C-G.09: Exploring twin genes with DupyliCate
Authors
Claudia Sterling
University of Bonn
Boas Pucker
University of Bonn
Keywords
DupyliCate, Gene duplications, Comparative genomics, Plants, Python3, Software
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Paralogs, copies of a gene, form an important basis for novelty during evolution. Analysis of such gene duplications is important to understand the emergence of novel evolutionary traits. DupyliCate is a Python tool that has been developed for the identification, classification, and characterization of gene copies. With the ability to process multiple datasets concurrently, flexible features, and parameters to set species-specific thresholds, DupyliCate offers a high-throughput method for gene duplicate array identification. It also facilitates downstream gene expression divergence analysis of the identified duplicates, enabling their fate prediction. DupyliCate was applied on the flavonoid synthase (FLS) gene family in Brassicales and subgroup 7 myeloblastosis (MYB) transcription factors (SG7 MYB) across a diverse range of plant species to understand the duplication dynamics of these important players in flavonoid biosynthesis. This helped uncover a potential radiation of FLS genes in the Brassicaceae and a deep duplication of the SG7 MYB lineage in some dicots. Further, DupyliCate was also used to identify gene duplications in other key genes of the flavonoid biosynthesis. A downstream expression analysis of these mined duplicates using the tool, combined with a systematic analysis of their promoter sequences helped ascertain the genetic triggers explaining the observed divergence and redundancy.
DupyliCate is available at: https://github.com/ShakNat/DupyliCate
Co-authors: Boas Pucker, Claudia Sterling
Contact Attendee
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