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Yang F, Zhao G, Zhou L, Li B. Complete mitochondrial genome of White-rumped Munia Lonchura striata swinhoei (Passeriformes: Estrildidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3028-9. [PMID: 26190080 DOI: 10.3109/19401736.2015.1063052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
White-rumped Munia Lonchura striata is a small passerine bird from the family of waxbill "finches" (Estrildidae), which are close relatives of the true finches (Fringillidae) and true sparrows (Passeridae). In this study, we determined the mitogenome of Lonchura striata swinhoei by the PCR-based method. The mitogenome (16 813 bp) comprises 13 protein-coding genes, 22 tRNA, two rRNA genes, and a control region. Gene order is identical to most of the other passerine birds. The DNA base composition is A, 31.70%; C, 13.70%; T, 31.40%, and G, 23.20%. All protein-coding genes start with a typical ATN codon except for the gene COI that uses GTG as the start codon. Conventional stop codon (TAA) has been assigned to seven of the PCGs, COIII, and ND4 terminate with T-. Both neighbor-joining and Bayesian analyses support that Lonchura striata swinhoei has close relative with Taeniopygia guttata.
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Affiliation(s)
- Fan Yang
- a School of Resources and Environmental Engineering, Anhui University , Hefei , PR China and.,b Anhui Biodiversity Information Center , Hefei , PR China
| | - Guanghong Zhao
- a School of Resources and Environmental Engineering, Anhui University , Hefei , PR China and.,b Anhui Biodiversity Information Center , Hefei , PR China
| | - Lizhi Zhou
- a School of Resources and Environmental Engineering, Anhui University , Hefei , PR China and.,b Anhui Biodiversity Information Center , Hefei , PR China
| | - Bo Li
- a School of Resources and Environmental Engineering, Anhui University , Hefei , PR China and.,b Anhui Biodiversity Information Center , Hefei , PR China
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52
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Burrell AS, Disotell TR, Bergey CM. The use of museum specimens with high-throughput DNA sequencers. J Hum Evol 2015; 79:35-44. [PMID: 25532801 PMCID: PMC4312722 DOI: 10.1016/j.jhevol.2014.10.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/08/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022]
Abstract
Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.
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Affiliation(s)
- Andrew S Burrell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
| | - Todd R Disotell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
| | - Christina M Bergey
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
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53
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Arbeláez-Cortés E, Torres MF, López-Álvarez D, Palacio-Mejía JD, Mendoza ÁM, Medina CA. COLOMBIAN FROZEN BIODIVERSITY: 16 YEARS OF THE TISSUE COLLECTION OF THE HUMBOLDT INSTITUTE. ACTA BIOLÓGICA COLOMBIANA 2015. [DOI: 10.15446/abc.v20n2.47102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Collections of tissue samples stand as keystone sources of molecular information to construct biodiversity knowledge, and are particularly useful in megadiverse countries. In 1998 the Humboldt Institute (<em>Instituto de Investigación de Recursos Biológicos Alexander von Humboldt</em>) began a tissue collection of Colombian biodiversity (IAvH-CT) and the aim of this work is to present a diagnostic and an historical narrative for that collection, constructed by compiling information and experiences on its management as well as by organizing and curating the information of each catalogued sample. After 16 years the IAvH-CT harbors 16469 samples, which represent around 2530 species from 1289 genera, and 323 families of the Colombian biodiversity. Samples are biased toward plants and birds (84 %), but also include other animal taxa. Geographically, IAvH-CT includes samples from all Colombian departments, but there is a broad variation in their coverage. When compared with other international collections IAvH-CT fulfills several standards of sample storage and data management, but have a major weakness that is that several tissues seem to lack a vouchered specimen. Tissues housed at IAvH-CT have been included in at least 48 studies published in several scientific journals. IAvH-CT is implementing strategies to improve curatorial standards, fill-up taxonomic gaps, and to explore the potential of its samples to understand the outstanding Colombian biota in a cooperative research frame among institutions.
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54
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Turner CR, Miller DJ, Coyne KJ, Corush J. Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.). PLoS One 2014; 9:e114329. [PMID: 25474207 PMCID: PMC4256254 DOI: 10.1371/journal.pone.0114329] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 11/06/2014] [Indexed: 02/04/2023] Open
Abstract
Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.
