KOPS - The Institutional Repository of the University of Konstanz

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Cite This

Files in this item

Checksum: MD5:3c755be1f37b9b64e9d9c7e540bb2c7c

MUELLER, Ralf, Patrik ELLSTRÖM, Kerstin HOWE, Marcela ULIANO-SILVA, Richard I. KUO, Katarzyna MIEDZINSKA, Amanda WARR, Olivier FEDRIGO, Björn OLSEN, Robert H. S. KRAUS, 2021. A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). In: GigaScience. Oxford University Press. 10(12), giab081. eISSN 2047-217X. Available under: doi: 10.1093/gigascience/giab081

@article{Mueller2021-12-20highq-56515, title={A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)}, year={2021}, doi={10.1093/gigascience/giab081}, number={12}, volume={10}, journal={GigaScience}, author={Mueller, Ralf and Ellström, Patrik and Howe, Kerstin and Uliano-Silva, Marcela and Kuo, Richard I. and Miedzinska, Katarzyna and Warr, Amanda and Fedrigo, Olivier and Olsen, Björn and Kraus, Robert H. S.}, note={Article Number: giab081} }

Fedrigo, Olivier Uliano-Silva, Marcela Warr, Amanda Kraus, Robert H. S. eng Kuo, Richard I. Miedzinska, Katarzyna 2021-12-20 Howe, Kerstin Olsen, Björn Olsen, Björn Warr, Amanda Kraus, Robert H. S. Ellström, Patrik Attribution 4.0 International Mueller, Ralf Uliano-Silva, Marcela Miedzinska, Katarzyna Mueller, Ralf A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck) 2022-02-10T13:13:02Z Kuo, Richard I. Ellström, Patrik 2022-02-10T13:13:02Z Background: The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.<br />Findings: This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families.<br />Conclusions: This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses. Howe, Kerstin Fedrigo, Olivier

Downloads since Feb 10, 2022 (Information about access statistics)

Mueller_2-cgdero73ndi67.pdf 55

This item appears in the following Collection(s)

Attribution 4.0 International Except where otherwise noted, this item's license is described as Attribution 4.0 International

Search KOPS


Browse

My Account