1
|
Gauthier M, Konecny‐Dupré L, Nguyen A, Elbrecht V, Datry T, Douady C, Lefébure T. Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. Mol Ecol Resour 2019; 20:79-96. [DOI: 10.1111/1755-0998.13088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Mailys Gauthier
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Lara Konecny‐Dupré
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | | | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph Ontario Canada
| | - Thibault Datry
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Christophe Douady
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | - Tristan Lefébure
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| |
Collapse
|
2
|
Govender A, Groeneveld J, Singh S, Willows-Munro S. The design and testing of mini-barcode markers in marine lobsters. PLoS One 2019; 14:e0210492. [PMID: 30677051 PMCID: PMC6345471 DOI: 10.1371/journal.pone.0210492] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/23/2018] [Indexed: 11/19/2022] Open
Abstract
Full-length mitochondrial cytochrome c oxidase I (COI) sequence information from lobster phyllosoma larvae can be difficult to obtain when DNA is degraded or fragmented. Primers that amplify smaller fragments are also more useful in metabarcoding studies. In this study, we developed and tested a method to design a taxon-specific mini-barcode primer set for marine lobsters. The shortest, most informative portion of the COI gene region was identified in silico, and a DNA barcode gap analysis was performed to assess its reliability as species diagnostic marker. Primers were designed, and cross-species amplification success was tested on DNA extracted from a taxonomic range of spiny-, clawed-, slipper- and blind lobsters. The mini-barcode primers successfully amplified both adult and phyllosoma COI fragments, and were able to successfully delimit all species analyzed. Previously published universal primer sets were also tested and sometimes failed to amplify COI from phyllosoma samples. The newly designed taxon-specific mini-barcode primers will increase the success rate of species identification in bulk environmental samples and add to the growing DNA metabarcoding toolkit.
Collapse
Affiliation(s)
- Ashrenee Govender
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Oceanographic Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Johan Groeneveld
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Oceanographic Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Sohana Singh
- Oceanographic Research Institute, Durban, KwaZulu-Natal, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| |
Collapse
|
3
|
Mariac C, Vigouroux Y, Duponchelle F, García-Dávila C, Nunez J, Desmarais E, Renno J. Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms. PLoS One 2018; 13:e0202976. [PMID: 30208069 PMCID: PMC6135497 DOI: 10.1371/journal.pone.0202976] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/13/2018] [Indexed: 12/04/2022] Open
Abstract
The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.
Collapse
Affiliation(s)
- C. Mariac
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- * E-mail:
| | - Y. Vigouroux
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
| | - F. Duponchelle
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN—CNRS-7208—UPMC—UCBN—IRD-207, Montpellier, France
| | - C García-Dávila
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- Instituto de Investigaciones de la Amazonía Peruana (IIAP), Laboratorio de Biología y Genética Molecular (LBGM), Iquitos, Perú
| | - J. Nunez
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN—CNRS-7208—UPMC—UCBN—IRD-207, Montpellier, France
| | - E. Desmarais
- Institut des Sciences de l’Évolution (UMR ISEM), Université Montpellier—CNRS—IRD—EPHE, Place Eugène Bataillon—France
| | - J.F. Renno
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN—CNRS-7208—UPMC—UCBN—IRD-207, Montpellier, France
| |
Collapse
|
4
|
Suntrarachun S, Chanhome L, Sumontha M. Phylogenetic analysis of the king cobra, Ophiophagus hannah in Thailand based on mitochondrial DNA sequences. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0802.289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background: Snakes possess adaptive characteristics of morphology that may result in incorrect reconstruction of phylogeny. Molecular approaches have become the major source of new information for advancing our understanding of evolutionary, genetic relationships, and species identification.
Objective: We studied DNA sequences of Ophiophagus hannah in different parts of Thailand and compared them with those of O. hannah from other countries.
Materials and Methods: We studied the mitochondrial NADH dehydrogenase subunit 2 (ND2) and control region (CR) sequences of 12 individuals O. hannah from different localities across Thailand. Phylogenetic analysis of DNA sequences were compared to the published sequences of O. hannah deposited in NCBI GenBank database from other countries.
Results: O. hannah could be categorized into 2 Clades, 5 haplotypes, and 4 localities based on 43 different nucleotide positions from the 736 bp of ND2 and 673 bp of CR. Clade A was haplotype A from southern Thailand. Clade B consisted of haplotypes B, C, D, and E. Haplotype B and C came from northern Thailand. Haplotype D came from western Thailand, while haplotype E was O. hannah from central Thailand. The DNA sequences of Clade B were similar to the sequences of O. hannah in Myanmar and southern China that are already deposited in NCBI GenBank database.
Conclusion: We found a different genotype of O. hannah from southern Thailand and suggest that this may be a new species of O. hannah.
Collapse
Affiliation(s)
- Sunutcha Suntrarachun
- Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Lawan Chanhome
- Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | | |
Collapse
|
5
|
Walker FM, Williamson CHD, Sanchez DE, Sobek CJ, Chambers CL. Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples. PLoS One 2016; 11:e0162342. [PMID: 27654850 PMCID: PMC5031397 DOI: 10.1371/journal.pone.0162342] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/22/2016] [Indexed: 11/25/2022] Open
Abstract
Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa.
