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Science China Life Sciences

, Volume 62, Issue 4, pp 498–506 | Cite as

Complete loss of RNA editing from the plastid genome and most highly expressed mitochondrial genes of Welwitschia mirabilis

  • Weishu Fan
  • Wenhu Guo
  • Lexis Funk
  • Jeffrey P. MowerEmail author
  • Andan ZhuEmail author
Research Paper
  • 32 Downloads

Abstract

Comparative genomics among gymnosperms suggested extensive loss of mitochondrial RNA editing sites from Welwitschia mirabilis based on predictive analysis. However, empirical or transcriptome data to confirm this massive loss event are lacking, and the potential mechanisms of RNA site loss are unclear. By comparing genomic sequences with transcriptomic and reverse-transcription PCR sequencing data, we performed a comprehensive analysis of the pattern of RNA editing in the mitochondrial and plastid genomes (mitogenome and plastome, respectively) of W. mirabilis and a second gymnosperm, Ginkgo biloba. For W. mirabilis, we found only 99 editing sites located in 13 protein-coding genes in the mitogenome and a complete loss of RNA editing from the plastome. The few genes having high editing frequency in the Welwitschia mitogenome showed a strong negative correlation with gene expression level. Comparative analyses with G. biloba, containing 1,405 mitochondrial and 345 plastid editing sites, revealed that the editing loss from W. mirabilis is mainly due to the substitution of editable cytidines to thymidines at the genomic level, which could be caused by retroprocessing. Our result is the first study to uncover massive editing loss from both the mitogenome and plastome in a single genus. Furthermore, our results suggest that gene expression level and retroprocessing both contributed to the evolution of RNA editing in plant organellar genomes.

Keywords

RNA editing massive loss expression levels organelle genomes Welwitschia 

Supplementary material

11427_2018_9450_MOESM1_ESM.pdf (518 kb)
Supplementary material, approximately 518 KB.
11427_2018_9450_MOESM2_ESM.xlsx (19 kb)
Table S1. RNA Editing Sites Distribution in Welwitschia mitogenome
11427_2018_9450_MOESM3_ESM.xlsx (13 kb)
Table S2. RT-PCR Validation of Welwitschia Mitogenes
11427_2018_9450_MOESM4_ESM.xlsx (71 kb)
Table S3. RNA Editing Sites Distribution in Ginkgo Mitogenome and Plastome
11427_2018_9450_MOESM5_ESM.xlsx (12 kb)
Table S4. Gene specific primers for Welwitschia mitogenes

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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Germplasm Bank of Wild Species, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
  2. 2.Center for Plant Science InnovationUniversity of NebraskaLincolnUSA
  3. 3.Department of Agronomy and HorticultureUniversity of NebraskaLincolnUSA
  4. 4.School of Biological SciencesUniversity of NebraskaLincolnUSA

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