Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris
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Abstract
Background
Hummingbirds 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.
Findings
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. 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.
Conclusions
We 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.
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Now published in GigaScience doi: 10.1093/gigascience/giy009
Rachael E. Workman 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexander M. Myrka 2Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada and Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth Tseng 4Pacific Biosciences, Menlo Park, California, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteG. William Wong 3Department of Physiology and Center for Metabolism and Obesity Research, Johns Hopkins University School of …
Now published in GigaScience doi: 10.1093/gigascience/giy009
Rachael E. Workman 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexander M. Myrka 2Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada and Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteElizabeth Tseng 4Pacific Biosciences, Menlo Park, California, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteG. William Wong 3Department of Physiology and Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKenneth C. Welch Jr.2Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada and Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, CanadaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kenneth C. Welch Jr.Winston Timp 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Winston Timp
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy009 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101011 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101012
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