Collapse
Affiliation(s)
- Faith M. Walker
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Charles H. D. Williamson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Daniel E. Sanchez
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Colin J. Sobek
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Carol L. Chambers
- Bat Ecology & Genetics Laboratory, School of Forestry, Northern Arizona University, Flagstaff, Arizona, United States of America
| |
Collapse
|
6
|
Lopez-Oceja A, Gamarra D, Borragan S, Jiménez-Moreno S, de Pancorbo MM. New cyt b gene universal primer set for forensic analysis. Forensic Sci Int Genet 2016; 23:159-165. [PMID: 27206224 DOI: 10.1016/j.fsigen.2016.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/28/2022]
Abstract
Analysis of mitochondrial DNA, and in particular the cytochrome b gene (cyt b), has become an essential tool for species identification in routine forensic practice. In cases of degraded samples, where the DNA is fractionated, universal primers that are highly efficient for the amplification of the target region are necessary. Therefore, in the present study a new universal cyt b primer set with high species identification capabilities, even in samples with highly degraded DNA, has been developed. In order to achieve this objective, the primers were designed following the alignment of complete sequences of the cyt b from 751 species from the Class of Mammalia listed in GenBank. A highly variable region of 148bp flanked by highly conserved sequences was chosen for placing the primers. The effectiveness of the new pair of primers was examined in 63 animal species belonging to 38 Families from 14 Orders and 5 Classes (Mammalia, Aves, Reptilia, Actinopterygii, and Malacostraca). Species determination was possible in all cases, which shows that the fragment analyzed provided a high capability for species identification. Furthermore, to ensure the efficiency of the 148bp fragment, the intraspecific variability was analyzed by calculating the concordance between individuals with the BLAST tool from the NCBI (National Center for Biotechnological Information). The intraspecific concordance levels were superior to 97% in all species. Likewise, the phylogenetic information from the selected fragment was confirmed by obtaining the phylogenetic tree from the sequences of the species analyzed. Evidence of the high power of phylogenetic discrimination of the analyzed fragment of the cyt b was obtained, as 93.75% of the species were grouped within their corresponding Orders. Finally, the analysis of 40 degraded samples with small-size DNA fragments showed that the new pair of primers permits identifying the species, even when the DNA is highly degraded as it is very common in forensic samples.
Collapse
Affiliation(s)
- A Lopez-Oceja
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain
| | - D Gamarra
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain
| | - S Borragan
- Parque de la Naturaleza de Cabárceno, 39693, Obregón, Cantabria, Spain
| | - S Jiménez-Moreno
- Area of Forensic and Legal Medicine, Pathology and Surgery Dept., Miguel Hernández University of Elche, 03550, Elche, Alicante, Spain
| | - M M de Pancorbo
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain.
| |
Collapse
|
7
|
Chambers EA, Hebert PDN. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections. PLoS One 2016; 11:e0154363. [PMID: 27116180 PMCID: PMC4846166 DOI: 10.1371/journal.pone.0154363] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 11/19/2022] Open
Abstract
Background High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. Methodology/Principal Findings This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. Conclusions/Significance This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.
Collapse
Affiliation(s)
- E. Anne Chambers
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
8
|
Lee PS, Sing KW, Wilson JJ. Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala) and a New DNA Mini-Barcode Target. PLoS One 2015; 10:e0123871. [PMID: 25898278 PMCID: PMC4405593 DOI: 10.1371/journal.pone.0123871] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/23/2015] [Indexed: 11/19/2022] Open
Abstract
Most tropical mammal species are threatened or data-deficient. Data collection is impeded by the traditional monitoring approaches which can be laborious, expensive and struggle to detect cryptic diversity. Monitoring approaches using mammal DNA derived from invertebrates are emerging as cost- and time-effective alternatives. As a step towards development of blowfly-derived DNA as an effective method for mammal monitoring in the biodiversity hotspot of Peninsular Malaysia, our objectives were (i) to determine the persistence period of amplifiable mammal mtDNA in blowfly guts through a laboratory feeding experiment (ii) to design and test primers that can selectively amplify mammal COI DNA mini-barcodes in the presence of high concentrations of blowfly DNA. The persistence period of amplifiable mammal mtDNA in blowfly guts was 24 h to 96 h post-feeding indicating the need for collecting flies within 24 h of capture to detect mammal mtDNA of sufficient quantity and quality. We designed a new primer combination for a COI DNA mini-barcode that did not amplify blowfly DNA and showed 89% amplification success for a dataset of mammals from Peninsular Malaysia. The short (205 bp) DNA mini-barcode could distinguish most mammal species (including separating dark taxa) and is of suitable length for high-throughput sequencing. Our new DNA mini-barcode target and a standardized trapping protocol with retrieval of blowflies every 24 h could point the way forward in the development of blowfly-derived DNA as an effective method for mammal monitoring.
