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Whole plastid transcriptomes reveal abundant RNA editing sites and differential editing status in Phalaenopsis aphrodite subsp. formosana

Overview of attention for article published in Botanical Studies, September 2017
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Title
Whole plastid transcriptomes reveal abundant RNA editing sites and differential editing status in Phalaenopsis aphrodite subsp. formosana
Published in
Botanical Studies, September 2017
DOI 10.1186/s40529-017-0193-7
Pubmed ID
Authors

Ting-Chieh Chen, Yu-Chang Liu, Xuewen Wang, Chi-Hsuan Wu, Chih-Hao Huang, Ching-Chun Chang

Abstract

RNA editing is a process of post-transcriptional level of gene regulation by nucleotide modification. Previously, the chloroplast DNA of Taiwan endemic moth orchid, P. aphrodite subsp. formosana was determined, and 44 RNA editing sites were identified from 24 plastid protein-coding transcripts of leaf tissue via RT-PCR and then conventional Sanger sequencing. However, the RNA editing status of whole-plastid transcripts in leaf and other distinct tissue types in moth orchids has not been addressed. To sensitively and extensively examine the plastid RNA editing status of moth orchid, RNA-Seq was used to investigate the editing status of whole-plastid transcripts from leaf and floral tissues by mapping the sequence reads to the corresponding cpDNA template. With the threshold of at least 5% C-to-U or U-to-C conversion events observed in sequence reads considered as RNA editing sites. In total, 137 edits with 126 C-to-U and 11 U-to-C conversions, including 93 newly discovered edits, were identified in plastid transcripts, representing an average of 0.09% of the nucleotides examined in moth orchid. Overall, 110 and 106 edits were present in leaf and floral tissues, respectively, with 79 edits in common. As well, 79 edits were involved in protein-coding transcripts, and the 58 nucleotide conversions caused the non-synonymous substitution. At least 32 edits showed significant (≧20%) differential editing between leaf and floral tissues. Finally, RNA editing in trnM is required for the formation of a standard clover-leaf structure. We identified 137 edits in plastid transcripts of moth orchid, the highest number reported so far in monocots. The consequence of RNA editing in protein-coding transcripts mainly cause the amino acid change and tend to increase the hydrophobicity as well as conservation among plant phylogeny. RNA editing occurred in non-protein-coding transcripts such as tRNA, introns and untranslated regulatory regions could affect the formation and stability of secondary structure, which might play an important role in the regulation of gene expression. Furthermore, some unidentified tissue-specific factors might be required for regulating RNA editing in moth orchid.

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Geographical breakdown

Country Count As %
Unknown 17 100%

Demographic breakdown

Readers by professional status Count As %
Other 4 24%
Student > Master 3 18%
Professor 3 18%
Researcher 2 12%
Student > Ph. D. Student 2 12%
Other 2 12%
Unknown 1 6%
Readers by discipline Count As %
Agricultural and Biological Sciences 7 41%
Biochemistry, Genetics and Molecular Biology 7 41%
Arts and Humanities 1 6%
Unknown 2 12%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 17 September 2017.
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#10,443,670
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Outputs from Botanical Studies
#68
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#224,964
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Outputs of similar age from Botanical Studies
#3
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