obesity were associated with alterations in gut microbiota and a muscle-specific increase in histone acetylation, leading to the transcriptional activation of circadian clock genes and their controlled genes.
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Affiliation(s)
- Jinyoung Shon
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03670, Republic of Korea; Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03670, Republic of Korea
| | - Yerim Han
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03670, Republic of Korea; Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03670, Republic of Korea
| | - Seungmin Song
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03670, Republic of Korea; Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03670, Republic of Korea
| | - So Young Kwon
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03670, Republic of Korea; Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03670, Republic of Korea
| | - Khuhee Na
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03670, Republic of Korea; Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03670, Republic of Korea
| | - Anders M Lindroth
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si 10408, Republic of Korea
| | - Yoon Jung Park
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03670, Republic of Korea; Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03670, Republic of Korea.
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7
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Han S, An X, He X, Ren X, Sichone J, Wu X, Zhang Y, Wang H, Sun F. Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering. Microorganisms 2024; 12:858. [PMID: 38792687 PMCID: PMC11124218 DOI: 10.3390/microorganisms12050858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.
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Affiliation(s)
- Shuaibo Han
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaojiao An
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xiaolong He
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xin Ren
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - John Sichone
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xinxing Wu
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Zhang
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Hui Wang
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Fangli Sun
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
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8
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Pertegal C, Barranco P, De Mas E, Moya-Laraño J. More Than 200 Years Later: Gluvia brunnea sp. nov. (Solifugae, Daesiidae), a Second Species of Camel Spider from the Iberian Peninsula. INSECTS 2024; 15:284. [PMID: 38667414 PMCID: PMC11050627 DOI: 10.3390/insects15040284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/01/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
We present the description of a new species of Solifugae from the Iberian Peninsula, Gluvia brunnea sp. nov., which has been found so far in southeast Spain. The morphological description is accompanied by molecular and multiple factor analyses, jointly giving full support to the specific status of the taxon. Finally, we discuss the intraspecific variability of both species, G. dorsalis and G. brunnea sp. nov., and the recent history of the genus. We also discuss the usefulness of multiple factor analysis for quantitatively separating species, and we stress that some specimens of this new species were found in Mesovoid Shallow Substratum stations, representing the very first time that Solifugae have been captured in this type of trap.
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Affiliation(s)
- Cristian Pertegal
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, (EEZA-CSIC) Ctra. de Sacramento s/n, La Cañada de San Urbano, 04120 Almería, Spain; (E.D.M.); (J.M.-L.)
- Departamento de Zoología, Universidad de Córdoba, Edificio C-1, Campus de Rabanales, 14071 Córdoba, Spain
| | - Pablo Barranco
- Departamento de Biología y Geología, CITE-IIB, Centro de Colecciones, CECOUAL, Universidad de Almería, Ctra. Sacramento, s/n, La Cañada, 04120 Almería, Spain;
| | - Eva De Mas
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, (EEZA-CSIC) Ctra. de Sacramento s/n, La Cañada de San Urbano, 04120 Almería, Spain; (E.D.M.); (J.M.-L.)
| | - Jordi Moya-Laraño
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, (EEZA-CSIC) Ctra. de Sacramento s/n, La Cañada de San Urbano, 04120 Almería, Spain; (E.D.M.); (J.M.-L.)
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9
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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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10
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Soh M, Tay YC, Lee CS, Low A, Orban L, Jaafar Z, Seedorf H. The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota. NPJ Biofilms Microbiomes 2024; 10:11. [PMID: 38374184 PMCID: PMC10876542 DOI: 10.1038/s41522-024-00484-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Studying the gut microbes of marine fishes is an important part of conservation as many fish species are increasingly threatened by extinction. The gut microbiota of only a small fraction of the more than 32,000 known fish species has been investigated. In this study we analysed the intestinal digesta microbiota composition of more than 50 different wild fish species from tropical waters. Our results show that the fish harbour intestinal digesta microbiota that are distinct from that of the surrounding water and that location, domestication status, and host intrinsic factors are strongly associated with the microbiota composition. Furthermore, we show that the vast majority (~97%) of the fish-associated microorganisms do not have any cultured representative. Considering the impact of the microbiota on host health and physiology, these findings underpin the call to also preserve the microbiota of host species, especially those that may be exposed to habitat destruction.
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Affiliation(s)
- Melissa Soh
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Ywee Chieh Tay
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Co Sin Lee
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Adrian Low
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6-Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore
| | - Laszlo Orban
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, 8360, Hungary
| | - Zeehan Jaafar
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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11
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Harl J, Fauchois A, Puech MP, Gey D, Ariey F, Izac B, Weissenböck H, Chakarov N, Iezhova T, Valkiūnas G, Duval L. Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species. Parasite 2024; 31:5. [PMID: 38334685 PMCID: PMC10854483 DOI: 10.1051/parasite/2023066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/18/2023] [Indexed: 02/10/2024] Open
Abstract
Avian haemosporidian parasites (order Haemosporida, phylum Apicomplexa) are blood and tissue parasites transmitted by blood-sucking dipteran insects. Three genera (Plasmodium, Haemoproteus and Leucocytozoon) have been most often found in birds, with over 270 species described and named in avian hosts based mainly on the morphological characters of blood stages. A broad diversity of Haemoproteus parasites remains to be identified and characterized morphologically and molecularly, especially those infecting birds of prey, an underrepresented bird group in haemosporidian parasite studies. The aim of this study was to investigate and identify Haemoproteus parasites from a large sample comprising accipitriform raptors of 16 species combining morphological and new molecular protocols targeting the cytb genes of this parasite group. This study provides morphological descriptions and molecular characterizations of two Haemoproteus species, H. multivacuolatus n. sp. and H. nisi Peirce and Marquiss, 1983. Haemoproteus parasites of this group were so far found in accipitriform raptors only and might be classified into a separate subgenus or even genus. Cytb sequences of these parasites diverge by more than 15% from those of all others known avian haemosporidian genera and form a unique phylogenetic clade. This study underlines the importance of developing new diagnostic tools to detect molecularly highly divergent parasites that might be undetectable by commonly used conventional tools.
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Affiliation(s)
- Josef Harl
- Institute of Pathology, Department of Pathobiology, University of Veterinary Medicine Vienna Veterinaerplatz 1 1210 Vienna Austria
| | - Anaïs Fauchois
- Département Adaptations du Vivant (AVIV), Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Muséum National d’Histoire Naturelle, CNRS, CP 52 57 rue Cuvier 75231 Cedex 05 Paris France
| | - Marie-Pierre Puech
- Hôpital de la faune sauvage des Garrigues et Cévennes – Goupil Connexion 34190 Brissac France
| | - Delphine Gey
- Département Adaptations du Vivant (AVIV), Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Muséum National d’Histoire Naturelle, CNRS, CP 52 57 rue Cuvier 75231 Cedex 05 Paris France
| | - Frédéric Ariey
- Université de Paris, INSERM 1016, Institut Cochin, Service de Parasitologie-Mycologie Hôpital Cochin Paris France
| | - Brigitte Izac
- Université de Paris, INSERM 1016, Institut Cochin, Service de Parasitologie-Mycologie Hôpital Cochin Paris France
| | - Herbert Weissenböck
- Institute of Pathology, Department of Pathobiology, University of Veterinary Medicine Vienna Veterinaerplatz 1 1210 Vienna Austria
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University Konsequenz 45 33615 Bielefeld Germany
| | | | | | - Linda Duval
- Département Adaptations du Vivant (AVIV), Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Muséum National d’Histoire Naturelle, CNRS, CP 52 57 rue Cuvier 75231 Cedex 05 Paris France
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12
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Srivathsan A, Meier R. Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing. Methods Mol Biol 2024; 2744:223-238. [PMID: 38683322 DOI: 10.1007/978-1-0716-3581-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA barcodes are useful in biodiversity research, but sequencing barcodes with dye termination methods ("Sanger sequencing") has been so time-consuming and expensive that DNA barcodes are not as widely used as they should be. Fortunately, MinION sequencers from Oxford Nanopore Technologies have recently emerged as a cost-effective and efficient alternative for barcoding. MinION barcodes are now suitable for large-scale species discovery and enable specimen identification when the target species are represented in barcode databases. With a MinION, it is possible to obtain 10,000 barcodes from a single flow cell at a cost of less than 0.10 USD per specimen. Additionally, a Flongle flow cell can be used for small projects requiring up to 300 barcodes (0.50 USD per specimen). We here describe a cost-effective laboratory workflow for obtaining tagged amplicons, preparing ONT libraries, sequencing amplicon pools, and analyzing the MinION reads with the software ONTbarcoder. This workflow has been shown to yield highly accurate barcodes that are 99.99% identical to Sanger barcodes. Overall, we propose that the use of MinION for DNA barcoding is an attractive option for all researchers in need of a cost-effective and efficient solution for large-scale species discovery and specimen identification.
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Affiliation(s)
- Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.
- Institute for Biology, Humboldt University, Berlin, Germany.
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13
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Noguerales V, Meramveliotakis E, Castro-Insua A, Andújar C, Arribas P, Creedy TJ, Overcast I, Morlon H, Emerson BC, Vogler AP, Papadopoulou A. Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests. Mol Ecol 2023; 32:6110-6128. [PMID: 34775647 DOI: 10.1111/mec.16275] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 01/04/2023]
Abstract
Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical data sets are required to account for taxon- and context-dependency, but relevant research in understudied areas is often compromised by the taxonomic impediment. Here we used haplotype-level community DNA metabarcoding, enabled by stringent filtering of amplicon sequence variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, operational taxonomic unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented Quercus alnifolia habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterizing metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.