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Affiliation(s)
- Cameron R. Turner
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Derryl J. Miller
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Kathryn J. Coyne
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, Delaware, United States of America
| | - Joel Corush
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
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55
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Rocha J, Coelho FJRC, Peixe L, Gomes NCM, Calado R. Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools. Sci Rep 2014; 4:6986. [PMID: 25384534 PMCID: PMC5381475 DOI: 10.1038/srep06986] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/24/2014] [Indexed: 11/23/2022] Open
Abstract
For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H′). Statistical analyses indicated that preservation significantly affects H′. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H′. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar & pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer.
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Affiliation(s)
- Joana Rocha
- 1] Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal [2] Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira n.° 228, 4050-313 Porto, Portugal
| | - Francisco J R C Coelho
- Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Luísa Peixe
- REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira n. ° 228, 4050-313 Porto, Portugal
| | - Newton C M Gomes
- Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ricardo Calado
- Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Terada ASSD, Silva LAFD, Galo R, Azevedo AD, Gerlach RF, Silva RHAD. The use of a DNA stabilizer in human dental tissues stored under different temperature conditions and time intervals. J Appl Oral Sci 2014; 22:331-5. [PMID: 25141206 PMCID: PMC4126830 DOI: 10.1590/1678-775720130683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 05/20/2014] [Indexed: 11/21/2022] Open
Abstract
Objective The present study evaluated the use of a reagent to stabilize the DNA extracted
from human dental tissues stored under different temperature conditions and time
intervals. Material and Methods A total of 161 teeth were divided into two distinct groups: intact teeth and
isolated dental pulp tissue. The samples were stored with or without the product
at different time intervals and temperature. After storage, DNA extraction and
genomic DNA quantification were performed using real-time PCR; the fragments of
the 32 samples that represented each possible condition were analyzed to find the
four pre-selected markers in STR analysis. Results The results of the quantification showed values ranging from 0.01 to 10,246.88
ng/μL of DNA. The statistical difference in the quantity of DNA was observed when
the factors related to the time and temperature of storage were analyzed. In
relation to the use of the specific reagent, its use was relevant in the group of
intact teeth when they were at room temperature for 30 and 180 days. The analysis
of the fragments in the 32 selected samples was possible irrespective of the
amount of DNA, confirming that the STR analysis using an automated method yields
good results. Conclusions The use of a specific reagent showed a significant difference in stabilizing DNA
in samples of intact human teeth stored at room temperature for 30 and 180 days,
while the results showed no justification for using the product under the other
conditions tested.
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Affiliation(s)
| | | | - Rodrigo Galo
- Ribeirão Preto School of Dentistry, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Aline de Azevedo
- Ribeirão Preto School of Dentistry, University of São Paulo, Ribeirão Preto, SP, Brazil
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57
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Chen L, Li B, Zhou L, Zhao G. The complete mitochondrial genome sequence of Predatory carp Chanodichthys erythropterus (Cypriniformes: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1119-20. [PMID: 25010069 DOI: 10.3109/19401736.2014.933328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Predatory carp Chanodichthys erythropterus is a small-sized economic cyprinid fish distributed in East Asia. We sequenced its complete mitochondrial genome by PCR-based method. The mitochondrial DNA is packaged in a compact 16,629 base pair (bp) circular molecule with A + T content of 56.1%. It contains 22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and the non-coding control region (D-loop). All PCGs are initiated by ATG codons, except for COI, which uses GTG as its start codon. Of the 13 PCGs, 12 stop with TAA and TAG, while Cyt b uses incomplete termination codon T. All tRNAs possess the classic cloverleaf secondary structure except for tRNA(Ser)(AGN), which lacks the ''DHU'' stem.
