Abstract
BackgroundThe 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.FindingsThis 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.ConclusionsThis 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.
Highlights
The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks
In contrast to mallards, which carry avian influenza A virus (AIV) largely asymptomatically, tufted ducks are less commonly infected with low pathogenic AIV (LPAIV) but experience high mortality in outbreaks of highly pathogenic AIV (HPAIV) [8,9,10,11]
This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project (VGP) pipeline [24] followed by manual curation [38], which we annotated with short- and long-read transcripts from 6 different tissues, and short reads from small RNAs from the same tissues
Summary
The tufted duck (Aythya fuligula, NCBI:txid219594) is a non-model organism that has received attention because of its role in the zoonotic ecology of avian influenza A viruses (AIVs). This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the VGP pipeline [24] followed by manual curation [38], which we annotated with short- and long-read transcripts from 6 different tissues, and short reads from small RNAs from the same tissues. In the Illumina short-read RNA-Seq transcript model reconstruction, more exons per gene were recovered on average than in the long-read pipeline (Table 3). ORFs G24916.7/8 and G46857.2/3/4 were flagged with “5prime degrade,” which means that the transcript might be incomplete on the 5 end Both genes were predicted in the short-read and long-read pipeline. An alignment of the mallard and tufted duck RIGI/DDX58 amino acid sequences revealed 15 variants (14 substitutions, 1 insertion), which were predicted to have no effect on the biological function of the protein (Supplementary Tables S4 and S5). The number of predicted and annotated covariance models overlapped for 237 RNA families, while 69 were only identified in the genome scan and 9 were only identified in the pooled tissue annotations
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