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Affiliation(s)
- Víctor Noguerales
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | | | | | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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14
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Arjona Y, Arribas P, Salces-Castellano A, López H, Emerson BC, Andújar C. Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest. Mol Ecol 2023; 32:6130-6146. [PMID: 36197789 DOI: 10.1111/mec.16716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 11/28/2022]
Abstract
Soils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromise the reliability of biodiversity inventories. Here, we explore the potential of a bioinformatic approach to jointly "denoise" and filter nonauthentic mitochondrial sequences from metabarcode reads to obtain reliable soil beetle inventories and address open questions in soil biodiversity research, such as the scale of dispersal constraints in different soil layers. We sampled cloud forest arthropod communities from 49 sites in the Anaga peninsula of Tenerife (Canary Islands). We performed whole organism community DNA (wocDNA) metabarcoding, and built a local reference database with COI barcode sequences of 310 species of Coleoptera for filtering reads and the identification of metabarcoded species. This resulted in reliable haplotype data after considerably reducing nuclear mitochondrial copies and other artefacts. Comparing our results with previous beetle inventories, we found: (i) new species records, potentially representing undescribed species; (ii) new distribution records, and (iii) validated phylogeographic structure when compared with traditional sequencing approaches. Analyses also revealed evidence for higher dispersal constraint within deeper soil beetle communities, compared to those closer to the surface. The combined power of barcoding and metabarcoding contribute to mitigate the important shortfalls associated with soil arthropod diversity data, and thus address unresolved questions for this vast biodiversity fraction.
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Affiliation(s)
- Yurena Arjona
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Antonia Salces-Castellano
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
- Department of Biology, Ecology and Evolution, University of Liege, Liege, Belgium
| | - Heriberto López
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
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15
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Melo M, Covas R, de Lima RF, Veiga da Horta O, do Bom Jesus C, Barros da Veiga M, Samba S, Fonseca R, Cabinda G, Viegas L, Silva TL, Mata VA, Beja P, Ferreira S. DNA Barcode library of the endemic-rich avifauna of the oceanic islands of the Gulf of Guinea. Biodivers Data J 2023; 11:e110428. [PMID: 37915315 PMCID: PMC10616780 DOI: 10.3897/bdj.11.e110428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
Background The BioSTP: DNA Barcoding of endemic birds from oceanic islands of the Gulf of Guinea dataset contains records of 155 bird specimens belonging to 56 species in 23 families, representing over 80% of the diversity of the breeding landbird community. All specimens were collected on Príncipe, São Tomé and Annobón Islands between 2002 and 2021 and morphologically identified to species or subspecies level by qualified ornithologists. The dataset includes all endemic species and 3/4 of the extant endemic subspecies of the islands. This dataset is the second release by BioSTP and it greatly increases the knowledge on the DNA barcodes of Gulf of Guinea birds. All DNA extractions are deposited at Associação BIOPOLIS - CIBIO, Research Center in Biodiversity and Genetic Resources. New information The dataset includes DNA barcodes for all 29 endemic bird species and for 11 of the 15 extant endemic bird subspecies from the oceanic islands of the Gulf of Guinea. This is the first major DNA barcode set of African birds. The three endemic subspecies of Crithagrarufobrunnea, an island endemic with three allopatric populations within the Archipelago, are also represented. Additionally, we obtained DNA barcodes for 16 of the 21 non-endemic landbirds and for one vagrant (Sylviacommunis). In total, forty-one taxa were new additions to the Barcode of Life Data System (BOLD), with another 11 corresponding to under-represented taxa in BOLD. Furthermore, the submitted sequences were found to cluster in 55 Barcode Index Numbers (BINs), 37 of which were new to BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and GenBank.
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Affiliation(s)
- Martim Melo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 VairaoVila do CondePortugal
- MHNC-UP, Museu de História Natural e da Ciência da Universidade do Porto, Porto, PortugalMHNC-UP, Museu de História Natural e da Ciência da Universidade do PortoPortoPortugal
- DST/NRF Centre of Excellence, FitzPatrick Institute, University of Cape Town, Rondebosch, South AfricaDST/NRF Centre of Excellence, FitzPatrick Institute, University of Cape TownRondeboschSouth Africa
| | - Rita Covas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 VairaoVila do CondePortugal
- DST/NRF Centre of Excellence, FitzPatrick Institute, University of Cape Town, Rondebosch, South AfricaDST/NRF Centre of Excellence, FitzPatrick Institute, University of Cape TownRondeboschSouth Africa
| | - Ricardo Faustino de Lima
- Gulf of Guinea Biodiversity Centre, São Tomé, São Tomé and PríncipeGulf of Guinea Biodiversity CentreSão ToméSão Tomé and Príncipe
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisboa, PortugalCentre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de LisboaLisboaPortugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, PortugalDepartamento de Biologia Animal, Faculdade de Ciências, Universidade de LisboaLisboaPortugal
- CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, PortugalCHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de LisboaLisboaPortugal
| | - Octávio Veiga da Horta
- Associação Monte Pico, Monte Café, São Tomé, São Tomé and PríncipeAssociação Monte Pico, Monte CaféSão ToméSão Tomé and Príncipe
| | - Ceciliano do Bom Jesus
- Parque Natural do Obô – Príncipe, Porto Real, Príncipe, São Tomé and PríncipeParque Natural do Obô – Príncipe, Porto RealPríncipeSão Tomé and Príncipe
| | - Martim Barros da Veiga
- Associação Monte Pico, Monte Café, São Tomé, São Tomé and PríncipeAssociação Monte Pico, Monte CaféSão ToméSão Tomé and Príncipe
| | - Seduney Samba
- Associação Monte Pico, Monte Café, São Tomé, São Tomé and PríncipeAssociação Monte Pico, Monte CaféSão ToméSão Tomé and Príncipe
| | - Ricardo Fonseca
- Associação Monte Pico, Monte Café, São Tomé, São Tomé and PríncipeAssociação Monte Pico, Monte CaféSão ToméSão Tomé and Príncipe
| | - Gabriel Cabinda
- Associação Monte Pico, Monte Café, São Tomé, São Tomé and PríncipeAssociação Monte Pico, Monte CaféSão ToméSão Tomé and Príncipe
| | - Lionel Viegas
- Parque Nacional do Obô - São Tomé, São Tomé, São Tomé and PríncipeParque Nacional do Obô - São ToméSão ToméSão Tomé and Príncipe
| | - Teresa L Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 VairaoVila do CondePortugal
| | - Vanessa A. Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 VairaoVila do CondePortugal
| | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 VairaoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 Vairao, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairao, Universidade do Porto, 4485-661 VairaoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 Vairao, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairao, 4485-661 VairaoVila do CondePortugal
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16
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Ferguson DK, Li C, Chakraborty A, Gittins DA, Fowler M, Webb J, Campbell C, Morrison N, MacDonald A, Hubert CRJ. Multi-year seabed environmental baseline in deep-sea offshore oil prospective areas established using microbial biodiversity. MARINE POLLUTION BULLETIN 2023; 194:115308. [PMID: 37517246 DOI: 10.1016/j.marpolbul.2023.115308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023]
Abstract
Microorganisms are the ocean's first responders to marine pollution events, yet baseline studies rarely focus on microbial communities. Temporal and spatial microbial biodiversity baselines were established using bacterial 16S rRNA gene amplicon sequencing of seafloor sediments in a deep-water oil prospective area along the Scotian Slope off Canada's east coast sampled during 2015-2018. Bacterial diversity was generally similar in space and time, with members of the family Woeseiaceae detected consistently in >1 % relative abundance, similar to seabed sediments in other parts of the world. Anomalous biodiversity results at one site featured lower Woeseiaceae as well as higher levels of bacterial groups specifically associated with cold seeps such as Aminicenantes. This was unexpected given that site selection was based on sediment geochemistry not revealing any petroleum hydrocarbons in these locations. This finding highlights the sensitivity and specificity of microbial DNA sequencing in environmental monitoring. Microbiome assessments like this one represent an important strategy for incorporating microbial biodiversity as a new and useful metric for establishing robust environmental baselines that are necessary for understanding ecosystem responses to marine pollution.
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Affiliation(s)
- Deidra K Ferguson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Anirban Chakraborty
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Daniel A Gittins
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Martin Fowler
- Applied Petroleum Technology Canada, Calgary, Alberta, Canada
| | - Jamie Webb
- Applied Petroleum Technology Canada, Calgary, Alberta, Canada
| | - Calvin Campbell
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Nova Scotia, Canada
| | - Natasha Morrison
- Nova Scotia Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Nova Scotia, Canada
| | - Adam MacDonald
- Nova Scotia Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Nova Scotia, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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17
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Lee YR, Ko KS, Lee HE, Lee ES, Han K, Yoo JY, Vu BN, Choi HN, Lee YN, Hong JC, Lee KO, Kim DS. CRISPR/Cas9-Mediated HY5 Gene Editing Reduces Growth Inhibition in Chinese Cabbage ( Brassica rapa) under ER Stress. Int J Mol Sci 2023; 24:13105. [PMID: 37685921 PMCID: PMC10487758 DOI: 10.3390/ijms241713105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Various stresses can affect the quality and yield of crops, including vegetables. In this study, CRISPR/Cas9 technology was employed to examine the role of the ELONGATED HYPOCOTYL 5 (HY5) gene in influencing the growth of Chinese cabbage (Brassica rapa). Single guide RNAs (sgRNAs) were designed to target the HY5 gene, and deep-sequencing analysis confirmed the induction of mutations in the bZIP domain of the gene. To investigate the response of Chinese cabbage to endoplasmic reticulum (ER) stress, plants were treated with tunicamycin (TM). Both wild-type and hy5 mutant plants showed increased growth inhibition with increasing TM concentration. However, the hy5 mutant plants displayed less severe growth inhibition compared to the wild type. Using nitroblue tetrazolium (NBT) and 3,3'-diaminobenzidine (DAB) staining methods, we determined the amount of reactive oxygen species (ROS) produced under ER stress conditions, and found that the hy5 mutant plants generated lower levels of ROS compared to the wild type. Under ER stress conditions, the hy5 mutant plants exhibited lower expression levels of UPR- and cell death-related genes than the wild type. These results indicate that CRISPR/Cas9-mediated editing of the HY5 gene can mitigate growth inhibition in Chinese cabbage under stresses, improving the quality and yield of crops.
