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Divne, Anna-Maria
Publications (4 of 4) Show all publications
Alneberg, J., Karlsson, C. M. G., Divne, A.-M., Bergin, C., Homa, F., Lindh, M. V., . . . Pinhassi, J. (2018). Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. Microbiome, 6, Article ID 173.
Open this publication in new window or tab >>Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
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2018 (English)In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 6, article id 173Article in journal (Refereed) Published
Abstract [en]

Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.

Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.

Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

Place, publisher, year, edition, pages
BMC, 2018
Keywords
Single-amplified genomes, Metagenome-assembled genomes, Metagenomics, Binning, Single-cell genomics
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:uu:diva-368105 (URN)10.1186/s40168-018-0550-0 (DOI)000446307400001 ()30266101 (PubMedID)
Funder
Swedish Research Council, 2011-4369Swedish Research Council, 2015-04254Swedish Research Council, 2011-5689Swedish Research Council, 2015-04959Swedish Research Council FormasEU, European Research Council, 310039-PUZZLE_CELLSwedish Foundation for Strategic Research
Available from: 2018-12-05 Created: 2018-12-05 Last updated: 2018-12-05Bibliographically approved
Troell, K., Hallstrom, B., Divne, A.-M., Alsmark, C., Arrighi, R., Huss, M., . . . Bertilsson, S. (2016). Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics, 17, Article ID 471.
Open this publication in new window or tab >>Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes
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2016 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 17, article id 471Article in journal (Refereed) Published
Abstract [en]

Background: Infectious disease involving multiple genetically distinct populations of pathogens is frequently concurrent, but difficult to detect or describe with current routine methodology. Cryptosporidium sp. is a widespread gastrointestinal protozoan of global significance in both animals and humans. It cannot be easily maintained in culture and infections of multiple strains have been reported. To explore the potential use of single cell genomics methodology for revealing genome-level variation in clinical samples from Cryptosporidium-infected hosts, we sorted individual oocysts for subsequent genome amplification and full-genome sequencing. Results: Cells were identified with fluorescent antibodies with an 80 % success rate for the entire single cell genomics workflow, demonstrating that the methodology can be applied directly to purified fecal samples. Ten amplified genomes from sorted single cells were selected for genome sequencing and compared both to the original population and a reference genome in order to evaluate the accuracy and performance of the method. Single cell genome coverage was on average 81 % even with a moderate sequencing effort and by combining the 10 single cell genomes, the full genome was accounted for. By a comparison to the original sample, biological variation could be distinguished and separated from noise introduced in the amplification. Conclusions: As a proof of principle, we have demonstrated the power of applying single cell genomics to dissect infectious disease caused by closely related parasite species or subtypes. The workflow can easily be expanded and adapted to target other protozoans, and potential applications include mapping genome-encoded traits, virulence, pathogenicity, host specificity and resistance at the level of cells as truly meaningful biological units.

Keywords
Apicomplexa, Single cell genomics, Whole genome amplification, Cryptosporidium, Multiple infection, FACS
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-299711 (URN)10.1186/s12864-016-2815-y (DOI)000378380600001 ()27338614 (PubMedID)
Funder
Swedish Civil Contingencies Agency, DNR2012-172 1109-2015-3.4.4Swedish Research Council, 2012-3892 2012-5095
Available from: 2016-07-26 Created: 2016-07-26 Last updated: 2017-11-28Bibliographically approved
Divne, A.-M., Nilsson, M., Calloway, C., Reynolds, R., Erlich, H. & Allen, M. (2005). Forensic casework analysis using the HVI/HVII mtDNA linear array assay.. Journal of Forensic Sciences, 50(3), 548-554
Open this publication in new window or tab >>Forensic casework analysis using the HVI/HVII mtDNA linear array assay.
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2005 (English)In: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 50, no 3, p. 548-554Article in journal (Refereed) Published
Abstract [en]

The mitochondrial hypervariable regions I and II have proven to be a useful target for analysis of forensic materials, in which the amount of DNA is limited or highly degraded. Conventional mitochondrial DNA (mtDNA) sequencing can be time-consuming and expensive, limitations that can be minimized using a faster and less expensive typing assay. We have evaluated the exclusion capacity of the linear array mtDNA HVI/HVII region-sequence typing assay (Roche Applied Science) in 16 forensic cases comprising 90 samples. Using the HVI/HVII mtDNA linear array, 56% of the samples were excluded and thus less than half of the samples require further sequencing due to a match or inconclusive results. Of all the samples that were excluded by sequence analysis, 79% could be excluded using the HVI/HVII linear array alone. Using the HVI/HVII mtDNA linear array assay, we demonstrate the potential to decrease sequencing efforts substantially and thereby reduce the cost and the turn-around time in casework analysis.

Keywords
Crime, DNA primers, DNA, mitochondrial/*analysis, female, forensic medicine/methods, hair/*chemistry, humans, male, oligonucleotide array sequence analysis/*methods, research support, non-U.S. Gov't, research support, U.S. Gov't, non-P.H.S., sequence analysis, DNA/*methods
National Category
Forensic Science
Identifiers
urn:nbn:se:uu:diva-78183 (URN)000228818800009 ()15932085 (PubMedID)
Available from: 2006-03-20 Created: 2009-03-26 Last updated: 2017-12-14Bibliographically approved
Allen, M. & Divne, A.-M. (2005). Universal tag arrays in forensic SNP analysis.. Methods in Molecular Biology, 297, 141-154
Open this publication in new window or tab >>Universal tag arrays in forensic SNP analysis.
2005 (English)In: Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029, Vol. 297, p. 141-154Article in journal (Refereed) Published
Abstract [en]

Microarray-based single nucleotide polymorphism (SNP) genotyping enables simultaneous and rapid detection of a large number of markers and is thus an attractive method for forensic individual acid identification. This assay relies on a one-color detection system and minisequencing in solution before hybridization to universal tag arrays. The minisequencing reaction is based on incorporation of a fluorescent dideoxynucleotide to a primer containing a tag-sequence flanking the position to be interrogated. This one-color system detects C and T polymorphisms in separate reactions on multiple polymerase chain reaction targets with the fluorophore TAMRA coupled to the respective dideoxynucleotide. After incorporation, tagged primer sequences are hybridized through their complementary sequence on the array, and positive signals are detected by a confocal laser-scanner.

Keywords
Base sequence, DNA primers, forensic medicine, humans, nucleic acid hybridization, polymerase chain reaction, polymorphism, single nucleotide, research support, non-U.S. Gov't, microarrays, universal tag-arrays, minisequencing, forensic, SNP
National Category
Forensic Science
Identifiers
urn:nbn:se:uu:diva-78180 (URN)15570105 (PubMedID)
Available from: 2006-03-20 Created: 2009-03-26 Last updated: 2017-12-18Bibliographically approved
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