Recently, it was announced by the Key Laboratory of Marine Genetics and Breeding of the Ministry of Education at the Ocean University of China and the Center for Marine Evolutionary Developmental Biology led by Professor Fang Zongxi, that significant progress has been made in the development of genomic system resolution tools under the direction of Chinese Academy of Engineering academician Bao Zhenmin and Professor Wang Shi. It is reported that the team has developed the world's first integrated macro/micro-evolutionary genome and functional genome comprehensive analysis tool, PanSyn. The research findings have been published in Nature Protocols.
PanSyn Workflow Overview
Elucidating the structure and function of genomes lies at the heart of decoding the evolutionary history and biodiversity of life on Earth. The revolutionary breakthroughs in high-throughput sequencing technology and the widespread application of various omics technologies have provided unprecedented opportunities for the life sciences, propelling research into the era of big data.
For most biological taxa, especially non-model marine organisms, there is still a lack of comprehensive genomic analysis tools to meet the growing demand for analyzing increasingly complex massive omics data, and to deeply unravel the fundamental laws governing genome structure and functional evolution.
Over the past decade, comparative genomics studies using micro/macro collinearity analysis have brought about many significant discoveries and breakthroughs in the field of biology. Currently, most collinearity analysis methods are mainly focused on the microevolutionary scale or only study either micro or macro single evolutionary scales, with few integrated analyses of both scales, severely hindering a comprehensive understanding of the pan-evolutionary process of genomes and the functional significance behind it.
To address the common challenges faced by the international genomics community, the research team has developed the most comprehensive and systematic integrated analysis tool to date, integrating macro/micro evolutionary genomics and functional genomics. It not only includes a comprehensive functional micro-collinearity analysis module but also greatly supplements the shortage of macro-collinearity analysis tools and innovatively proposes an integrated analysis module that integrates micro and macro collinearity as well as regulatory omics data.
Compared to mainstream software and tools, this tool has significant advantages. In terms of micro-collinearity analysis, it can achieve comprehensive micro-collinearity analysis from single to multiple alignments, from simple to complex ploidy, from low-dimensional to high-dimensional networks, and from structure to function. In terms of macro-collinearity analysis, it can achieve ancestral genome reconstruction, ancient gene family clustering, estimation of karyotype conservatism, and systematic inference of chromosomal evolutionary processes. In terms of integrated analysis modules, it introduces for the first time a dual integration strategy from micro to macro and from macro to micro, realizing systematic deduction and analysis of the pan-evolutionary scale between ancestral and extant species' genomes. At the same time, it integrates multi-dimensional functional omics data to provide a more comprehensive and in-depth functional interpretation perspective for understanding genome evolution.
The research team provides detailed instructions and application demonstrations for PanSyn, whose highly customizable features can meet the specific analysis needs of users for species or taxa of interest. PanSyn is the world's first integrated analysis tool for macro/micro evolutionary genomics and functional genomics. PanSyn will provide powerful tools for comprehensive analysis of genome evolution and function, gene resource development and utilization, etc., to promote innovative discoveries and major breakthroughs in the field of life sciences and ultimately depict the overall development and evolution of the tree of life.
This research was supported by the Laoshan National Laboratory, the National Natural Science Foundation of China, the National Key Research and Development Program, the Shandong Provincial Key Research and Development Program, and the Taishan Scholar Program, among others.
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