Abstract
BackgroundHummingbirds oxidize ingested nectar sugars directly to fuel foraging but cannot sustain this fuel use during fasting periods, such as during the night or during long-distance migratory flights. Instead, fasting hummingbirds switch to oxidizing stored lipids that are derived from ingested sugars. The hummingbird liver plays a key role in moderating energy homeostasis and this remarkable capacity for fuel switching. Additionally, liver is the principle location of de novo lipogenesis, which can occur at exceptionally high rates, such as during premigratory fattening. Yet understanding how this tissue and whole organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation.FindingsWe generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, then clustered isoforms into gene families to generate de novo gene contigs using Cogent. We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. Finally, we closely examined homology of critical lipid metabolism genes between our transcriptome data and avian and human genomes.ConclusionsWe confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the hepatic lipogenic pathways. Our results leverage cutting-edge technology and a novel bioinformatics pipeline to provide a first direct look at the transcriptome of this incredible organism.
Highlights
Hummingbirds are the only avian group to engage in sustained hovering flight as a means for accessing floral nectar, their primary caloric energy source
We generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions
As the initial impetus for our investigation centered on the exceptional metabolism and energetics of hummingbirds, we focused our investigation on orthologs tagged as part of the “metabolic process (GO:0008152)” grouping
Summary
Hummingbirds are the only avian group to engage in sustained hovering flight as a means for accessing floral nectar, their primary caloric energy source. Small hummingbirds, such as the ruby-throated hummingbird (Archilochus colubris), achieve some of the highest mass-specific metabolic rates observed among vertebrates [1,2] Given their specialized, sugar-rich diet, it is not surprising that hummingbirds are able to fuel this intense form of exercise exclusively by oxidizing carbohydrates [3,4]. Completed sequencing of the Anna’s hummingbird (Calypte anna) genome provides a powerful new tool in the arsenal of biologists seeking to understand variation in metabolic physiology in hummingbirds and other groups [20] Despite their extreme catabolic and anabolic capabilities, hummingbirds have the smallest genomes among birds [21] and, in general, have among the smallest vertebrate genomes [22]. Full-length sequences greatly enhance the likelihood of detecting novel or rare splice variants, which is crucial for fully characterizing the transcriptomes of lesser studied, nonmodel organisms such as the hummingbird
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