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系統識別號 U0026-1507202014580900
論文名稱(中文) 台灣白花蝴蝶蘭葉片及花朵轉錄組之胞器RNA編輯分析
論文名稱(英文) Analysis of organellar RNA editing from leaf and floral transcriptomes of Phalaenopsis aphrodite subsp. formosana
校院名稱 成功大學
系所名稱(中) 生物科技與產業科學系
系所名稱(英) Department of Biotechnology and Bioindustry Sciences
學年度 108
學期 2
出版年 109
研究生(中文) 陳亭潔
研究生(英文) Ting-Chieh Chen
學號 L68001159
學位類別 博士
語文別 英文
論文頁數 245頁
口試委員 指導教授-張清俊
口試委員-吳文鑾
口試委員-陳虹樺
口試委員-詹明才
口試委員-陳福旗
口試委員-謝明勳
中文關鍵字 葉綠體  粒線體  RNA編輯  原生種蝴蝶蘭  台灣白花蝴蝶蘭 
英文關鍵字 plastid  mitochondria  RNA editing  moth orchids  Phalaenopsis aphrodite 
學科別分類
中文摘要 台灣白花蝴蝶蘭(Phalaenopsis aphrodite subsp. formosana)是台灣兩種原生種的蝴蝶蘭之一。 RNA編輯是在基因轉錄後通過核苷酸修飾進行調控的重要機制。在本研究中,我們通過次世代定序的方法分析了蝴蝶蘭葉片和花朵中胞器的轉錄組。將RNA定序讀數對應到葉綠體和粒線體DNA模板序列後,由C-U或U-C轉換的讀數超過總讀數5%定義為RNA編輯。在台灣白花蝴蝶蘭葉綠體和粒線體轉錄組中分別鑑定出137次和1032次C-U和/或U-C轉換,這是迄今為止單子葉植物報導的最高數量。在葉和花組織中,葉綠體分別存在110和106個編輯位點,共有79個編輯位點。在蛋白質編碼轉錄本含有79個編輯位點,其中58個編輯位點引起了非同義替換。在葉和花組織中,粒線體分別存在978和898個編輯位點,共有844個編輯位點。在蛋白質編碼轉錄本中含有790個編輯位點,其中621個編輯位點引起了非同義替換。此外,至少31和142個編輯位點分別顯示葉綠體或粒線體中的葉片和花朵之間的顯著(≥20%)差異編輯,推測可能存在一些未知的組織特異性因子來調節蝴蝶蘭的RNA編輯。最後,在葉綠體trnM中進行的RNA編輯與形成典型的三葉草結構相關。
英文摘要 SUMMARY
Previously, 44 plastid RNA editing sites have been identified from 24 protein-coding transcripts of leaf by using Sanger sequencing in Phalaenopsis aphrodite subsp. formosana. In this study, we analyzed the organelle-enriched transcriptomes from leaf and floral tissues of moth orchid by next-generation sequencing (NGS). RNA editing sites were determined with the threshold of more than 5% of C-to-U or U-to-C conversion after mapping the sequencing reads to the reference plastid and mitochondrial DNA templates. In total, 137 and 1,032 edits of C-to-U and/or U-to-C conversions were identified in plastid and mitochondrial transcriptomes of P. aphrodite, respectively, the highest number reported so far in monocots. In plastid, 110 and 106 edits were present in leaf and flower, respectively, with 91 edits in common. As well, 79 edits were involved in protein-coding transcripts, and the 58 edits caused the non-synonymous substitution. In mitochondria, 978 and 898 edits were present in leaf and flower, respectively, with 847 edits in common. As well, 790 edits were involved in protein-coding transcripts, and the 621 edits caused the non-synonymous substitution. Furthermore, at least 31 and 142 edits showed significantly (≧20%) differential editing between leaf and floral tissues in either plastid or mitochondria, respectively, which it suggested that some unidentified tissue-specific factors might be required for regulating RNA editing in moth orchid.Finally, RNA editing in plastid trnM is required for the formation of a standard cloverleaf structure.