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Affiliation(s)
- Lin Chen
- a School of Resources and Environmental Engineering, Anhui University , Hefei , P. R. China and.,b Anhui Biodiversity Information Center , Hefei , P. R. China
| | - Bo Li
- a School of Resources and Environmental Engineering, Anhui University , Hefei , P. R. China and.,b Anhui Biodiversity Information Center , Hefei , P. R. China
| | - Lizhi Zhou
- a School of Resources and Environmental Engineering, Anhui University , Hefei , P. R. China and.,b Anhui Biodiversity Information Center , Hefei , P. R. China
| | - Guanghong Zhao
- a School of Resources and Environmental Engineering, Anhui University , Hefei , P. R. China and.,b Anhui Biodiversity Information Center , Hefei , P. R. China
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58
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U'Ren JM, Riddle JM, Monacell JT, Carbone I, Miadlikowska J, Arnold AE. Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. Mol Ecol Resour 2014; 14:1032-48. [PMID: 24628864 DOI: 10.1111/1755-0998.12252] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 02/14/2014] [Indexed: 12/23/2022]
Abstract
Next-generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next-generation methods can lead to difficult-to-detect errors in estimating fungal community richness, distributions and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design and various quality-control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first contrast 454 data sets generated contemporaneously from subsets of the same plant and lichen tissues that were stored in CTAB buffer, dried in silica gel or freshly frozen prior to DNA extraction. We show that storage in silica gel markedly limits the recovery of sequence data and yields a small fraction of the diversity observed by the other two methods. Using lichen mycobiont sequences as internal positive controls, we next show that despite careful filtering of raw reads and utilization of current best-practice OTU clustering methods, homopolymer errors in sequences representing rare taxa artificially increased estimates of richness c. 15-fold in a model data set. Third, we show that inferences regarding endolichenic diversity can be improved using a novel primer that reduces amplification of the mycobiont. Together, our results provide a rationale for selecting tissue treatment regimes prior to DNA extraction, demonstrate the efficacy of reducing mycobiont amplification in studies of the fungal microbiomes of lichen thalli and highlight the difficulties in differentiating true information about fungal biodiversity from methodological artefacts.
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Affiliation(s)
- Jana M U'Ren
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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59
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Homolka L. Preservation of live cultures of basidiomycetes – Recent methods. Fungal Biol 2014; 118:107-25. [DOI: 10.1016/j.funbio.2013.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/30/2013] [Accepted: 12/05/2013] [Indexed: 11/26/2022]
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60
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Allen-Hall A, McNevin D. Non-cryogenic forensic tissue preservation in the field: a review. AUST J FORENSIC SCI 2013. [DOI: 10.1080/00450618.2013.789077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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61
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Carrió E, Rosselló JA. Salt drying: a low-cost, simple and efficient method for storing plants in the field and preserving biological repositories for DNA diversity research. Mol Ecol Resour 2013; 14:344-51. [DOI: 10.1111/1755-0998.12170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Elena Carrió
- Botanical Garden ICBiBE; University of Valencia; Quart 80 Valencia 46008 Spain
| | - Josep A. Rosselló
- Botanical Garden ICBiBE; University of Valencia; Quart 80 Valencia 46008 Spain
- Marimurtra Botanic Garden; Carl Faust Foundation; PO Box 112, E-17300 Blanes Catalonia Spain
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62
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Straube D, Juen A. Storage and shipping of tissue samples for DNA analyses: A case study on earthworms. EUROPEAN JOURNAL OF SOIL BIOLOGY 2013; 57:13-18. [PMID: 26109838 PMCID: PMC4461180 DOI: 10.1016/j.ejsobi.2013.04.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 04/05/2013] [Accepted: 04/11/2013] [Indexed: 06/04/2023]
Abstract
Nowadays, molecular analyses play an important role in studies of soil dwelling animals, for example in taxonomy, phylogeography or food web analyses. The quality of the DNA, used for later molecular analyses, is an important factor and depends on collection and preservation of samples prior to DNA extraction. Ideally, DNA samples are frozen immediately upon collection, but if samples are collected in the field, suitable preservation methods might be limited due to unavailability of resources or remote field sites. Moreover, shipping samples over long distances can cause loss of DNA quality e.g. by thawing or leaking of preservation liquid. In this study we use earthworms, a key organism in soil research, to compare three different DNA preservation methods - freezing at -20 °C, storing in 75% ethanol, and freeze drying. Samples were shipped from the United States of America to Austria. The DNA of the samples was extracted using two different extraction methods, peqGOLD™ and Chelex® 100. The DNA amplification success was determined by amplifying four DNA fragments of different length. The PCR amplification success is significantly influenced by preservation method and extraction method and differed significantly depending on the length of the DNA fragment. Freeze drying samples was the best preservation method when samples were extracted using the silica based extraction method peqGOLD™. For samples that were extracted with Chelex® 100, storage in ethanol was the best preservation method. However, the overall amplification success was significantly lower for the extraction procedure based on Chelex® 100. The detection of the small DNA fragments was higher and independent from the extraction method, while the amplification success was significantly reduced for the longer DNA fragments. We recommend freeze drying of DNA samples, especially when they have to be shipped for longer distances. No special packaging or declaration is needed for freeze dried samples, and the risk of thawing is excluded. Storage of freeze dried samples also reduces costs because samples can be kept at room temperature in a desiccator. It should be noted, that the extraction methods showed significant differences in DNA amplification success. Thus, the extraction method should be taken into account when choosing the preservation method.
