An Extreme Metabolism: Iso-Seq analysis of the Ruby-Throated Hummingbird Transcriptome

There are many features of natural and evolutionary history, morphology, and physiology that distinguish our study species, the ruby-throated hummingbird (Archilochus colubris). They sustain the highest metabolic rates among all vertebrates; even while engaging in an annual migratory journey between Eastern North America and Central America. Notably, hummingbirds can switch rapidly (20-30 minutes) between a fuel of lipids to newly ingested sugars.

This remarkable metabolism is supported by enzymes which operate at the extreme limit of catalytic efficiency. Understanding the molecular basis of enzymatic action will provide a foundation enabling rational engineering of metabolic circuits in other systems.

To do this, we generated a de novo transcriptome of the hummingbird liver using PacBio IsoSeq, yielding a total of 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed the data with the SMRTAnalysis IsoSeq pipeline, including classification of reads, clustering of isoforms (ICE) followed by error-correction (Quiver). IsoSeq data is unique in that it provides full length mRNA transcripts, giving clear insight into coding sequences for novel protein products.

We used BLAST+ to search for human and chicken gene orthologs in our polished transcriptome.  We also aligned our transcriptome against the Calypte draft genome where possible. Our characterization of the resulting protein coding sequences provides clues into how the hummingbird achieves its extreme metabolism.