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Affiliation(s)
- Ye Rin Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju-gun 55365, Republic of Korea; (Y.R.L.); (H.E.L.); (E.S.L.); (K.H.)
| | - Ki Seong Ko
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (K.S.K.); (J.Y.Y.); (J.C.H.)
| | - Hye Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju-gun 55365, Republic of Korea; (Y.R.L.); (H.E.L.); (E.S.L.); (K.H.)
| | - Eun Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju-gun 55365, Republic of Korea; (Y.R.L.); (H.E.L.); (E.S.L.); (K.H.)
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju-gun 55365, Republic of Korea; (Y.R.L.); (H.E.L.); (E.S.L.); (K.H.)
| | - Jae Yong Yoo
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (K.S.K.); (J.Y.Y.); (J.C.H.)
| | - Bich Ngoc Vu
- Division of Life Science, Division of Applied Life Sciences (BK4 Program), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (B.N.V.); (H.N.C.); (Y.N.L.)
| | - Ha Na Choi
- Division of Life Science, Division of Applied Life Sciences (BK4 Program), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (B.N.V.); (H.N.C.); (Y.N.L.)
| | - Yoo Na Lee
- Division of Life Science, Division of Applied Life Sciences (BK4 Program), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (B.N.V.); (H.N.C.); (Y.N.L.)
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (K.S.K.); (J.Y.Y.); (J.C.H.)
- Division of Life Science, Division of Applied Life Sciences (BK4 Program), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (B.N.V.); (H.N.C.); (Y.N.L.)
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (K.S.K.); (J.Y.Y.); (J.C.H.)
- Division of Life Science, Division of Applied Life Sciences (BK4 Program), Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; (B.N.V.); (H.N.C.); (Y.N.L.)
| | - Do Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju-gun 55365, Republic of Korea; (Y.R.L.); (H.E.L.); (E.S.L.); (K.H.)
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18
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Zwick P, Zwick A. Revision of the African Neoperla Needham, 1905 (Plecoptera: Perlidae: Perlinae) based on morphological and molecular data. Zootaxa 2023; 5316:1-194. [PMID: 37518401 DOI: 10.11646/zootaxa.5316.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Adults of the African species of the genus Neoperla Needham, 1905 (Plecoptera: Perlidae: Perlinae) are revised, and 82 valid species are recognised. Of the original 29 named species, 14 valid ones are redescribed from types, nine lectotypes are designated, and nine new synonymies are proposed. Sixty-two new species are named, and several additional new species only known from material insufficient for formal description are listed. There are one unavailable nomen nudum and three doubtful names. Diagnostic morphological traits of the recognised species are described and illustrated in detail where available of males, females, and eggs. Dichotomous keys to all species are provided. Mitochondrial DNA-data of 71 species-group taxa are available, which permits reliable association of sexes and minimises the risk of synonymies between species known from only one sex. Importantly, this includes DNA sequences from 50 holotypes. The DNA-data will also permit future monitoring with eDNA sequencing and identification of nymphs, which are probably important but so far unidentifiable bioindicators in streams. The genus Neoperla occurs largely in the northern hemisphere and in Africa, where it is restricted to the Ethiopian region south of the Sahara but unknown from Madagascar. A single specimen not clearly distinct from a widespread mainland species was taken on Comoro Island. All African species are endemic, but one African species group has a few outlying members in Asia. The Asian N. montivaga-group is not known from Africa. The following new species are described and named: N. aethiopica n. sp., N. amoena n. sp., N. angolana n. sp., N. bareensis n. sp., N. bella n. sp., N. benti n. sp., N. beta n. sp., N. bipolaris n. sp., N. biserrata n. sp., N. brachyphallus n. sp., N. caeleps n. sp., N. cataractae n. sp., N. claviger n. sp., N. coffea n. sp., N. costata n. sp., N. crenulata n. sp., N. crustata n. sp., N. decorata n. sp., N. dianae n. sp., N. dolium n. sp., N. dundoana n. sp., N. duodeviginti n. sp., N. erinaceus n. sp., N. excavata n. sp., N. filamentosa n. sp., N. funiculata n. sp., N. gibbosa n. sp., N. gordius n. sp., N. heideae n. sp., N. ivanloebli n. sp., N. juxtadidita n. sp., N. kalengonis n. sp., N. larvata n. sp., N. lineata n. sp., N. luhohonis n. sp., N. massevensis n. sp., N. multiserrata n. sp., N. muyukae n. sp., N. nichollsi n. sp., N. occulta n. sp., N. orthonema n. sp., N. pallidogigas n. sp., N. panafricana n. sp., N. pickeri n. sp., N. pilulifera n. sp., N. pirus n. sp., N. planidorsum n. sp., N. plicata n. sp., N. proxima n. sp., N. pusilla n. sp., N. rostrata n. sp., N. sambarua n. sp., N. sassandrae n. sp., N. schuelei n. sp., N. serrula n. sp., N. simplex n. sp., N. socia n. sp., N. sorella n. sp., N. spaghetti n. sp., N. spectabilis n. sp., N. spironema n. sp., N. tangana n. sp., N. tansanica n. sp., N. usambara n. sp., and N. vicina n. sp..
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Affiliation(s)
| | - Andreas Zwick
- Australian National Insect Collection; National Research Collections Australia; CSIRO; Canberra; ACT 2601; Australia.
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Long K, Yin R, Kardol P, Wei Q, Li Y, Huang J. Bamboo invasion alters Collembola community composition varying with life-forms. PEST MANAGEMENT SCIENCE 2023; 79:2517-2526. [PMID: 36864785 DOI: 10.1002/ps.7434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 02/11/2023] [Accepted: 03/02/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Plant invasions are a global concern. In eastern China, bamboo is rapidly expanding, negatively influencing neighbouring forest communities. However, studies on how bamboo invasion affects belowground communities, especially for soil invertebrates, are still lacking. In the present study, we focused on a highly abundant and diverse fauna taxon - Collembola. Collembola communities have three typical life-forms (i.e., epedaphic, hemiedaphic, and euedaphic) inhabiting different soil layers and playing distinct roles in ecological processes. Specifically, we studied their abundance, diversity, and community composition at the three stages of bamboo invasion: uninvaded secondary broadleaf forest, moderately invaded mixed bamboo forest, and completely invaded bamboo (Phyllostachys edulis) forest. RESULTS Our results showed that bamboo invasion negatively influenced Collembola communities by decreasing their abundance and diversity. Moreover, Collembola life-forms differed in their responses to bamboo invasion, with surface-dwelling Collembola being more vulnerable to bamboo invasion than soil-living Collembola. CONCLUSION Our findings indicate differential response patterns to bamboo invasion within Collembola communities. The negative effects of bamboo invasion on soil surface-dwelling Collembola may further influence ecosystem functioning. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Kui Long
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Rui Yin
- Department of Community Ecology, Helmholtz-Centre for Environmental Research-UFZ, Halle (Saale), Germany
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Paul Kardol
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Science, Uppsala, Sweden
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Qiaoyu Wei
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Yongchun Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Junhao Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Ceríaco LMP, Marques MP, de Sousa ACA, Veríssimo J, Beja P, Ferreira S. Illustrated keys and a DNA barcode reference library of the amphibians and terrestrial reptiles (Amphibia, Reptilia) of São Tomé and Príncipe (Gulf of Guinea, West Africa). Zookeys 2023; 1168:41-75. [PMID: 37415718 PMCID: PMC10320720 DOI: 10.3897/zookeys.1168.101334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/18/2023] [Indexed: 07/08/2023] Open
Abstract
The herpetofauna of São Tomé and Príncipe consists of nine species of amphibians, all endemic, and 21 species of terrestrial reptiles, of which 17 are endemic. Our current knowledge regarding its natural history, ecology, and distribution is limited. Here two important tools are provided to support researchers, conservationists, and local authorities in the identification of the country's herpetofauna: an illustrated key to the herpetofauna of the two islands and surroundings islets and a DNA barcode reference library. The keys allow a rapid and unambiguous morphological identification of all occurring species. The DNA barcodes for the entire herpetofauna of the country were produced from 79 specimens, all of which are deposited in museum collections. The barcodes generated are available in online repositories and can be used to provide unambiguous molecular identification of most of the species. Future applications and use of these tools are briefly discussed.
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Affiliation(s)
- Luis Miguel Pires Ceríaco
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Av. Bartolomeu de Gusmão 875, São Cristóvão, 20941-160 Rio de Janeiro, Brasil
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Mariana Pimentel Marques
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
| | | | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
| | - Pedro Beja
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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21
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An X, Han S, Ren X, Sichone J, Fan Z, Wu X, Zhang Y, Wang H, Cai W, Sun F. Succession of Fungal Community during Outdoor Deterioration of Round Bamboo. J Fungi (Basel) 2023; 9:691. [PMID: 37367627 DOI: 10.3390/jof9060691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Bamboo's mechanical and aesthetic properties are significantly influenced by fungi. However, few studies have been conducted to investigate the structure and dynamics of fungal communities in bamboo during its natural deterioration. In this study, fungal community succession and characteristic variations of round bamboo in roofed and unroofed environments over a period of 13 weeks of deterioration were deciphered using high-throughput sequencing and multiple characterization methods. A total of 459 fungal Operational Taxonomic Units (OTUs) from eight phyla were identified. The fungal community's richness of roofed bamboo samples showed an increasing trend, whereas that of unroofed bamboo samples presented a declining trend during deterioration. Ascomycota and Basidiomycota were the dominant phyla throughout the deterioration process in two different environments: Basidiomycota was found to be an early colonizer of unroofed bamboo samples. Principal Coordinates Analysis (PCoA) analysis suggested that the deterioration time had a greater impact on fungal community variation compared to the exposure conditions. Redundancy analysis (RDA) further revealed that temperature was a major environmental factor that contributed to the variation in fungal communities. Additionally, the bamboo epidermis presented a descending total amount of cell wall components in both roofed and unroofed conditions. The correlation analysis between the fungal community and relative abundance of three major cell wall components elucidated that Cladosporium was negatively correlated with hemicellulose in roofed samples, whereas they presented a positive correlation with hemicellulose and a negative correlation with lignin in unroofed samples. Furthermore, the contact angle decreased during the deterioration process in the roofed as well as unroofed samples, which could arise from the degradation of lignin. Our findings provide novel insights into the fungal community succession on round bamboo during its natural deterioration and give useful information for round bamboo protection.
