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Molecular Genetics and Genomics

, Volume 288, Issue 9, pp 445–457 | Cite as

RNA editing events in mitochondrial genes by ultra-deep sequencing methods: a comparison of cytoplasmic male sterile, fertile and restored genotypes in cotton

  • Hideaki Suzuki
  • Jiwen Yu
  • Scott A. Ness
  • Mary A. O’Connell
  • Jinfa ZhangEmail author
Original Paper

Abstract

Cytoplasmic male sterility (CMS) is a maternally inherited trait resulting in failure to produce functional pollen and is widely used in the production of hybrid seed. Improper RNA editing is implicated as the molecular basis for some CMS systems. However, the mechanism of CMS in cotton is unknown. This study compared RNA editing events in eight mitochondrial genes (atp1, 4, 6, 8, 9, and cox1, 2, 3) among three lines (maintainer B, CMS A, and restorer R). These events were quantified by ultra-deep sequencing of mitochondrial transcripts and sequencing of cloned versions of these genes as cDNAs. A comparison of genomic PCR and RT-PCR products detected 72 editing sites in coding sequences in the eight genes and four partial editing sites in the 3′-untranslated region of atp6. The most frequent alteration (61.4 %) resulted in changes of hydrophilic amino acids to hydrophobic amino acids and the most common alteration was proline (P) to leucine (L) (26.7 %). In atp6, RNA editing created a stop codon from a glutamine in the genomic sequence. Statistical analysis of the frequencies of RNA editing events detected differences between mtDNA genes, but no differences between cotton cytoplasms that could account for the CMS phenotype or restoration. This study represents the first work to use next-generation sequencing to identify RNA editing positions and efficiency, and possible association with CMS and restoration in plants.

Keywords

Cotton  Cytoplasmic male sterility  Restoration  RNA editing  Ultra-deep sequencing 

Notes

Acknowledgments

The research was supported in part by New Mexico Agricultural Experiment Station. The authors thank Anthony Aragon and Jeremy Edwards for help with the Ion Torrent sequencing. Some of the experiments used the Keck-UNM Genomics Resource in the University of New Mexico Cancer Center. Parts of this work were supported by USPHS/NIH grant 1R01CA170250-01 (to SAN).

Supplementary material

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Supplementary material 1 (DOCX 50 kb)
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Supplementary material 2 (XLS 62 kb)
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Supplementary material 3 (XLSX 16 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Hideaki Suzuki
    • 1
    • 3
  • Jiwen Yu
    • 1
    • 2
  • Scott A. Ness
    • 3
  • Mary A. O’Connell
    • 1
  • Jinfa Zhang
    • 1
    Email author
  1. 1.Department of Plant and Environmental SciencesNew Mexico State UniversityLas CrucesUSA
  2. 2.State Key Laboratory in Cotton Biology, Cotton Research InstituteChinese Academy of Agricultural ScienceAnyangChina
  3. 3.Molecular Genetics and MicrobiologyUniversity of New Mexico Health Sciences CenterAlbuquerqueUSA

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