A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). Issue 12 (20th December 2021)

• Record Type: Journal Article
• Authors: Mueller, Ralf C; Ellström, Patrik; Howe, Kerstin; Uliano-Silva, Marcela; Kuo, Richard I; Miedzinska, Katarzyna; Warr, Amanda; Fedrigo, Olivier; Haase, Bettina; Mountcastle, Jacquelyn; Chow, William; Torrance, James; Wood, Jonathan M D; Järhult, Josef D; Naguib, Mahmoud M; Olsen, Björn; Jarvis, Erich D; Smith, Jacqueline; Eöry, Lél; Kraus, Robert H S
• Is Part Of: GigaScience. Volume 10:Issue 12(2021)
• Publication Date: 2021-12-20
• Subjects: tufted duck -- Aythya fuligula -- genome annotation -- transcriptome sequencing -- Vertebrate Genomes Project -- Iso-Seq -- Pacific Biosciences -- RNA sequencing -- small RNA; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giab081
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: 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. 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. 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.