%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Bethune, Kévin
%A Mariac, Cédric
%A Couderc, Marie
%A Scarcelli, Nora
%A Santoni, S.
%A Ardisson, M.
%A Martin, J. F.
%A Montufar, R.
%A Klein, V.
%A Sabot, François
%A Vigouroux, Yves
%A Couvreur, Thomas
%T Long-fragment targeted capture for long-read sequencing of plastomes
%D 2019
%L fdi:010075713
%G ENG
%J Applications in Plant Sciences
%@ 2168-0450
%K de novo assembly ; DNA probes ; long-range PCR ; MinION ; whole plastome ; sequencing
%M ISI:000468315800007
%N 5
%P e1243 [13 ]
%R 10.1002/aps3.1243
%U https://www.documentation.ird.fr/hor/fdi:010075713
%> https://www.documentation.ird.fr/intranet/publi/2019/06/010075713.pdf
%V 7
%W Horizon (IRD)
%X Premise Third-generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. Methods and Results The protocol uses cost-effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel-dried leaves. Our protocol successfully captured long-read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel-dried leaves led to low-quality plastome assemblies when compared to DNA extracted from fresh tissue. Conclusions Our protocol could also be generalized to capture long sequences from specific nuclear fragments.
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