作者
Pengchuan Sun, Beibei Jiao, Yongzhi Yang, Lanxing Shan, Ting Li, Xiaonan Li, Zhenxiang Xi, Xiyin Wang, Jianquan Liu
发表日期
2021
期刊
bioRxiv
页码范围
2021.04.29
出版商
Cold Spring Harbor Laboratory
简介
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 …
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