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\begin{document}

\title{Museomic approaches to genotype historic Cinchona barks}



\author[1]{Nataly Canales}%
\author[2]{Elliot Gardner}%
\author[1]{Tobias Gress H.}%
\author[3]{Kim Walker}%
\author[4]{Vanessa Bieker}%
\author[5]{Michael Martin}%
\author[3]{Mark  Nesbitt}%
\author[3]{Alexandre  Antonelli}%
\author[1]{Nina Rønsted}%
\author[6]{Christopher Barnes}%
\affil[1]{University of Copenhagen}%
\affil[2]{Florida International University}%
\affil[3]{Royal Botanic Gardens Kew}%
\affil[4]{NTNU}%
\affil[5]{Norwegian University of Science and Technology}%
\affil[6]{University of Copenhagen Faculty of Health Sciences}%


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  \date{May 25, 2024}


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\begin{abstract}
Over the last few centuries, millions of plant specimens have
accumulated within herbaria and biocultural collections. These include
type specimens, used to define species, and populations that are rare,
extinct or difficult to access. They therefore represent a considerable
resource for a broad range of scientific uses. However, collections
degrade over time, and become increasingly difficult to characterise
their genetic signatures, even considering exponential advancements in
sequencing technologies. Here, we tested the genotyping performance on
highly degraded samples using a commonly used high-throughput sequencing
(HtS) technique, genome skimming, against a recent alternative target
capture kit, the universal set Angiosperm-353. We performed phylogenomic
analyses of modern leaf and historical barks of Cinchona, including 23
historical barks and six fresh leaf specimens. DNA within historical
barks is highly degraded, therefore a customised DNA extraction method
was developed before library preparation. We show that sample
degradation over time directly impacted the quantity and quality of the
data produced by both methodologies (in terms of reads mapped to the
references). However, we find that both approaches generate enough data
to infer phylogenetic relationships, even between highly degraded
specimens that are over 230 years old. Within historical barks, the
target capture kit is more advantageous than genome skimming in
profiling Cinchona species since it was possible to retrieve nuclear and
plastid data to infer phylogenies. This study showcases the value of
historical samples in genetic studies and paves the way for further
experiments across different taxonomic groups with varying levels of
genetic variation or hybridisation.%
\end{abstract}%



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\verb`museomics_cinchona_methods_submission.docx`  available at \url{https://authorea.com/users/739545/articles/713068-museomic-approaches-to-genotype-historic-cinchona-barks}\selectlanguage{english}
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\verb`Table1_reedit.xlsx`  available at \url{https://authorea.com/users/739545/articles/713068-museomic-approaches-to-genotype-historic-cinchona-barks}

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