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Affiliation(s)
- Xiaojiao An
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuaibo Han
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Xin Ren
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - John Sichone
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhiwei Fan
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinxing Wu
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Zhang
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Hui Wang
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Wei Cai
- Anji Zhujing Bamboo Technology Co., Ltd., Huzhou 313300, China
| | - Fangli Sun
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
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22
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Karin BR, Arellano S, Wang L, Walzer K, Pomerantz A, Vasquez JM, Chatla K, Sudmant PH, Bach BH, Smith LL, McGuire JA. Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes. BMC Genomics 2023; 24:229. [PMID: 37131128 PMCID: PMC10155392 DOI: 10.1186/s12864-023-09277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/24/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods. RESULTS With the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80-90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes. CONCLUSIONS This method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.
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Affiliation(s)
- Benjamin R Karin
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA.
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.
| | - Selene Arellano
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Laura Wang
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Kayla Walzer
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Aaron Pomerantz
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Juan Manuel Vasquez
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Peter H Sudmant
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Lydia L Smith
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Jimmy A McGuire
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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23
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Sultana S, Azlan A, Desa MNM, Mahyudin NA. Multiplex platforms in biosensor based analytical approaches: Opportunities and challenges for the speciation of animal species in food chain. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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24
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Rosa P, Wood T, Silva TLL, Veríssimo J, Mata VA, Michez D, Beja P, Ferreira S. The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of cuckoo wasps, with the description of new species from the Iberian Peninsula (Hymenoptera, Chrysididae). Biodivers Data J 2023; 11:e98743. [PMID: 38327368 PMCID: PMC10848353 DOI: 10.3897/bdj.11.e98743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/25/2023] [Indexed: 03/05/2023] Open
Abstract
Background DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present a part of the InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of cuckoo wasps (Hymenoptera, Chrysididae) dataset representing 144 specimens and 103 species, covering approximately 44% of the Iberian and 21% of the European fauna. The InBIO Barcoding Initiative (IBI - DNA Barcoding Portuguese terrestrial invertebrate biodiversity) aims to fill the barcoding gap for the terrestrial invertebrate taxa. All DNA extractions are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources and specimens are deposited in the University of Mons collection (Belgium) and in the Natur-Museum in Lucerne (Switzerland). New information This dataset increases the knowledge on the DNA barcodes and distribution of 102 species of cuckoo wasps. A total of 52 species, from 11 different genera, were new additions to the Barcode of Life Data System (BOLD), with DNA barcodes for another 44 species added from under-represented taxa in BOLD. All specimens have their DNA barcodes publicly accessible through the BOLD online database. Nine cuckoo wasp species are newly recorded for Portugal. Additionally, two new species for science are described: Chrysiscrossi Rosa, sp. nov. from southern Portugal and Hedychridiumcalcarium Rosa, sp. nov. from eastern Spain. Several taxonomic changes are proposed and Hedychrumrutilans Dahlbom, 1845 is found to consist of two different taxa that can be found in sympatry, Hedychrumrutilans s. str. and Hedychrumviridaureum Tournier, 1877 stat. nov. Stilbumwestermanni Dahlbom, 1845 stat. nov. is confirmed as distinct from Stilbumcalens (Fabricius, 1781), with the latter species not confirmed as present in Iberia; barcoded Stilbum material from Australia is distinct and represents Stilbumamethystium (Fabricius, 1775) sp. resurr.; Portuguese material identified as Hedychridiumchloropygum Buysson, 1888 actually belongs to Hedychridiumcaputaureum Trautmann & Trautmann, 1919, the first confirmed record of this species from Iberia. Philoctetesparvulus (Dahlbom, 1845) is confirmed to be a synonym of Philoctetespunctulatus (Dahlbom, 1845). Chrysislusitanica Bischoff, 1910 is confirmed as a valid species. Chrysishebraeica Linsenmaier, 1959 stat. nov. is raised to species status.
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Affiliation(s)
- Paolo Rosa
- University of Mons, Research Institute for Biosciences, Laboratory of Zoology, Place du parc 20, 7000, Mons, BelgiumUniversity of Mons, Research Institute for Biosciences, Laboratory of Zoology, Place du parc 20, 7000MonsBelgium
| | - Thomas Wood
- University of Mons, Research Institute for Biosciences, Laboratory of Zoology, Place du parc 20, 7000, Mons, BelgiumUniversity of Mons, Research Institute for Biosciences, Laboratory of Zoology, Place du parc 20, 7000MonsBelgium
| | - Teresa Luísa L. Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
| | - Vanessa A. Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
| | - Denis Michez
- University of Mons, Research Institute for Biosciences, Laboratory of Zoology, Place du parc 20, 7000, Mons, BelgiumUniversity of Mons, Research Institute for Biosciences, Laboratory of Zoology, Place du parc 20, 7000MonsBelgium
| | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
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25
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Ouyang X, Fan Q, Chen A, Huang J. Effects of trunk injection with emamectin benzoate on arthropod diversity. PEST MANAGEMENT SCIENCE 2023; 79:935-946. [PMID: 36309931 DOI: 10.1002/ps.7264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pine wood nematode is a major plant quarantine object in the world. Trunk injection is an effective method for controlling pests that cause disease. To evaluate the ecological safety of trunk injection with emamectin benzoates in forests of Pinus massoniana, the community diversity and community composition of soil arthropods and flying insects (Hymenoptera) were studied at different stages of trunk injection. RESULTS The dominant taxonomic groups of soil arthropods were Collembola (30.80%), Insecta (26.42%), and Arachnida (23.84%). The taxonomic groups of flying insects (Hymenoptera) were Ichneumonidae (48.94%), Formicidae (14.10%), and Braconidae (8.44%). Trunk injection with emamectin benzoate has no significant effect on the community diversity indices of total soil arthropods and flying insects (Hymenoptera). However, it has a significant effect on the community diversity indices of detritivores for soil arthropods. It changed the community composition of soil arthropods but did not impact the community composition of flying insects (Hymenoptera). Redundancy analysis of arthropod community structure and environmental variables showed that total potassium, residual of green leaf, and residual of litter leaf have a significant impact on the community structure of soil arthropods, and total phosphorus, total nitrogen, water content, organic matter, and total potassium have a significant impact on the community structure of flying insects (Hymenoptera). CONCLUSION Trunk injection with emamectin benzoate is safe for the ecological environment. This study provides a new insight into the field for the prevention and control of pine wood nematode disease, which is of great significance to forest management and pest control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xianheng Ouyang
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Qingbin Fan
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Anliang Chen
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Junhao Huang
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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26
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Seo H, Yoon SY, ul-Haq A, Jo S, Kim S, Rahim MA, Park HA, Ghorbanian F, Kim MJ, Lee MY, Kim KH, Lee N, Won JH, Song HY. The Effects of Iron Deficiency on the Gut Microbiota in Women of Childbearing Age. Nutrients 2023; 15:nu15030691. [PMID: 36771397 PMCID: PMC9919165 DOI: 10.3390/nu15030691] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Iron deficiency anemia (IDA) is the most prevalent and common nutritional deficiency worldwide and is a global health problem with significant risk, particularly among women of reproductive age. Oral iron supplementation is the most widely used and cost-effective treatment for iron deficiency and IDA. However, there are limitations regarding side effects such as enteritis, treatment compliance, and bioavailability. Intestinal microbiome characteristic research has been recently conducted to overcome these issues, but more is needed. Against this background, a metagenomics study on the 16S gene in the feces of young women vulnerable to IDA was conducted. As a result of analyzing 16 normal subjects and 15 IDA patients, significant differences in bacterial community distribution were identified. In particular, a significant decrease in Faecalibacterium was characteristic in IDA patients compared with normal subjects. Furthermore, in the case of patients who recovered from IDA following iron supplementation treatment, it was confirmed that Faecalibacterium significantly recovered to normal levels. However, no significance in beta diversity was seen compared with before treatment. There were also no differences in the beta diversity results between the recovered and normal subjects. Therefore, intestinal dysbiosis during the disease state was considered to be restored as IDA improved. Although the results were derived from a limited number of subjects and additional research is needed, the results of this study are expected to be the basis for developing treatment and prevention strategies based on host-microbiome crosstalk in IDA.
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Affiliation(s)
- Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si 31538, Republic of Korea
| | - Seug Yun Yoon
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Asad ul-Haq
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si 31538, Republic of Korea
| | - Sujin Jo
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si 31538, Republic of Korea
| | - Md Abdur Rahim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
| | - Hyun-A Park
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
| | - Fatemeh Ghorbanian
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
| | - Min Jung Kim
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Min-Young Lee
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Kyoung Ha Kim
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Namsu Lee
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
| | - Jong-Ho Won
- Division of Hematology & Medical Oncology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul 04401, Republic of Korea
- Correspondence: (J.-H.W.); (H.-Y.S.)
| | - Ho-Yeon Song
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan-si 31538, Republic of Korea
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan-si 31151, Republic of Korea
- Correspondence: (J.-H.W.); (H.-Y.S.)
