1
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Burian A, Bruce K, Tovela E, Bakker J, Balcells L, Bennett R, Chordekar S, Costa HM, Crampton-Platt A, de Boer H, Ross-Gillespie V, de Sacramento A, Sidat N, Simbine L, Ready J, Tang C, Mauvisseau Q. Merging two eDNA metabarcoding approaches and citizen-science-based sampling to facilitate fish community monitoring along vast Sub-Saharan coastlines. Mol Ecol Resour 2023; 23:1641-1655. [PMID: 37464467 DOI: 10.1111/1755-0998.13839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
The coastline of Sub-Saharan Africa hosts highly diverse fish communities of great conservation value, which are also key resources for local livelihoods. However, many costal ecosystems are threatened by overexploitation and their conservation state is frequently unknown due to their vast spatial extent and limited monitoring budgets. Here, we evaluated the potential of citizen science-based eDNA surveys to alleviate such chronic data deficiencies and assessed fish communities in Mozambique using two 12S metabarcoding primer sets. Samples were either collected by scientific personnel or trained community members and results from the two metabarcoding primers were combined using a new data merging approach. Irrespective of the background of sampling personnel, a high average fish species richness was recorded (38 ± 20 OTUs per sample). Individual sections of the coastline largely differed in the occurrence of threatened and commercially important species, highlighting the need for regionally differentiated management strategies. A detailed comparison of the two applied primer sets revealed an important trade-off in primer choice with MiFish primers amplifying a higher number of species but Riaz primers performing better in the detection of threatened fish species. This trade-off could be partly resolved by applying our new data-merging approach, which was especially designed to increase the robustness of multiprimer assessments in regions with poor reference libraries. Overall, our study provides encouraging results but also highlights that eDNA-based monitoring will require further improvements of, for example, reference databases and local analytical infrastructure to facilitate routine applications in Sub-Saharan Africa.
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Affiliation(s)
- Alfred Burian
- Department of Computational Landscape Ecology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
- Marine Ecology Department, Lurio University, Nampula, Mozambique
| | | | - Erica Tovela
- Natural History Museum, University Eduardo Mondlane, Maputo, Mozambique
| | | | | | | | | | - Hugo M Costa
- Wildlife Conservation Society, Maputo, Mozambique
| | | | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | | | | | - Luisa Simbine
- Instituto Oceanográfico de Moçambique, Ministério do Mar, Águas Interiores e Pescas, Maputo, Mozambique
| | - Jonathan Ready
- Universidade Federal do Pará, Grupo de Investigação Biológica Integrada, Centro de Estudos Avançados da Biodiversidade, Belem, Brazil
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2
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Chua PYS, Carøe C, Crampton-Platt A, Reyes-Avila CS, Jones G, Streicker DG, Bohmann K. A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus). MBMG 2022. [DOI: 10.3897/mbmg.6.78756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n = 8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and mtDNA contig assembly) to identify prey. After validating our results from detections made through metabarcoding, we accurately identified the common vampire bats’ prey in six out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138 bp to 3231 bp (median = 770 bp, Q1 = 262 bp, Q3 = 1766 bp). This opens the potential to conduct phylogenetic and phylogeographic monitoring of elusive prey species in future studies, through the analyses of blood meal metagenomic data.
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3
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Chua PYS, Crampton-Platt A, Lammers Y, Alsos IG, Boessenkool S, Bohmann K. Metagenomics: A viable tool for reconstructing herbivore diet. Mol Ecol Resour 2021; 21:2249-2263. [PMID: 33971086 PMCID: PMC8518049 DOI: 10.1111/1755-0998.13425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 04/08/2021] [Accepted: 05/04/2021] [Indexed: 11/28/2022]
Abstract
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
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Affiliation(s)
- Physilia Y S Chua
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Youri Lammers
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Inger G Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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4
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Axtner J, Crampton-Platt A, Hörig LA, Mohamed A, Xu CCY, Yu DW, Wilting A. An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies. Gigascience 2019; 8:giz029. [PMID: 30997489 PMCID: PMC6461710 DOI: 10.1093/gigascience/giz029] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/12/2018] [Accepted: 03/07/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation. FINDINGS Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples. CONCLUSIONS Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods.
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Affiliation(s)
- Jan Axtner
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Alex Crampton-Platt
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Lisa A Hörig
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Azlan Mohamed
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Charles C Y Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd, Kunming, Yunnan 650223, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
- Redpath Museum and Department of Biology, McGill University 859 Sherbooke Street West, Montreal, PQ, Canada H3A 2K6
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Rd, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Department of Ecological Dynamics, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
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Linard B, Crampton-Platt A, Moriniere J, Timmermans MJ, Andújar C, Arribas P, Miller KE, Lipecki J, Favreau E, Hunter A, Gómez-Rodríguez C, Barton C, Nie R, Gillett CP, Breeschoten T, Bocak L, Vogler AP. The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera. Mol Phylogenet Evol 2018; 128:1-11. [DOI: 10.1016/j.ympev.2018.07.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 03/09/2018] [Indexed: 12/16/2022]
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6
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Choo LQ, Crampton-Platt A, Vogler AP. Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum. Mol Ecol 2017; 26:5086-5098. [PMID: 28742928 DOI: 10.1111/mec.14258] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 07/10/2017] [Indexed: 11/29/2022]
Abstract
Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA mixtures of mass-trapped arthropods ("mitochondrial metagenomics"), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small-bodied fraction was the by far most species-rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small-bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log-linear, indicating a uniformly filled abundance spectrum, especially for small-bodied species. Small-bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria.
