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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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IPOP: An Integrative Plant Multi-omics Platform for Cross-species Comparison and Evolutionary Study.

Wenyue Huang1, Xiaona Hu2, Yanlin Ren1

  • 1State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.

Molecular Biology and Evolution
|November 23, 2023
PubMed
Summary

The Integrative Plant Omics Platform (IPOP) provides evolutionary and multi-omics data for 13 plant species. This resource aids researchers in cross-species gene evolutionary and functional analysis.

Keywords:
evolutionary genomicsfunctional genomicsintegrationmulti-omicsplant

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Area of Science:

  • Plant biology
  • Genomics
  • Bioinformatics

Background:

  • High-throughput sequencing generates vast plant omics data, valuable for comparative analysis.
  • Existing platforms lack comprehensive evolutionary annotation and multi-species omics data, hindering gene analysis.
  • A need exists for advanced platforms for timely, accurate, and high-caliber omics information.

Purpose of the Study:

  • To develop an advanced plant multi-omics platform (IPOP) for evolutionary and functional gene analysis.
  • To provide standardized, reanalyzed omics data and evolutionary annotations for multiple plant species.
  • To integrate online analysis tools for comprehensive evolutionary and functional studies.

Main Methods:

  • Collected and reanalyzed 7 types of omics data from 13 plant species (monocots, dicots, moss) using standardized pipelines.
  • Furnished homology, duplication events, and phylostratigraphic stages for evolutionary examination.
  • Developed IPOP with tools like Multi-omics Integration Analysis and Transcriptome-wide Association Analysis.

Main Results:

  • The IPOP platform integrates 7 omics data types and evolutionary information for 13 plant species.
  • Online tools facilitate multi-omics integration and linking functional analysis with phenotype.
  • A case study on YTH domain genes revealed shared functionalities and varied evolutionary patterns.

Conclusions:

  • IPOP addresses the need for cross-species comparison and evolutionary research platforms in plant science.
  • The platform offers valuable evolutionary insights and multi-omics data for the scientific community.
  • All IPOP data and tools are freely accessible for academic research.