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Pauperio J, Gonzalez LM, Martinez J, González MA, Martins FMS, Veríssimo J, Puppo P, Pinto J, Chaves C, Pinho CJ, Grosso-Silva JM, Quaglietta L, Silva TLL, Sousa P, Alves PC, Fonseca N, Beja P, Ferreira S. The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot. Biodivers Data J 2023; 11:e97484. [PMID: 38327295 PMCID: PMC10848855 DOI: 10.3897/bdj.11.e97484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Background The Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically identified Trichoptera specimens, representing 142 Iberian taxa, was constructed. The InBIO Barcoding Initiative (IBI) Trichoptera 01 dataset contains records of 438 sequenced specimens. The species of this dataset correspond to about 37% of Iberian Trichoptera species diversity. Specimens were collected between 1975 and 2018 and are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources, Portugal) or in the collection Marcos A. González at the University of Santiago de Compostela (Spain). New information Twenty-nine species, from nine different families, were new additions to the Barcode of Life Data System (BOLD). A success identification rate of over 80% was achieved when comparing morphological identifications and DNA barcodes for the species analysed. This encouraging step advances incorporation of informed Environmental DNA tools in biomonitoring schemes, given the shortcomings of morphological identifications of larvae and adult Caddisflies in such studies. DNA barcoding was not successful in identifying species in six Trichoptera genera: Hydropsyche (Hydropsychidae), Athripsodes (Leptoceridae), Wormaldia (Philopotamidae), Polycentropus (Polycentropodidae) Rhyacophila (Rhyacophilidae) and Sericostoma (Sericostomatidae). The high levels of intraspecific genetic variability found, combined with a lack of a barcode gap and a challenging morphological identification, rendered these species as needing additional studies to resolve their taxonomy.
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Affiliation(s)
- Joana Pauperio
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United KingdomEuropean Molecular Biology Laboratory, European Bioinformatics InstituteHinxton, CambridgeUnited Kingdom
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Luis Martin Gonzalez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Jesus Martinez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Marcos A González
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Filipa MS Martins
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Joana Veríssimo
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007PortoPortugal
| | - Pamela Puppo
- Marshall University, Department of Biological Sciences, Huntington, United States of AmericaMarshall University, Department of Biological SciencesHuntingtonUnited States of America
| | - Joana Pinto
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Cátia Chaves
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Catarina J. Pinho
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007PortoPortugal
| | - José Manuel Grosso-Silva
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Lorenzo Quaglietta
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Teresa Luísa L Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Pedro Sousa
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Paulo Celio Alves
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
| | - Nuno Fonseca
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Pedro Beja
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Sónia Ferreira
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
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Olds CG, Berta‐Thompson JW, Loucks JJ, Levy RA, Wilson AW. Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11508. [PMID: 36818783 PMCID: PMC9934593 DOI: 10.1002/aps3.11508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/18/2023]
Abstract
Premise Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor-efficient and cost-effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once. Methods We applied a two-step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 Lactarius specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de-noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens. Results The taxonomic identities derived from the nrITS2 sequence data were >90% accurate across all specimens sampled. A phylogenetic analysis of the Lactarius sequences identified 20 MOTUs. Discussion The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.
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Affiliation(s)
- C. Gary Olds
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
- The Department of Integrative BiologyUniversity of Colorado DenverDenverColoradoUSA
| | | | - Justin J. Loucks
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
| | - Richard A. Levy
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
| | - Andrew W. Wilson
- The Department of Research and ConservationDenver Botanic GardensDenverColoradoUSA
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29
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Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome. Microbiol Spectr 2022; 10:e0251322. [PMID: 36409146 PMCID: PMC9769941 DOI: 10.1128/spectrum.02513-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The evolution of sequencing technology and multiplexing has rapidly expanded our ability to characterize fungal diversity in the environment. However, obtaining an unbiased assessment of the fungal community using ribosomal markers remains challenging. Longer amplicons were shown to improve taxonomic resolution and resolve ambiguities by reducing the risk of spurious operational taxonomic units. We examined the implications of barcoding strategies by amplifying and sequencing two ribosomal DNA fragments. We analyzed the performance of the full internal transcribed spacer (ITS) and a longer fragment including also a part of the 28S ribosomal subunit replicated on 60 grapevine trunk core samples. Grapevine trunks harbor highly diverse fungal communities with implications for disease development. Using identical handling, amplification, and sequencing procedures, we obtained higher sequencing depths for the shorter ITS amplicon. Despite the more limited access to polymorphism, the overall diversity in amplified sequence variants was higher for the shorter ITS amplicon. We detected no meaningful bias in the phylogenetic composition due to the amplicon choice across analyzed samples. Despite the increased resolution of the longer ITS-28S amplicon, the higher and more consistent yields of the shorter amplicons produced a clearer resolution of the fungal community of grapevine stem samples. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals. IMPORTANCE Surveying fungal communities is key to our understanding of ecological functions of diverse habitats. Fungal communities can inform about the resilience of agricultural ecosystems, risks to human health, and impacts of pathogens. Community compositions are typically analyzed using ribosomal DNA sequences. Due to technical limitations, most fungal community surveys were based on amplifying a short but highly variable fragment. Advances in sequencing technology enabled the use of longer fragments that can address some limitations of species identification. In this study, we examined the implications of choosing either a short or long ribosomal sequence fragment by replicating the analyses on 60 grapevine wood core samples. Using highly accurate long-read sequencing, we found that the shorter fragment produced substantially higher yields. The shorter fragment also revealed more sequence and species diversity. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.
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30
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Chaemsaithong P, Romero R, Pongchaikul P, Vivithanaporn P, Lertrut W, Jaovisidha A, Mongkolsuk P, Nitayanon P, Pongsuktavorn K, Kamlungkuea T, Jung E, Suksai M, Singhsnaeh A, Jenjaroenpun P, Thaipisuttikul I, Wongsurawat T. Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing. J Perinat Med 2022:jpm-2022-0504. [PMID: 36503654 DOI: 10.1515/jpm-2022-0504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Early diagnosis and treatment of intra-amniotic infection is crucial. Rapid pathogen identification allows for a definite diagnosis and enables proper management. We determined whether the 16S amplicon sequencing performed by a nanopore sequencing technique make possible rapid bacterial identification at the species level in intra-amniotic infection. METHODS Five cases of confirmed intra-amniotic infection, determined by either cultivation or 16S rDNA polymerase chain reaction (PCR) Sanger sequencing, and 10 cases of women who underwent mid-trimester genetic amniocentesis were included. DNA was extracted from amniotic fluid and PCR was performed on the full-length 16S rDNA. Nanopore sequencing was performed. The results derived from nanopore sequencing were compared with those derived from cultivation and Sanger sequencing methods. RESULTS Bacteria were successfully detected from amniotic fluid using nanopore sequencing in all cases of intra-amniotic infection. Nanopore sequencing identified additional bacterial species and polymicrobial infections. All patients who underwent a mid-trimester amniocentesis had negative cultures, negative 16S PCR Sanger sequencing and nanopore sequencing. Identification of the microorganisms using nanopore sequencing technique at the bacterial species level was achieved within 5-9 h from DNA extraction. CONCLUSIONS This is the first study demonstrating that the nanopore sequencing technique is capable of rapid diagnosis of intra-amniotic infection using fresh amniotic fluid samples.
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Affiliation(s)
- Piya Chaemsaithong
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Perinatalogy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA.,National Institutes of Health, Bethesda, MD, USA
| | - Roberto Romero
- Perinatalogy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA.,National Institutes of Health, Bethesda, MD, USA.,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.,Detroit Medical Center, Detroit, MI, USA
| | - Pisut Pongchaikul
- Faculty of Medicine Ramathibodi Hospital, Chakri Naruebodindra Medical Institute, Mahidol University, Samut Prakarn, Thailand.,Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakorn Pathom, Thailand.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Pornpun Vivithanaporn
- Faculty of Medicine Ramathibodi Hospital, Chakri Naruebodindra Medical Institute, Mahidol University, Samut Prakarn, Thailand
| | - Waranyu Lertrut
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Adithep Jaovisidha
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Paninee Mongkolsuk
- Faculty of Medicine Ramathibodi Hospital, Chakri Naruebodindra Medical Institute, Mahidol University, Samut Prakarn, Thailand
| | - Perapon Nitayanon
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Khontawan Pongsuktavorn
- Siriraj Genomics, Molecular Genetics Laboratory, Office of the Dean, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Threebhorn Kamlungkuea
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Eunjung Jung
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Perinatalogy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - Manaphat Suksai
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Perinatalogy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - Arunee Singhsnaeh
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Long-Read Lab (Si-LoL), Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Iyarit Thaipisuttikul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Long-Read Lab (Si-LoL), Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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31
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Dopheide A, Brav-Cubitt T, Podolyan A, Leschen RAB, Ward D, Buckley TR, Dhami MK. Fast-tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation. Mol Ecol Resour 2022. [PMID: 36345645 DOI: 10.1111/1755-0998.13733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
Despite recent advances in high-throughput DNA sequencing technologies, a lack of locally relevant DNA reference databases limits the potential for DNA-based monitoring of biodiversity for conservation and biosecurity applications. Museums and national collections represent a compelling source of authoritatively identified genetic material for DNA database development, yet obtaining DNA barcodes from long-stored specimens may be difficult due to sample degradation. Here we demonstrate a sensitive and efficient laboratory and bioinformatic process for generating DNA barcodes from hundreds of invertebrate specimens simultaneously via the Illumina MiSeq system. Using this process, we recovered full-length (334) or partial (105) COI barcodes from 439 of 450 (98%) national collection-held invertebrate specimens. This included full-length barcodes from 146 specimens which produced low-yield DNA and no visible PCR bands, and which produced as little as a single sequence per specimen, demonstrating high sensitivity of the process. In many cases, the identity of the most abundant sequences per specimen were not the correct barcodes, necessitating the development of a taxonomy-informed process for identifying correct sequences among the sequencing output. The recovery of only partial barcodes for some taxa indicates a need to refine certain PCR primers. Nonetheless, our approach represents a highly sensitive, accurate and efficient method for targeted reference database generation, providing a foundation for DNA-based assessments and monitoring of biodiversity.
