ArticleGigaScience2018
Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 90 citations in OpenAlex.
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- Deciphering triterpenoid saponin biosynthesis by leveraging transcriptome response to methyl jasmonate elicitation in Saponaria vaccaria.Nature communications · 2023Article
- Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1.Heliyon · 2023Article
- Genomic insights into metabolic flux in hummingbirds.Genome research · 2023Article
- Transcript- and annotation-guided genome assembly of the European starling.Molecular ecology resources · 2022Article
- Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates.Plant biotechnology journal · 2022Article
- Combination analysis of single-molecule long-read and Illumina sequencing provides insights into the anthocyanin accumulation mechanism in an ornamental grass, Pennisetum setaceum cv. Rubrum.Plant molecular biology · 2022Article
- Seed Germination Mechanism ofFrontiers in plant science · 2022Article
- A reference genome for the nectar-robbing Black-throated Flowerpiercer (Diglossa brunneiventris).G3 (Bethesda, Md.) · 2021Article
- Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish.Genome research · 2021Article
- An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids.The plant genome · 2021Article
- Comparative physiological and full-length transcriptome analyses reveal the molecular mechanism of melatonin-mediated salt tolerance in okra (Abelmoschus esculentus L.).BMC plant biology · 2021Article
- Single-Molecule Long-Read Sequencing of Purslane (Plants (Basel, Switzerland) · 2021Article
- PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress inFrontiers in genetics · 2021Article
- Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing.Scientific reports · 2020Article
- Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses inInternational journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.