Hummingbird Transcriptome: Iso-Seq Analysis of the Ruby-Throated Hummingbird Archilochus colubris

The hummingbird occupies a unique place in the vertebrate world. It has the highest known metabolic rate, needed to fuel incredible energetic demands of hovering flight the bird performs daily to collect nectar from flowers. To sustain hovering flight, a hummingbird needs to maintain a wing beat up to 200 beats per second. This remarkable feat is made possible by extremely high metabolic rates in the liver, with certain enzymes operating at the very limit of catalytic efficiency. Understanding the molecular basis of such extreme physiology will provide foundational knowledge to enable rational engineering of metabolic circuits in mammalian cells.

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 data with the SMRTAnalysis IsoSeq platform, including classification of reads, clustering of isoforms (ICE) followed by error-correction (Quiver).  We then 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.

IsoSeq data is in the unique position of providing full length mRNA transcripts, giving clear insight into coding sequences for novel protein products.  A genome assembly exists for Anna’s hummingbird (Calypte anna), but the gene annotation produced by homology-based annotation is still missing several key orthologs important in metabolism.  Using the transcriptome data, we identified important full coding sequences and discovered homologies to human and chicken genomes.