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Affiliation(s)
| | | | | | | | - Darren Ward
- Manaaki Whenua Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Thomas R Buckley
- Manaaki Whenua Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Hévin NM, Hansen S, Addison P, Benoit L, Kergoat GJ, Haran J. Late Cenozoic environmental changes drove the diversification of a weevil genus endemic to the Cape Floristic Region. ZOOL SCR 2022. [DOI: 10.1111/zsc.12563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noémie M.‐C. Hévin
- CBGP INRAE, CIRAD, IRD, Institut Agro, Univ. Montpellier Montpellier France
- Université de Poitiers Poitiers France
| | | | | | - Laure Benoit
- CBGP CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier Montpellier France
| | - Gael J. Kergoat
- CBGP INRAE, CIRAD, IRD, Institut Agro, Univ. Montpellier Montpellier France
| | - Julien Haran
- CBGP CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier Montpellier France
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Andújar C, Arribas P, López H, Arjona Y, Pérez-Delgado A, Oromí P, Vogler AP, Emerson BC. Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island. Mol Ecol 2022; 31:4078-4094. [PMID: 35665980 PMCID: PMC9544582 DOI: 10.1111/mec.16560] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/04/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
Abstract
Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here, we take advantage of a relatively young and dynamic oceanic island to advance our understanding of ecoevolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable haplotype‐level DNA sequence data for soil mesofaunal assemblages sampled across the four main habitats within the island of Tenerife. Community ecological and metaphylogeographic analyses have been performed at multiple levels of genetic similarity, from haplotypes to species and supraspecific groupings. Broadly consistent patterns of local‐scale species richness across different insular habitats have been found, whereas local insular richness is lower than in continental settings. Our results reveal an important role for niche conservatism as a driver of insular community assembly of soil mesofauna, with only limited evidence for habitat shifts promoting diversification. Furthermore, support is found for a fundamental role of habitat in the assembly of soil mesofauna, where habitat specialism is mainly due to colonization and the establishment of preadapted species. Hierarchical patterns of distance decay at the community level and metaphylogeographical analyses support a pattern of geographic structuring over limited spatial scales, from the level of haplotypes through to species and lineages, as expected for taxa with strong dispersal limitations. Our results demonstrate the potential for wocDNA metabarcoding to advance our understanding of biodiversity.
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Affiliation(s)
- Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
| | - Heriberto López
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
| | - Yurena Arjona
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
| | - Antonio Pérez-Delgado
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain.,School of Doctoral and Postgraduate Studies, University of La Laguna, La Laguna Tenerife, Canary Islands, Spain
| | - Pedro Oromí
- Department of Animal Biology, Edaphology and Geology, University of La Laguna, La Laguna Tenerife, Canary Islands, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, UK.,Department of Life Sciences, Imperial College London Silwood Park Campus, Ascot, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna Tenerife, Canary Islands, Spain
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Gomes-de-Sá S, Barradas P, Queirós-Reis L, Matas IM, Amorim I, Cardoso L, Muñoz-Mérida A, Mesquita JR. De Novo Assembly of the Dirofilaria immitis Genome by Long-Read Nanopore-Based Sequencing Technology on an Adult Worm from a Canine Cardiopulmonary Dirofilariosis Case. Animals (Basel) 2022; 12:ani12111342. [PMID: 35681811 PMCID: PMC9179477 DOI: 10.3390/ani12111342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Dirofilaria immitis is a zoonotic parasite that infects canids and other vertebrates. We expanded the use of long-read nanopore-based sequencing technology by performing genomic de novo assembly of a D. immitis specimen retrieved from a canine cardiopulmonary dirofilariasis case by using the ONT MinION platform. We also identified loci previously characterized as being associated to macrocyclic lactone resistance selection pressure. The identification of a resistant zoonotic parasite alerts for the overuse of macrocyclic lactone in the region. Abstract Dirofilaria immitis is a zoonotic parasitic nematode that infects domestic and wild canids, among its vertebrate hosts. The genetic analysis of D. immitis nowadays transcends the need for genetic taxonomy of nematodes, such as the study of resistance to macrocyclic lactone. We expanded the use of long-read nanopore-based sequencing technology on nematodes by performing genomic de novo assembly of a D. immitis specimen retrieved from a canine cardiopulmonary dirofilariasis case using the ONT MinION platform, followed by the study of macrocyclic lactone resistance. The assembled genome of D. immitis consists of 110 contigs with an N50 of 3687191. The genome size is 87899012 and contains a total of 9741 proteins; 6 ribosomal RNAs, with three belonging to the small subunit (18S) and three to the large subunit (28S); and 73 tRNAs. Subsequent analysis of six loci previously characterized as being associated to macrocyclic lactone resistance selection pressure showed that four have a genotype associated with either some loss of efficacy or the resistance phenotype. Considering the zoonotic potential of D. immitis, the identification of a resistant parasite alerts for the overuse of macrocyclic lactone in the region, which poses a potential risk to both veterinary and human public health.
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Affiliation(s)
- Sónia Gomes-de-Sá
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (S.G.-d.-S.); (L.Q.-R.); (I.A.)
| | - Patrícia Barradas
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal;
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-600 Porto, Portugal
- Department of Sciences, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal
| | - Luís Queirós-Reis
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (S.G.-d.-S.); (L.Q.-R.); (I.A.)
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal;
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-600 Porto, Portugal
| | - Isabel M. Matas
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/InBIO), Universidade do Porto, Vairão, 4485-661 Porto, Portugal; (I.M.M.); (A.M.-M.)
| | - Irina Amorim
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (S.G.-d.-S.); (L.Q.-R.); (I.A.)
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4220-135 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
| | - Luís Cardoso
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences, University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Animal and Veterinary Research Centre (CECAV), UTAD, 5000-801 Vila Real, Portugal
| | - Antonio Muñoz-Mérida
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/InBIO), Universidade do Porto, Vairão, 4485-661 Porto, Portugal; (I.M.M.); (A.M.-M.)
| | - João R. Mesquita
- ICBAS—School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; (S.G.-d.-S.); (L.Q.-R.); (I.A.)
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal;
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-600 Porto, Portugal
- Correspondence:
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Gomez Palacios LR, Bracamonte AG. Development of nano- and microdevices for the next generation of biotechnology, wearables and miniaturized instrumentation. RSC Adv 2022; 12:12806-12822. [PMID: 35496334 PMCID: PMC9047444 DOI: 10.1039/d2ra02008d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/15/2022] [Indexed: 12/27/2022] Open
Abstract
This is a short communication based on recent high-impact publications related to how various chemical materials and substrate modifications could be tuned for nano- and microdevices, where their application for high point-of-care bioanalysis and further applications in life science is discussed. Hence, they have allowed different high-impact research topics in a variety of fields, from the control of nanoscale to functional microarchitectures embedded in various support materials to obtain a device for a given application or use. Thus, their incorporation in standard instrumentation is shown, as well as in new optical setups to record different classical and non-classical light, signaling, and energy modes at a variety of wavelengths and energy levels. Moreover, the development of miniaturized instrumentation was also contemplated. In order to develop these different levels of technology, the chemistry, physics and engineering of materials were discussed. In this manner, a number of subjects that allowed the design and manufacture of devices could be found. The following could be mentioned by way of example: (i) nanophotonics; (ii) design, synthesis and tuning of advanced nanomaterials; (iii) classical and non-classical light generation within the near field; (iv) microfluidics and nanofluidics; (v) signal waveguiding; (vi) quantum-, nano- and microcircuits; (vii) materials for nano- and microplatforms, and support substrates and their respective modifications for targeted functionalities. Moreover, nano-optics in in-flow devices and chips for biosensing were discussed, and perspectives on biosensing and single molecule detection (SMD) applications. In this perspective, new insights about precision nanomedicine based on genomics and drug delivery systems were obtained, incorporating new advanced diagnosis methods based on lab-on-particles, labs-on-a-chip, gene therapies, implantable devices, portable miniaturized instrumentation, single molecule detection for biophotonics, and neurophotonics. In this manner, this communication intends to highlight recent reports and developments of nano- and microdevices and further approaches towards the incorporation of developments in nanophotonics and biophotonics in the design of new materials based on different strategies and enhanced techniques and methods. Recent proofs of concept are discussed that could allow new substrates for device manufacturing. Thus, physical phenomena and materials chemistry with accurate control within the nanoscale were introduced into the discussion. In this manner, new potential sources of ideas and strategies for the next generation of technology in many research and development fields are showcased.