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Affiliation(s)
- Daniela Straube
- Corresponding author. Tel.: +43 (0) 512 507 51678; fax: +43 (0) 512 507 51799.
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Camacho-Sanchez M, Burraco P, Gomez-Mestre I, Leonard JA. Preservation of RNA and DNA from mammal samples under field conditions. Mol Ecol Resour 2013; 13:663-73. [PMID: 23617785 DOI: 10.1111/1755-0998.12108] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 03/18/2013] [Accepted: 03/21/2013] [Indexed: 11/27/2022]
Abstract
Ecological and conservation genetics require sampling of organisms in the wild. Appropriate preservation of the collected samples, usually by cryostorage, is key to the quality of the genetic data obtained. Nevertheless, cryopreservation in the field to ensure RNA and DNA stability is not always possible. We compared several nucleic acid preservation solutions appropriate for field sampling and tested them on rat (Rattus rattus) blood, ear and tail tip, liver, brain and muscle. We compared the efficacy of a nucleic acid preservation (NAP) buffer for DNA preservation against 95% ethanol and Longmire buffer, and for RNA preservation against RNAlater (Qiagen) and Longmire buffer, under simulated field conditions. For DNA, the NAP buffer was slightly better than cryopreservation or 95% ethanol, but high molecular weight DNA was preserved in all conditions. The NAP buffer preserved RNA as well as RNAlater. Liver yielded the best RNA and DNA quantity and quality; thus, liver should be the tissue preferentially collected from euthanized animals. We also show that DNA persists in nonpreserved muscle tissue for at least 1 week at ambient temperature, although degradation is noticeable in a matter of hours. When cryopreservation is not possible, the NAP buffer is an economical alternative for RNA preservation at ambient temperature for at least 2 months and DNA preservation for at least 10 months.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain.
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Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates. PLoS One 2013; 8:e51273. [PMID: 23308097 PMCID: PMC3537618 DOI: 10.1371/journal.pone.0051273] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022] Open
Abstract
Molecular methods, such as DNA barcoding, have the potential to enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvertebrates. Using higher volumes or concentrations of ethanol, requirements for shorter holding times, or the need to include additional filtering may increase cost and logistical constraints to existing biomonitoring programs. To address this issue we evaluated the efficacy of various ethanol-based sample preservation methods at maintaining DNA integrity. We evaluated a series of methods that were minimally modified from typical field protocols in order to identify an approach that can be readily incorporated into existing monitoring programs. Benthic macroinvertebrates were collected from a minimally disturbed stream in southern California, USA and subjected to one of six preservation treatments. Ten individuals from five taxa were selected from each treatment and processed to produce DNA barcodes from the mitochondrial gene cytochrome c oxidase I (COI). On average, we obtained successful COI sequences (i.e. either full or partial barcodes) for between 93–99% of all specimens across all six treatments. As long as samples were initially preserved in 95% ethanol, successful sequencing of COI barcodes was not affected by a low dilution ratio of 2∶1, transfer to 70% ethanol, presence of abundant organic matter, or holding times of up to six months. Barcoding success varied by taxa, with Leptohyphidae (Ephemeroptera) producing the lowest barcode success rate, most likely due to poor PCR primer efficiency. Differential barcoding success rates have the potential to introduce spurious results. However, routine preservation methods can largely be used without adverse effects on DNA integrity.
