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- Title
Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns.
- Authors
Lu, Yuan; Boswell, Mikki; Boswell, William; Salinas, Raquel Ybanez; Savage, Markita; Reyes, Jose; Walter, Sean; Marks, Rebecca; Gonzalez, Trevor; Medrano, Geraldo; Warren, Wesley C.; Schartl, Manfred; Walter, Ronald B.
- Abstract
Background: Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period. Results: Our results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs. Conclusions: These observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.
- Subjects
GENE expression; MOLECULAR evolution; GENES; GENE expression profiling; DATA mining; SCIENTIFIC visualization; XIPHOPHORUS maculatus
- Publication
BMC Genomics, 2020, Vol 21, Issue 1, pN.PAG
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/s12864-020-07202-9