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Affiliation(s)
- Le Qin Choo
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
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7
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Linard B, Arribas P, Andújar C, Crampton-Platt A, Vogler AP. Lessons from genome skimming of arthropod-preserving ethanol. Mol Ecol Resour 2016; 16:1365-1377. [DOI: 10.1111/1755-0998.12539] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/06/2016] [Indexed: 01/16/2023]
Affiliation(s)
- B. Linard
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - P. Arribas
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - C. Andújar
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - A. Crampton-Platt
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - A. P. Vogler
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
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8
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Abstract
‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT UK
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, Yunnan Province 650223 China ; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ UK
| | - Xin Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province 518083 China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY UK
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9
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Linard B, Arribas P, Andújar C, Crampton-Platt A, Vogler AP. The mitogenome of Hydropsyche pellucidula (Hydropsychidae): first gene arrangement in the insect order Trichoptera. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:71-72. [PMID: 26677912 DOI: 10.3109/19401736.2015.1110803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We describe the mitochondrial genome of Hydropsyche pellucidula Curtis 1834, which is first described for the suborder Annulipalpia and the first in the order Trichoptera to show a non-canonical gene order. The mitogenome was obtained by de novo assembly of shotgun sequenced total genomic DNA using Illumina Miseq technology, which produced an average coverage of 115× and a minimum coverage of 48×. The mitochondrial genome includes 13 protein-coding genes, 2 rRNAs and 22 tRNAs. The genome is characterized by a rearrangement in the relative position of protein-coding and ribosomal genes. This mitogenome sequence will be useful for studying the family Hydropsychidae, which is commonly used for freshwater pollution biomonitoring.
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Affiliation(s)
- B Linard
- a Department of Life Sciences , Natural History Museum , London , UK
| | - P Arribas
- a Department of Life Sciences , Natural History Museum , London , UK.,b Department of Life Sciences , Imperial College London , Silwood Park Campus , Ascot , UK
| | - C Andújar
- a Department of Life Sciences , Natural History Museum , London , UK.,b Department of Life Sciences , Imperial College London , Silwood Park Campus , Ascot , UK
| | - A Crampton-Platt
- a Department of Life Sciences , Natural History Museum , London , UK.,c Department of Genetics , Evolution and Environment, University College London , London , UK
| | - A P Vogler
- a Department of Life Sciences , Natural History Museum , London , UK.,b Department of Life Sciences , Imperial College London , Silwood Park Campus , Ascot , UK
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10
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Linard B, Crampton-Platt A, Gillett CPDT, Timmermans MJTN, Vogler AP. Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics. Genome Biol Evol 2015; 7:1474-89. [PMID: 25979752 PMCID: PMC4494052 DOI: 10.1093/gbe/evv086] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2015] [Indexed: 01/08/2023] Open
Abstract
Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by "genome skimming," which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and known repeat elements of high and low complexity, including numerous copies of rRNA and histone genes. Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous "clusters" of scaffolds mapped to the same genomic site revealed intra- and/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The "metagenome skimming" approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.
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Affiliation(s)
- Benjamin Linard
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | | | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
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11
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Andújar C, Arribas P, Ruzicka F, Crampton-Platt A, Timmermans MJ, Vogler AP. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Mol Ecol 2015; 24:3603-17. [DOI: 10.1111/mec.13195] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/03/2015] [Accepted: 04/08/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Carmelo Andújar
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Paula Arribas
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Filip Ruzicka
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Alex Crampton-Platt
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Martijn J.T.N. Timmermans
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
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12
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Crampton-Platt A, Timmermans MJTN, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, Vogler AP. Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample. Mol Biol Evol 2015; 32:2302-16. [PMID: 25957318 PMCID: PMC4540967 DOI: 10.1093/molbev/msv111] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, Faculty of Life Sciences, University College London, London, United Kingdom
| | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Matthew L Gimmel
- Department of Biology, Faculty of Education, Palacký University, Olomouc, Czech Republic
| | | | - Timothy D Cockerill
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chey Vun Khen
- Entomology Section, Forest Research Centre, Forestry Department, Sandakan, Sabah, Malaysia
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
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13
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Gillett CPDT, Crampton-Platt A, Timmermans MJTN, Jordal BH, Emerson BC, Vogler AP. Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Mol Biol Evol 2014; 31:2223-37. [PMID: 24803639 PMCID: PMC4104315 DOI: 10.1093/molbev/msu154] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based "bait" sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge.
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Affiliation(s)
- Conrad P D T Gillett
- Department of Life Sciences, Natural History Museum, London, United KingdomSchool of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, United Kingdom
| | - Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| | - Bjarte H Jordal
- The Natural History Museum, University Museum of Bergen, Bergen, Norway
| | - Brent C Emerson
- School of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, United KingdomIsland Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología, La Laguna, Tenerife, Canary Islands, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
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