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Structural variations in papaya genomes.

Zhenyang Liao1, Xunxiao Zhang1, Shengcheng Zhang1

  • 1College of Life Science, Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.

BMC Genomics
|May 11, 2021
PubMed
Summary
This summary is machine-generated.

Structural variations (SVs) are key to papaya domestication, influencing traits like reproduction and environmental adaptability. This study identified numerous SVs and copy number variant genes (CNV-genes), providing insights into papaya evolution.

Keywords:
Carica papayaDomesticationStructural variationWGCNA

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Area of Science:

  • Genomics
  • Plant Biology
  • Evolutionary Biology

Background:

  • Structural variations (SVs) are mutations less studied in plants compared to animals.
  • SVs are implicated in animal domestication, suggesting a similar role in plants.
  • Understanding SVs in papaya can reveal impacts on phenotype and adaptability during domestication.

Purpose of the Study:

  • To comprehensively detect and analyze structural variations (SVs) in the papaya genome.
  • To investigate the role of SVs in papaya domestication, focusing on phenotype and environmental adaptability.
  • To provide genomic resources for developing molecular markers in papaya.

Main Methods:

  • Genome-wide detection of structural variations (SVs), including deletions, tandem duplications, and insertions.
  • Analysis of gene overlap with SVs and expression patterns in different tissues.
  • Weighted gene co-expression network analysis (WGCNA) and functional enrichment analysis.
  • Identification of copy number variant genes (CNV-genes) associated with selection.

Main Results:

  • Detected 8083 SVs, with deletions being the most prevalent.
  • Identified 1794 genes overlapping with SVs, with 1350 expressed in at least one tissue.
  • WGCNA revealed co-expression networks between SVs-genes and tissues, linked to growth and environmental responses.
  • Discovered domesticated SVs and CNV-genes related to environmental adaptability, sexual reproduction, and agronomic traits.

Conclusions:

  • Structural variations (SVs) are crucial for papaya domestication, particularly for reproductive traits in hermaphrodite plants.
  • Genome-wide SV and CNV-gene analysis between cultivated and wild populations offers insights into papaya's evolutionary trajectory.
  • This research provides a foundation for understanding the evolution of sex determination and trait development in papaya.