Ioannis Chrysostomakis

Sep 27, 2024 | biorxiv.org | Bernhard Bein |Ioannis Chrysostomakis |Larissa S. Arantes |Tom Brown

AbstractMuseum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit.

Mar 7, 2024 | biorxiv.org | Ioannis Chrysostomakis |Larissa S. Arantes |Tom Brown |Bernhard Bein

AbstractAdvances in long-read sequencing technology have shifted a key challenge in biodiversity genomics from DNA sequencing and genome assembly to obtaining suitable samples. Although flash-frozen samples remain the gold standard, they are often unattainable. In contrast, natural history collections worldwide harbor millions of ethanol-preserved samples, but such samples remain largely unutilized for long-read sequencing.

Dec 7, 2023 | genome.cshlp.org | Astrid Böhne |Ioannis Chrysostomakis |Simon Vitt |Zeynep Oğuzhan

2 1Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn, Germany; 2Bonn Institute of Organismic Biology (BIOB), Department of Animal Biodiversity, University of Bonn, 53121 Bonn, Germany; 3Evolutionary Biology, Bielefeld University, 33615 Bielefeld, Germany Corresponding authors: a.boehne{at}leibniz-lib.de, tthuenke{at}uni-bonn.de Footnotes [Supplemental material is available for this article.] Article published online before print.

Dec 1, 2023 | biorxiv.org | Madlen Stange |Sebastian Martin |Temitope O Oriowo |Ioannis Chrysostomakis

AbstractIn this study we present an in-depth analysis of the Eurasian Minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 25) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).