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65
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Allen-Hall A, McNevin D. Human tissue preservation for disaster victim identification (DVI) in tropical climates. Forensic Sci Int Genet 2012; 6:653-7. [DOI: 10.1016/j.fsigen.2011.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 12/09/2011] [Accepted: 12/19/2011] [Indexed: 11/28/2022]
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Wong PBY, Wiley EO, Johnson WE, Ryder OA, O’Brien SJ, Haussler D, Koepfli KP, Houck ML, Perelman P, Mastromonaco G, Bentley AC, Venkatesh B, Zhang YP, Murphy RW. Tissue sampling methods and standards for vertebrate genomics. Gigascience 2012; 1:8. [PMID: 23587255 PMCID: PMC3626508 DOI: 10.1186/2047-217x-1-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 07/12/2012] [Indexed: 11/18/2022] Open
Abstract
The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual); three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 μg of DNA); and one-star (ethanol-preserved tissue for 700 μg of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species' natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota.
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Affiliation(s)
- Pamela BY Wong
- Department of Ecology and Evolutionary Biology, University of Toronto, 25
Willcocks St., Toronto, Ontario, M5S 3B2, Canada
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100
Queen`s Park, Toronto, Ontario, M5S 2C6, Canada
| | - Edward O Wiley
- Division of Ichthyology, Biodiversity Institute, University of Kansas, 1345
Jayhawk Boulevard, Lawrence, Kansas, 66045, USA
| | - Warren E Johnson
- Laboratory of Genomic Diversity, National Cancer Institute, 31 Center Drive,
Frederick, Maryland, 21702-1201, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road,
Escondido, California, 92027, USA
| | - Stephen J O’Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State
University, 8 Viborgskaya Street, St. Petersburg, 194044, Russia
| | - David Haussler
- Center for Biomolecular Science and Engineering, University of California Santa
Cruz, 1156 High Street, Santa Cruz, California, 95064, USA
| | - Klaus-Peter Koepfli
- Laboratory of Genomic Diversity, National Cancer Institute, 31 Center Drive,
Frederick, Maryland, 21702-1201, USA
| | - Marlys L Houck
- San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road,
Escondido, California, 92027, USA
| | - Polina Perelman
- Laboratory of Animal Cytogenetics, Institute of Molecular and Cellular Biology,
Lavrentiev 10, Novosibirsk, 630090, Russia
| | - Gabriela Mastromonaco
- Reproductive Physiology, Toronto Zoo, 361A Old Finch Avenue, Scarborough, Ontario,
M1B 5K7, Canada
| | - Andrew C Bentley
- Division of Ichthyology, Biodiversity Institute, University of Kansas, 1345
Jayhawk Boulevard, Lawrence, Kansas, 66045, USA
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR,
Biopolis, Singapore, 138673, Singapore
| | - Ya-ping Zhang
- State Key Laboratory of Genetic Resource and Evolution, Kunming Institute of
Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan,
650223, China
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, 2
North Cuihu Road, Kunming, Yunnan, 650091, China
| | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25
Willcocks St., Toronto, Ontario, M5S 3B2, Canada
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100
Queen`s Park, Toronto, Ontario, M5S 2C6, Canada
- State Key Laboratory of Genetic Resource and Evolution, Kunming Institute of
Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan,
650223, China
| | - G10KCOS
- Genome 10 K Community of Scientists. http://www.genome10k.org/, Santa Cruz,
California, USA
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Szinwelski N, Fialho VS, Yotoko KSC, Seleme LR, Sperber CF. Ethanol fuel improves arthropod capture in pitfall traps and preserves DNA. Zookeys 2012:11-22. [PMID: 22679388 PMCID: PMC3361084 DOI: 10.3897/zookeys.196.3130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 05/15/2012] [Indexed: 11/25/2022] Open
Abstract
We tested the value of ethanol fuel as a killing solution in terms of sampling efficiency (species richness and accumulated abundance) and DNA preservation of Ensifera ground-dwelling specimens. Sampling efficiency was evaluated comparing abundance and species richness of pitfall sampling using 100% ethanol fuel, with two alternative killing solutions. We evaluated the DNA preservation efficiency of the killing solutions and of alternative storage solutions. Ethanol fuel was the most efficient killing solution, and allowed successful DNA preservation. This solution is cheaper than other preserving liquids, and is easily acquired near field study sites since it is available at every fuel station in Brazil and at an increasing number of fuel stations in the U.S. We recommend the use of ethanol fuel as a killing and storage solution, because it is a cheap and efficient alternative for large-scale arthropod sampling, both logistically and for DNA preservation. For open habitat sampling with high day temperatures, we recommend doubling the solution volume to cope with high evaporation, increasing its efficacy over two days.
