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The rise and fall of miRNA-directed PTGS modules in polyploidy: insights from Gossypium hirsutum and its closely related diploids

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  • Author(s): Zhang, Zijie
  • Document Type:
    Electronic Resource
  • Online Access:
    https://hdl.handle.net/2346/100527
  • Additional Information
    • Publisher Information:
      2024-08
    • Abstract:
      MicroRNA-directed post-transcriptional gene silencing (miRNA-PTGS) is an evolutionarily ancient regulatory mechanism found in both plants and animals. While current data suggest the independent evolution of miRNAs in the two kingdoms, the emergence and evolution of miRNA-PTGS modules remain poorly understood. Proposed mechanisms for miRNA evolution in plants include gene duplication and transposable element insertion. Polyploidy, which arises from genome doubling events and plays a significant role in plant evolution, represents an extreme form of gene duplication; and therefore, serves as a fertile ground for tracking the evolutionary dynamics of miRNA-PTGS associated with polyploid formation. The genus Gossypium, which contains recently (1.5-2 MYA) formed allotetraploids (AtDt genome) and extant diploid progenitors, represents an attractive system for such studies, particularly with the recent publication of their genome sequences. Through extensive small RNA sequencing (sRNA-seq) and computational analysis using ShortStack4, we globally identified miRNA-producing (MIRNA) loci in upland cotton (G. hirsutum), a widely cultivated allotetraploid, along with two A-genome diploids, G. herbaceum (A1) and G. arboreum (A2), and one D-genome diploid, G. raimondii (D5). Reliable identification of miRNA regulatory targets was achieved through computational prediction using TargetFinder, coupled with degradome sequencing. This analysis revealed distinct repertoires of miRNA-PTGS modules in each species, identifying unique miRNA families in both the A- and D-genome diploids, as well as the allotetraploid, in addition to those shared by all. One of the novel miRNAs uniquely identified in G. hirsutum, tentatively named miRc1230, may be expressed from two genomic loci on chromosome 6 of the A and D subgenomes: MIRc1230A (A6) and MIRc1230B (D6), respectively. These loci would produce mature miRc1230 with an identical sequence but distinct miRc1230* sequences. miRc1230 was found to
    • Subject Terms:
      microRNAs; miRNA-mediated PTGS; miRNA evolution; Gossypium allotetraploids; Polyphenol oxidase; Dissertation
    • Availability:
      Open access content. Open access content
      Restricted until 09/2030. To request the author grant access, click on the PDF link to the left.
    • Note:
      English
    • Other Numbers:
      ILU oai:ttu-ir.tdl.org:2346/100527
      1500163371
    • Contributing Source:
      TEXAS TECH UNIV
      From OAIster®, provided by the OCLC Cooperative.
    • Accession Number:
      edsoai.on1500163371
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