Supporting data for "Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris"

Dataset type: Transcriptomic
Data released on February 07, 2018

Workman RE; Myrka AM; Tseng E; Wong GW; Welch KC; Timp W (2018): Supporting data for "Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris" GigaScience Database. http://dx.doi.org/10.5524/100403

DOI10.5524/100403

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, 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.
We generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding a total of 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.
Our results leverage cutting-edge technology and a novel bioinformatics pipeline to provide a first direct look at the transcriptome of this incredible organism.

Additional details

Read the peer-reviewed publication(s):

Workman, R. E., Myrka, A. M., Wong, G. W., Tseng, E., Welch, K. C., & Timp, W. (2018). Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris. GigaScience, 7(3). doi:10.1093/gigascience/giy009

Additional information:

https://github.com/reworkman/hummingbird

http://dx.doi.org/10.5281/zenodo.1054086

Accessions (data included in GigaDB):

PROJECT: PRJNA369257





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
A.colubris_Illumia190676  Archilochus colubris Description:Liver transcriptome of Ruby-throated H...
Analyte type:RNA
Sex:male
...
+
SAMN06282498190676  Archilochus colubris Description:Liver transcriptome of Ruby-throated H...
Analyte type:RNA
Sex:male
...
+
Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Mixed archiveTAR25.01 MB2018-02-07
Mixed archiveTAR310.51 KB2018-02-07
Mixed archiveTAR3.74 MB2018-02-07
AlignmentsBAM18.13 MB2018-02-07
GitHub archivearchive9.7 KB2018-02-07
Mixed archiveTAR190.36 KB2018-02-07
Mixed archiveTAR3.09 MB2018-02-07
TextUNKNOWN20.52 KB2018-02-07
TextUNKNOWN24.92 KB2018-02-07
TextUNKNOWN3 KB2018-02-07
Displaying 11-20 of 61 File(s).
Funding body Awardee Award ID Comments
Human Frontier Science Program Dr. Kenneth C. Welch RGP0062/2016
Natural Sciences and Engineering
Research Council of Canada Dr. Kenneth C. Welch 386466
Date Action
February 7, 2018 Dataset publish
March 30, 2018 Manuscript Link added : 10.1093/gigascience/giy009