Satellite DNA evolution in Corvoidea inferred from short and long reads

Peona, Valentina, Kutschera, Verena E., Blom, Mozes P.K., Irestedt, Martin and Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992 (2022) Satellite DNA evolution in Corvoidea inferred from short and long reads. Molecular Ecology. ISSN 0962-1083

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Abstract

Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.

Item Type: Article
Additional Information: Funding Information: We thank Marco Ricci, Francisco J. Ruiz‐Ruano, Julie Blommaert, and Octavio M. Palacios‐Gimenez for comments on earlier versions of this manuscript. We also thank Francisco J. Ruiz Ruano and Octavio M. Palacios‐Gimenez for their help with running RepeatExplorer2. This study was supported by the Swedish Research Council Vetenskapsrådet (2016‐05139 and 2020‐04436 to Alexander Suh; 621‐2014‐5113 and 2019‐03900 to Martin Irestedt), and the Swedish Research Council Formas (2017‐01597 to Alexander Suh). Computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) through Uppsala Multidisciplinary Centre for Advanced Computational Science (UPPMAX). We also thank the Bioinformatic Advisory Programme from Science for Life Laboratory for the support in designing the initial analysis. Verena E. Kutschera is financially supported by the Knut and Alice Wallenberg Foundation as part of the National Bioinformatics Infrastructure Sweden at SciLifeLab. Publisher Copyright: © 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.
Uncontrolled Keywords: base composition,birds,birds-of-paradise,comparative genomics,crow,genomic dark matter,satellitome,ecology, evolution, behavior and systematics,genetics ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 21 Sep 2022 12:30
Last Modified: 25 Sep 2022 03:35
URI: https://ueaeprints.uea.ac.uk/id/eprint/88556
DOI: 10.1111/mec.16484

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