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Affiliation(s)
- Luna R Gomez Palacios
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC) Ciudad Universitaria 5000 Córdoba Argentina
| | - A Guillermo Bracamonte
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC) Ciudad Universitaria 5000 Córdoba Argentina
- Department of Chemistry, University of Victoria (UVic) Vancouver Island V8W 2Y2 British Columbia (BC) Canada
- Département de chimie and Centre d'optique, photonique et laser (COPL), Université Laval Québec (QC) G1V 0A6 Canada
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Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment. Nat Protoc 2022; 17:1415-1443. [DOI: 10.1038/s41596-022-00682-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
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Roman MG, Gutierrez R, Houston R. Massively parallel sequencing of Cannabis sativa chloroplast hotspots for forensic typing. J Cannabis Res 2022; 4:13. [PMID: 35300721 PMCID: PMC8928601 DOI: 10.1186/s42238-022-00123-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Marijuana (Cannabis sativa) is the most commonly used illicit drug in the USA, and the use of DNA barcodes could assist drug trafficking investigations by indicating the biogeographical origin and crop type of a sample and providing a means for linking cases. Additionally, the legality of marijuana in the USA remains complicated with some states fully legalizing marijuana for recreational use while federally marijuana remains completely illegal. Massively parallel sequencing (MPS) offers distinct advantages over capillary electrophoresis (CE), including more comprehensive coverage of target loci, analysis of hundreds of markers simultaneously, and high throughput capabilities. METHODS This study reports on the development of a MiSeq FGx® assay targeting seven "hotspot" regions in the Cannabis sativa chloroplast genome that are highly polymorphic and informative in attempts to determine biogeographical origin and distinguishing between marijuana and hemp. Sequencing results were compared to previous studies that used CE-based genotyping methods. RESULTS A total of 49 polymorphisms were observed, 16 of which have not been previously reported. Additionally, sequence data revealed isoalleles at one locus, which were able to differentiate two samples that had the same haplotype using CE-based methods. This study reports preliminary results from sequencing 14 hemp and marijuana samples from different countries using the developed MPS assay. CONCLUSION Future studies should genotype a more comprehensive sample set from around the world to build a haplotype database, which could be used to provide investigative leads for law enforcement agencies investigating marijuana trafficking.
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Affiliation(s)
- Madeline G Roman
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA
| | - Ryan Gutierrez
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA
| | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA.
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Kyrö K, Kankaanpää T, Vesterinen EJ, Lehvävirta S, Kotze DJ. Arthropod Communities on Young Vegetated Roofs Are More Similar to Each Other Than to Communities at Ground Level. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.785448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Vegetated roofs are human-manufactured ecosystems and potentially promising conservation tools for various taxa and habitats. Focussing on arthropods, we conducted a 3 year study on newly constructed vegetated roofs with shallow substrates (up to 10 cm) and vegetation established with pre-grown mats, plug plants and seeds to describe pioneer arthropod communities on roofs and to compare them with ground level communities. We vacuum sampled arthropods from the roofs and nearby ground level sites with low, open vegetation, i.e., potential source habitats. We showed that the roofs and ground sites resembled each other for ordinal species richness but differed in community composition: with time the roofs started to resemble each other rather than their closest ground level habitats. Species richness increased with time on roofs and at ground level, but the roofs had consistently less species than the ground sites and only a few species were unique to the roofs. Also, the proportion of predators increased on roofs, while not at ground level. We conclude that vegetated roofs established with similar substrates and vegetation, filter arthropods in a way that produces novel communities that are different from those at ground level but similar to one another. The role of these insular communities in species networks and ecosystem function remains to be investigated.
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Huang J, Miao X, Wang Q, Menzel F, Tang P, Yang D, Wu H, Vogler AP. Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem. Ecol Evol 2022; 12:e8535. [PMID: 35127039 PMCID: PMC8796913 DOI: 10.1002/ece3.8535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/08/2021] [Accepted: 12/22/2021] [Indexed: 11/07/2022] Open
Abstract
Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera communities on Tianmu Mountain, Zhejiang, China, using DNA metabarcoding technology, and evaluated their dynamic responses to the effects of slope aspect, season, and altitudinal zone. A total of 5,092 operational taxonomic units (OTUs) were discovered and tentatively assigned to 72 dipteran families, including 2 family records new for China and 30 family records new for the locality. Cecidomyiidae, Sciaridae, and Phoridae were the predominant families, representing 53.6% of total OTUs, while 52 families include >95% unidentified and presumed undescribed species. We found that the community structure of Diptera was significantly affected by aspect, seasonality (month) and elevation, with richer diversity harbored in north-facing than south-facing slopes, and seasonality a more profound driver of community structure and diversity than elevation. Overall, massive species diversity of Diptera communities was discovered in this subtropical ecosystem of east China. The huge diversity of potentially undescribed species only revealed by metabarcoding now requires more detailed taxonomic study, as a step toward an evolutionary integration that accumulates information on species' geographic ranges, ecological traits, functional roles, and species interactions, and thus places the local communities in the context of the growing knowledge base of global biodiversity and its response to environmental change.
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Affiliation(s)
- Junhao Huang
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Xiaoqian Miao
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Qingyun Wang
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Frank Menzel
- Senckenberg Deutsches Entomologisches InstitutMünchebergGermany
| | - Pu Tang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural EntomologyInstitute of Insect SciencesZhejiang UniversityHangzhouChina
| | - Ding Yang
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Hong Wu
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Alfried P. Vogler
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
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DNA barcoding of insects from India: Current status and future perspectives. Mol Biol Rep 2022; 49:10617-10626. [PMID: 35716293 PMCID: PMC9206398 DOI: 10.1007/s11033-022-07628-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/01/2022]
Abstract
Insect fauna occupy the largest proportion of animal biodiversity on earth, but the assessment or quantification in terms of species diversity is far from complete. Several recent studies have demonstrated the rapid pace at which insect population decline is occurring. There is an urgent need to document and quantify the diversity of insect fauna for a proper understanding of terrestrial ecosystems. This can be achieved by using modern technology to identify species much faster than relying on traditional methods alone. In line with this, the molecular approach through DNA barcoding coupled with morphological identification needs to be focused and accelerated. The present paper describes the current status of barcoding of insect species in India along with the gaps that need to be remedied. This analysis shows that barcoded specimens cover a very meagre proportion of less than 3.73% of the known taxa/described species and the most represented orders are Lepidoptera and Hemiptera followed by Diptera and Coleoptera. There is a need to expedite insect species discovery and documentation in a collaborative mode between traditional taxonomists and molecular biologists, to accomplish the DNA barcoding of all known insect taxa from India.
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Leite BR, Vieira PE, Troncoso JS, Costa FO. Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.70063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA metabarcoding has great potential to improve marine biomonitoring programs by providing a rapid and accurate assessment of species composition in zoobenthic communities. However, some methodological improvements are still required, especially regarding failed detections, primers efficiency and incompleteness of databases. Here we assessed the efficiency of two different marker loci (COI and 18S) and three primer pairs in marine species detection through DNA metabarcoding of the macrozoobenthic communities colonizing three types of artificial substrates (slate, PVC and granite), sampled between 3 and 15 months of deployment. To accurately compare detection success between markers, we also compared the representativeness of the detected species in public databases and revised the reliability of the taxonomic assignments. Globally, we recorded extensive complementarity in the species detected by each marker, with 69% of the species exclusively detected by either 18S or COI. Individually, each of the three primer pairs recovered, at most, 52% of all species detected on the samples, showing also different abilities to amplify specific taxonomic groups. Most of the detected species have reliable reference sequences in their respective databases (82% for COI and 72% for 18S), meaning that when a species was detected by one marker and not by the other, it was most likely due to faulty amplification, and not by lack of matching sequences in the database. Overall, results showed the impact of marker and primer applied on species detection ability and indicated that, currently, if only a single marker or primer pair is employed in marine zoobenthos metabarcoding, a fair portion of the diversity may be overlooked.
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Morrill A, Kaunisto KM, Mlynarek JJ, Sippola E, Vesterinen EJ, Forbes MR. Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets. PeerJ 2021; 9:e12634. [PMID: 35003931 PMCID: PMC8686731 DOI: 10.7717/peerj.12634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Sexes often differ in foraging and diet, which is associated with sex differences in size, trophic morphology, use of habitats, and/or life history tactics. Herein, strikingly similar diets were found for adult sexes of a dragonfly (Leucorrhinia intacta), based on comparing 141 dietary taxa identified from the metabarcoding of mitochondrial DNA archived in feces. Arthropods in > 5% of samples included five species of dipterans, two hemipterans, two spider species and one parasitic mite. The mite was not traditional prey as its presence was likely due to DNA contamination of samples arising through parasitism or possibly via accidental consumption during grooming, and therefore the mite was excluded from diet characterizations. Common prey species were found with statistically indistinguishable frequencies in male and female diets, with one exception of an aphid more often found in male diets, although this pattern was not robust to corrections for multiple statistical tests. While rare prey species were often found in diets of only one sex, instances of this were more frequent in the more oft-sampled females, suggesting sampling artefact. Sexes did not differ in the mean prey species richness in their diets. Overall, sexes showed statistically indistinguishable diets both on a prey species-by-species basis and in terms of multivariate characterizations of diet composition, derived from presence-absence data of prey species analyzed via PERMANOVA and accumulation curves. Males and females may have similar diets by being both opportunistic and generalist predators of arthropods, using the same foraging habitats and having similar sizes and flight agilities. Notably, similarities in diet between sexes occur alongside large interindividual differences in diet, within sexes. Researchers intending on explaining adaptive sex differences in diet should consider characteristics of species whose sexes show similar diets.
