Sökning: WFRF:(Komoroske Lisa M.) >
Benchmarking ultra-...
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
-
- Dahn, Hollis A. (författare)
- Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.
-
- Mountcastle, Jacquelyn (författare)
- Rockefeller Univ, New York, NY 10065 USA.
-
- Balacco, Jennifer (författare)
- Rockefeller Univ, New York, NY 10065 USA.
-
visa fler...
-
- Winkler, Sylke (författare)
- Max Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
-
- Bista, Iliana (författare)
- Wellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.;Univ Cambridge, Dept Genet, Cambridge CB2 3EH, Cambs, England.
-
- Schmitt, Anthony D. (författare)
- Arima Genom Inc, San Diego, CA 92121 USA.
-
- Vinnere, Olga (författare)
- Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab
-
- Formenti, Giulio (författare)
- Rockefeller Univ, New York, NY 10065 USA.
-
- Oliver, Karen (författare)
- Wellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.
-
- Smith, Michelle (författare)
- Wellcome Sanger Inst, Tree Life Program, Hinxton CB10 1SA, Cambs, England.
-
- Tan, Wenhua (författare)
- Max Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
-
- Kraus, Anne (författare)
- Max Planck Inst Mol Cell Biol & Genet, D-01307 Saxony, Germany.
-
- Mac, Stephen (författare)
- Arima Genom Inc, San Diego, CA 92121 USA.
-
- Komoroske, Lisa M. (författare)
- Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
-
- Lama, Tanya (författare)
- Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
-
- Crawford, Andrew J. (författare)
- Univ Los Andes, Dept Biol Sci, Bogota 111711, Colombia.
-
- Murphy, Robert W. (författare)
- Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.
-
- Brown, Samara (författare)
- Rockefeller Univ, New York, NY 10065 USA.
-
- Scott, Alan F. (författare)
- Johns Hopkins Univ, Dept Med, Baltimore, MD 21287 USA.
-
- Morin, Phillip A. (författare)
- NOAA, Southwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, La Jolla, CA 92037 USA.
-
- Jarvis, Erich D. (författare)
- Rockefeller Univ, New York, NY 10065 USA.;Howard Hughes Med Inst, Chevy Chase, MD 20815 USA.
-
- Fedrigo, Olivier (författare)
- Rockefeller Univ, New York, NY 10065 USA.
-
visa färre...
-
Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada Rockefeller Univ, New York, NY 10065 USA. (creator_code:org_t)
- 2022-08-10
- 2022
- Engelska.
-
Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 11
- Relaterad länk:
-
https://doi.org/10.1...
-
visa fler...
-
https://uu.diva-port... (primary) (Raw object)
-
https://urn.kb.se/re...
-
https://doi.org/10.1...
-
visa färre...
Abstract
Ämnesord
Stäng
- Background: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types.Results: We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.Conclusion: We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Nyckelord
- long-read sequencing
- genome assembly
- tissue preservation
- HMW DNA extraction
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas
- Av författaren/redakt...
-
Dahn, Hollis A.
-
Mountcastle, Jac ...
-
Balacco, Jennife ...
-
Winkler, Sylke
-
Bista, Iliana
-
Schmitt, Anthony ...
-
visa fler...
-
Vinnere, Olga
-
Formenti, Giulio
-
Oliver, Karen
-
Smith, Michelle
-
Tan, Wenhua
-
Kraus, Anne
-
Mac, Stephen
-
Komoroske, Lisa ...
-
Lama, Tanya
-
Crawford, Andrew ...
-
Murphy, Robert W ...
-
Brown, Samara
-
Scott, Alan F.
-
Morin, Phillip A ...
-
Jarvis, Erich D.
-
Fedrigo, Olivier
-
visa färre...
- Om ämnet
-
- NATURVETENSKAP
-
NATURVETENSKAP
-
och Biologi
-
och Genetik
- Artiklar i publikationen
-
GigaScience
- Av lärosätet
-
Uppsala universitet