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Affiliation(s)
- Neucir Szinwelski
- Postgraduate Programme in Entomology, Department of Entomology, Federal University of Viçosa, Avenida P.H. Rolfs s/n, Centro, Viçosa, Minas Gerais, Brazil
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68
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Justine JL, Briand MJ, Bray RA. A quick and simple method, usable in the field, for collecting parasites in suitable condition for both morphological and molecular studies. Parasitol Res 2012; 111:341-51. [DOI: 10.1007/s00436-012-2845-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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Dowell FE, Noutcha AEM, Michel K. Short report: The effect of preservation methods on predicting mosquito age by near infrared spectroscopy. Am J Trop Med Hyg 2012; 85:1093-6. [PMID: 22144450 PMCID: PMC3225158 DOI: 10.4269/ajtmh.2011.11-0438] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Determining mosquito age is important to evaluate vector control programs because the ability to transmit diseases is age dependent. Current age-grading techniques require dissection or RNA extraction. Near infrared spectroscopy has been used to rapidly and nondestructively determine the age of fresh mosquitoes and specimens stored in RNAlater, but other preservation techniques have not been examined. Thus, in this study, we investigate whether age can be predicted from insects preserved by various common methods. Results from this study show that age can be predicted from mosquitoes preserved with desiccants, ethanol, Carnoy, RNAlater, or refrigeration with confidence intervals < 1.4 days. The best results were generally obtained from mosquitoes stored using desiccants, RNAlater, or refrigeration.
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Affiliation(s)
- Floyd E Dowell
- Engineering and Wind Erosion Research Unit, Center for Grain and Animal Health Research, United States Department of Agriculture, Agricultural Research Service, Manhattan, Kansas 66502, USA.
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70
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Abstract
Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.
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Affiliation(s)
- Miguel Vences
- Division of Evolutionary Biology Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
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71
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Töpfer T, Gamauf A, Haring E. Utility of arsenic-treated bird skins for DNA extraction. BMC Res Notes 2011; 4:197. [PMID: 21676254 PMCID: PMC3138465 DOI: 10.1186/1756-0500-4-197] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 06/15/2011] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Natural history museums receive a rapidly growing number of requests for tissue samples from preserved specimens for DNA-based studies. Traditionally, dried vertebrate specimens were treated with arsenic because of its toxicity and insect-repellent effect. Arsenic has negative effects on in vivo DNA repair enzymes and consequently may inhibit PCR performance. In bird collections, foot pad samples are often requested since the feet were not regularly treated with arsenic and because they are assumed to provide substantial amounts of DNA. However, the actual influence of arsenic on DNA analyses has never been tested. FINDINGS PCR success of both foot pad and body skin samples was significantly lower in arsenic-treated samples. In general, foot pads performed better than body skin samples. Moreover, PCR success depends on collection date in which younger samples yielded better results. While the addition of arsenic solution to the PCR mixture had a clear negative effect on PCR performance after the threshold of 5.4 μg/μl, such high doses of arsenic are highly unlikely to occur in dried zoological specimens. CONCLUSIONS While lower PCR success in older samples might be due to age effects and/or DNA damage through arsenic treatment, our results show no inhibiting effect on DNA polymerase. We assume that DNA degradation proceeds more rapidly in thin tissue layers with low cell numbers that are susceptible to external abiotic influences. In contrast, in thicker parts of a specimen, such as foot pads, the outermost horny skin may act as an additional barrier. Since foot pads often performed better than body skin samples, the intention to preserve morphologically important structures of a specimen still conflicts with the aim to obtain optimal PCR success. Thus, body skin samples from recently collected specimens should be considered as alternative sources of DNA.
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Affiliation(s)
- Till Töpfer
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt/M,, Germany.
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