Collapse
Affiliation(s)
- Ping-Shin Lee
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- * E-mail: (PSL); (JJW)
| | - Kong-Wah Sing
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - John-James Wilson
- Museum of Zoology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Ecology and Biodiversity Program, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- * E-mail: (PSL); (JJW)
| |
Collapse
|
9
|
Dong W, Liu H, Xu C, Zuo Y, Chen Z, Zhou S. A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs. BMC Genet 2014; 15:138. [PMID: 25526752 PMCID: PMC4293818 DOI: 10.1186/s12863-014-0138-z] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 11/26/2014] [Indexed: 01/20/2023] Open
Abstract
Background Universal conventional DNA barcodes will become more and more popular in biological material identifications. However, in many cases such as processed medicines or canned food, the universal conventional barcodes are unnecessary and/or inapplicable due to DNA degradation. DNA mini-barcode is a solution for such specific purposes. Here we exemplify how to develop the best mini-barcodes for specific taxa using the ginseng genus (Panax) as an example. Results The chloroplast genome of P. notoginseng was sequenced. The genome was compared with that of P. ginseng. Regions of the highest variability were sought out. The shortest lengths which had the same discrimination powers of conventional lengths were considered the best mini-barcodes. The results showed that the chloroplast genome of P. notoginseng is 156,387 bp. There are only 464 (0.30%) substitutions between the two genomes. The intron of rps16 and two regions of the coding gene ycf1, ycf1a and ycf1b, evolved the quickest and served as candidate regions. The mini-barcodes of Panax turned out to be 60 bp for ycf1a at a discrimination power of 91.67%, 100 bp for ycf1b at 100%, and 280 bp for rps16 at 83.33%. Conclusions The strategy by searching the whole chloroplast genomes, identifying the most variable regions, shortening the focal regions for mini-barcodes are believed to be efficient in developing taxon-specific DNA mini-barcodes. The best DNA mini-barcodes are guaranteed to be found following this strategy. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0138-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Han Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Yunjuan Zuo
- Shanghai Chenshan Plant Science Research Center, the Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan College, Wenshan, 663000, Yunnan, China.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| |
Collapse
|
10
|
Tang M, Tan M, Meng G, Yang S, Su X, Liu S, Song W, Li Y, Wu Q, Zhang A, Zhou X. Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Res 2014; 42:e166. [PMID: 25294837 PMCID: PMC4267667 DOI: 10.1093/nar/gku917] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species >15 kb and the remaining >10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
Collapse
Affiliation(s)
- Min Tang
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Meihua Tan
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100094, China
| | - Guanliang Meng
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China China University of Geosciences, 388 Lumo Road, Wuhan 430074, China
| | - Shenzhou Yang
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Xu Su
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Shanlin Liu
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Wenhui Song
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Yiyuan Li
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Qiong Wu
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Aibing Zhang
- Capital Normal University, Beijing 100094, China
| | - Xin Zhou
- China National GeneBank, BGI-Shenzhen, Beishan Road, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| |
Collapse
|
11
|
Zhou X, Li Y, Liu S, Yang Q, Su X, Zhou L, Tang M, Fu R, Li J, Huang Q. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience 2013; 2:4. [PMID: 23587339 PMCID: PMC3637469 DOI: 10.1186/2047-217x-2-4] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/01/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities. RESULTS Mitochondrial enrichment directly followed by Illumina shotgun sequencing, at an ultra-high sequence volume, enabled the recovery of Cytochrome c Oxidase subunit 1 (COI) barcode sequences, which allowed for the estimation of species composition at high fidelity for a terrestrial insect community. With 15.5 Gbp Illumina data, approximately 97% and 92% were detected out of the 37 input Operational Taxonomic Units (OTUs), whether the reference barcode library was used or not, respectively, while only 1 novel OTU was found for the latter. Additionally, relatively strong correlation between the sequencing volume and the total biomass was observed for species from the bulk sample, suggesting a potential solution to reveal relative abundance. CONCLUSIONS The ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs. However, further improvement for mitochondrial enrichment is likely needed for the application of the new pipeline in analyzing arthropod communities at higher diversity.
Collapse
Affiliation(s)
- Xin Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
- China National GeneBank-Shenzhen, Yantian District, Shenzhen, Guangdong Province 518083, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, Shenzhen, Guangdong Province 518083, China
| | - Yiyuan Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
- China National GeneBank-Shenzhen, Yantian District, Shenzhen, Guangdong Province 518083, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, Shenzhen, Guangdong Province 518083, China
| | - Shanlin Liu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
- China National GeneBank-Shenzhen, Yantian District, Shenzhen, Guangdong Province 518083, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, Shenzhen, Guangdong Province 518083, China
| | - Qing Yang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Xu Su
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
- China National GeneBank-Shenzhen, Yantian District, Shenzhen, Guangdong Province 518083, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, Shenzhen, Guangdong Province 518083, China
| | - Lili Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
- China National GeneBank-Shenzhen, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Min Tang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
- China National GeneBank-Shenzhen, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Ribei Fu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Jiguang Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Quanfei Huang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| |
Collapse
|