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Affiliation(s)
- André Morrill
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | | | | | - Ella Sippola
- Biodiversity Unit, University of Turku, Turku, Finland
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Eero J. Vesterinen
- Department of Biology, University of Turku, Turku, Finland
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mark R. Forbes
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
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Lee HT, Liao CH, Hsu TH. Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood. BIOLOGY 2021; 10:1132. [PMID: 34827127 PMCID: PMC8614924 DOI: 10.3390/biology10111132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 01/08/2023]
Abstract
Seafood, especially the traditional one in Taiwan, is rarely sourced from a fixed species and routinely from similar species depending on their availability. Hence, the species composition of seafood can be complicated. While a DNA-based approach has been routinely utilized for species identification, a large scale of seafood identification in fish markets and restaurants could be challenging (e.g., elevated cost and time-consuming only for a limited number of species identification). In the present study, we aimed to identify the majority of fish species potentially consumed in fish markets and nearby seafood restaurants using environmental DNA (eDNA) metabarcoding. Four eDNA samplings from a local fish market and nearby seafood restaurants were conducted using Sterivex cartridges. Nineteen universal primers previously validated for fish species identification were utilized to amplify the fragments of mitochondrial DNA (12S, COI, ND5) of species in eDNA samples and sequenced with NovaSeq 6000 sequencing. A total of 153 fish species have been identified based on 417 fish related operational taxonomic units (OTUs) generated from 50,534,995 reads. Principal Coordinate Analysis (PCoA) further showed the differences in fish species between the sampling times and sampling sites. Of these fish species, 22 chondrichthyan fish, 14 Anguilliformes species, and 15 Serranidae species were respectively associated with smoked sharks, braised moray eels, and grouper fish soups. To our best knowledge, this work represents the first study to demonstrate the feasibility of a large scale of seafood identification using eDNA metabarcoding approach. Our findings also imply the species diversity in traditional seafood might be seriously underestimated and crucial for the conservation and management of marine resources.
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Affiliation(s)
- Hung-Tai Lee
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.L.); (C.-H.L.)
| | - Cheng-Hsin Liao
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.L.); (C.-H.L.)
| | - Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
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45
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Paula DP. Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution. NEOTROPICAL ENTOMOLOGY 2021; 50:679-696. [PMID: 34374956 DOI: 10.1007/s13744-021-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.
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Wei Q, Yin R, Huang J, Vogler AP, Li Y, Miao X, Kardol P. The diversity of soil mesofauna declines after bamboo invasion in subtropical China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:147982. [PMID: 34052488 DOI: 10.1016/j.scitotenv.2021.147982] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Plant invasions often act as ecosystem 'simplifiers' to simplify diversity and community structure of soil biota. However, inconsistent relationships between plant invasion and soil fauna have been found and few studies have addressed how soil fauna communities change upon plant invasions across taxa and feeding guilds. Here, we investigated the effects of moso bamboo (Phyllostachys edulis) invasion in subtropical China on soil mesofauna communities using novel high-throughput sequencing (HTS). Specifically, we analyzed the spatio-temporal dynamics of fauna diversity and feeding guilds in the litter and soil layers for three stages of moso bamboo invasion, i.e., uninvaded (secondary broadleaved forest), moderately invaded (mixed bamboo forest) and completely invaded (P. edulis forest). Overall, we found that the completely invaded bamboo forest decreased species richness and diversity of total fauna, herbivores, and microbivores consistently across different soil layers, but less so detritivores and predators. Although we did not find any interaction effects of bamboo invasion and soil layers on soil fauna diversity indices, significant interaction effects were found on the community composition, for total fauna and their feeding guilds. Specifically, the detrimental effects of bamboo invasion on the trophic structure of soil fauna communities were more profound in the litter layer than in the soil layer, suggesting that a litter layer with more diverse taxa does not mean higher resistance to plant invasion in maintaining the soil food web structure. Taken together, our findings suggest that different responses within fauna feeding guilds to plant invasion were pervasive, and a deeper soil layer may better alleviate the negative effects of pant invasion on fauna community structure. These shifts in soil biodiversity may further degrade ecosystem functioning.
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Affiliation(s)
- Qiaoyu Wei
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Rui Yin
- Helmholtz-Centre for Environmental Research-UFZ, Department of Community Ecology, Theodor-Lieser-Strasse 4, 06110 Halle (Saale), Germany; Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Junhao Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Yongchun Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaoqian Miao
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Paul Kardol
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901-83 Umeå, Sweden
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Srivathsan A, Lee L, Katoh K, Hartop E, Kutty SN, Wong J, Yeo D, Meier R. ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 2021; 19:217. [PMID: 34587965 PMCID: PMC8479912 DOI: 10.1186/s12915-021-01141-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer. RESULTS We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. CONCLUSIONS We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
| | - Emily Hartop
- Zoology Department, Stockholms Universitet, Stockholm, Sweden
- Station Linné, Öland, Sweden
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Johnathan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany.
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Gálvez-Reyes N, Arribas P, Andújar C, Emerson BC, Piñero D, Mastretta-Yanes A. Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: Evidence from community metabarcoding. Mol Ecol 2021; 30:6611-6626. [PMID: 34564919 DOI: 10.1111/mec.16195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 01/04/2023]
Abstract
Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale patterns of arthropod community assembly to understand the role of dispersal limitation and landscape features as drivers of diversity. We sampled whole-communities of arthropods for eight orders at a spatial scale ranging from 50 m to 19 km, using whole community metabarcoding. We explored multiple hierarchical levels, from individual haplotypes to lineages at 0.5, 1.5, 3, 5, and 7.5% similarity thresholds, to evaluate patterns of richness, turnover, and distance decay of similarity with isolation-by-distance and isolation-by-resistance (costs to dispersal given by landscape features) approaches. Our results showed that distance and altitude influence distance decay of similarity at all hierarchical levels. This holds for arthropod groups of contrasting dispersal abilities, but with different strength depending on the spatial scale. Our results support a model where local-scale differentiation mediated by dispersal constraints, combined with long-term persistence of lineages, is an important driver of diversity within tropical sky islands.
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Affiliation(s)
- Nancy Gálvez-Reyes
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), CDMX, Mexico.,Consejo Nacional de Ciencia y Tecnología, Benito Juárez (CONACYT), CDMX, Mexico
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Ferreira S, Oosterbroek P, Starý J, Sousa P, Mata VA, da Silva LP, Paupério J, Beja P. The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae. Biodivers Data J 2021; 9:e69841. [PMID: 34690515 PMCID: PMC8486732 DOI: 10.3897/bdj.9.e69841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/01/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The InBIO Barcoding Initiative (IBI) Diptera 02 dataset contains records of 412 crane fly specimens belonging to the Diptera families: Limoniidae, Pediciidae and Tipulidae. This dataset is the second release by IBI on Diptera and it greatly increases the knowledge on the DNA barcodes and distribution of crane flies from Portugal. All specimens were collected in Portugal, including six specimens from the Azores and Madeira archipelagos. Sampling took place from 2003 to 2019. Specimens have been morphologically identified to species level by taxonomists and belong to 83 species in total. The species, represented in this dataset, correspond to about 55% of all the crane fly species known from Portugal and 22% of crane fly species known from the Iberian Peninsula. All DNA extractions and most specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. NEW INFORMATION Fifty-three species were new additions to the Barcode of Life Data System (BOLD), with another 18 species' barcodes added from under-represented species in BOLD. Furthermore, the submitted sequences were found to cluster in 88 BINs, 54 of which were new to BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and its collection data can be accessed through the Global Biodiversity Information Facility (GBIF). One species, Gonomyiatenella (Limoniidae), is recorded for the first time from Portugal, raising the number of crane flies recorded in the country to 145 species.
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Affiliation(s)
- Sónia Ferreira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVila do CondePortugal
| | - Pjotr Oosterbroek
- Naturalis Biodiversity Center, Leiden, NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
| | - Jaroslav Starý
- Olomouc-Nedvězí & Silesian Museum, Nádražní okruh 31, CZ-746 01 Opava, Olomouc, Czech RepublicOlomouc-Nedvězí & Silesian Museum, Nádražní okruh 31, CZ-746 01 OpavaOlomoucCzech Republic
| | - Pedro Sousa
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVila do CondePortugal
| | - Vanessa A. Mata
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVila do CondePortugal
| | - Luis P da Silva
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVila do CondePortugal
| | - Joana Paupério
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVila do CondePortugal
| | - Pedro Beja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vila do Conde, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVila do CondePortugal
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Vila do Conde, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017Vila do CondePortugal
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50
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Oliveira D, Chaves C, Pinto J, Paupério J, Fonseca N, Beja P, Ferreira S. DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida). Zookeys 2021; 1054:67-84. [PMID: 34393563 PMCID: PMC8355005 DOI: 10.3897/zookeys.1054.64608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 11/12/2022] Open
Abstract
The orders Neuroptera and Raphidioptera include the species of insects known as lacewings and snakeflies, respectively. In Portugal, these groups account for over 100 species, some of which are very difficult to identify by morphological analysis. This work is the first to sample and DNA sequence lacewings and snakeflies of Portugal. A reference collection was built with captured specimens that were identified morphologically. DNA barcode sequences of 658 bp were obtained from 243 specimens of 54 species. The results showed that most species can be successfully identified through DNA barcoding, with the exception of seven species of Chrysopidae (Neuroptera). Additionally, the first published distribution data are presented for Portugal for the neuropterans Gymnocnemiavariegata (Schneider, 1845) and Myrmecaelurus (Myrmecaelurus) trigrammus (Pallas, 1771).
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Affiliation(s)
- Daniel Oliveira
- CIBIO/InBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, 4485–661 Vairão, PortugalCentro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoVairãoPortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, PortugalUniversidade do PortoPortoPortugal
| | - Cátia Chaves
- CIBIO/InBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, 4485–661 Vairão, PortugalCentro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoVairãoPortugal
| | - Joana Pinto
- CIBIO/InBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, 4485–661 Vairão, PortugalCentro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoVairãoPortugal
| | - Joana Paupério
- CIBIO/InBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, 4485–661 Vairão, PortugalCentro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoVairãoPortugal
| | - Nuno Fonseca
- CIBIO/InBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, 4485–661 Vairão, PortugalCentro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoVairãoPortugal
| | - Pedro Beja
- CIBIO/InBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, 4485–661 Vairão, PortugalCentro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoVairãoPortugal
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalUniversidade de LisboaLisboaPortugal
| | - Sónia Ferreira
- CIBIO/InBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, 4485–661 Vairão, PortugalCentro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoVairãoPortugal
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