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WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes.
- Source :
-
Molecular Plant (Cell Press) . Dec2022, Vol. 15 Issue 12, p1841-1851. 11p. - Publication Year :
- 2022
-
Abstract
- Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth. To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses, there is a need for convenient and accurate toolkits. To meet this need, we developed WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosome karyotyping) that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes. Significantly, it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution. This toolkit is freely available at GitHub (https://github.com/SunPengChuan/wgdi). As an example of its application, WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots. This work reports an integrated and user-friendly toolkit, WGDI,for polyploid inference, hierarchical inference of genomic homology, and ancestral chromosome karyotyping. WGDI can improve the detection of whole-genome duplication and facilitates dynamic illumination of karyotype evolution. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 16742052
- Volume :
- 15
- Issue :
- 12
- Database :
- Academic Search Index
- Journal :
- Molecular Plant (Cell Press)
- Publication Type :
- Academic Journal
- Accession number :
- 160535174
- Full Text :
- https://doi.org/10.1016/j.molp.2022.10.018