INTRODUCTION
RNA editing refers to a post-transcriptional modification of nucleotides at the RNA level, which the nucleotide sequence of the transcripts did not consistently reflect the sequence of the corresponding template DNA. In land plants, the C-to-U RNA editing event was first found in mitochondrial transcripts (Covello and Gray, 1989; Gualberto et al., 1989; Hiesel et al., 1989). The amino acid changed after RNA editing results in more similar to other orthologous proteins in other plants at the corresponding position (Gualberto et al., 1989). Editing in both plastid and mitochondrion were subsequently reported in different lineages of land plant including angiosperms, gymnosperms, ferns, lycophytes and bryophytes.

Phalaenopsis aphrodite subsp. formosana is one of the two endemic moth orchids in Taiwan. Previously, using Sanger sequencing, 42 editing sites were found in the 24 chloroplast transcripts of P. aphrodite, and two editing sites were found in the non-protein coding region (Zeng et al., 2007). However, the RNA editing status of the whole organelle transcriptome have not been fully understood, so in this study, by using high-throughput sequencing, the transcripts of the chloroplast and mitochondrion from leaves and flowers of P. aphrodite, were analyzed to obtain the detailed RNA editing status.

MATERIALS AND METHODS
The Phalaenopsis aphrodite subsp. formosana cultivar TS97 used in this study was purchased from Taiwan Sugar Corporation (Tainan, Taiwan). Plastid and mitochondrion were isolated from leaf and flower by using Percoll step gradient. The genomic DNA were purified by using Tri-Plant Genomic DNA Reagent Kit (Geneaid, Taiwan). The mtDNA was sequenced by using both Roche 454 pyrosequencing and Illumina HiSeq2500 platforms. Sequencing reads from two different platforms of Illumina and Roche 454 were assembled by SPAdes. For gene annotation of mitochondrial gene, the ORF Finder and BlastX were used to search protein-coding gene. In addition, the tRNAscan-SE was used to search for potential tRNA genes and Ribosomal RNA Blast was used to search the rRNA sequence. The putative editing sites were predicted by using the PREP-chloroplast and PREP-mitochondrion search program with the plastid and mitochondrial genome sequence. The RNA from leaf or floral tissue were purified by using Trizol reagent (Omic Bio, Taiwan). RNA from leaf and floral tissues underwent NGS with Ion Proton and Illumina Hiseq 2000 platforms, respectively. Transcriptome analysis involved the use of CLC Genomic Workbench 7.5.1 (CLC Bio, Aarhus, Denmark). The RNA sequence reads were mapped to the cpDNA (Accession number: AY916449) and mtDNA template of P. aphrodite. to determine the location of the RNA editing site, the total read count and depth of coverage were calculated. The degree of nucleotide conversion at each site was based on the reading of nucleotide conversion divided by the total reads. The frequency of C-to-U or U-to-C conversion at a specific nucleotide position must be greater than 5%, which is defined as the RNA editing site. In addition, we manually deleted more than five RNA edits in the homopolymer region, which was considered a potential sequencing error. The reads per kilobase of exon model per million mapped reads (RPKM) values was measured to estimate the gene expression profile.

RESULTS AND DISCUSSION
In plastid transcripts, we identified total 137 edits with 126 C-to-U and 11 U-to-C conversions, representing an average of 0.09% of the nucleotides examined in moth orchid. Compared with previous study, 93 sites were newly discovered. The 137 RNA edits revealing an average of 0.09% of the plastid nucleotides (149 kb). In leaf and floral tissues, we found 110 and 106 RNA edits, respectively. There are 79 edits commonly present in the two tissues, and 31 and 27 edits are specific in the leaf and floral tissues, respectively. Among 137 edits, 79 edits were involved in protein‑coding transcripts, and the 58 nucleotide conversions caused the non‑synonymous substitution (Table 1). In the trnM (cau) transcript, both leaf and floral tissues showed efficient RNA editing (>60%) at 52,826 genomic position. The result of C-to-U conversion in the trnM (cau) of Phalaenopsis resulted in increased nucleotide conservation among plant species and prompted the standard clover‑leaf structure of trnM (cau).

The mtDNA of P. aphrodite was sequenced and assembled into 77 contigs. After selection, 44 contigs with a total length of 576,203 bp that are considered mtDNA. After annotation the mtDNA of Phalaenopsis encodes 38 protein-coding, 3 rRNA and 9 tRNA genes. In addition, among sequence derived from plastid DNA, we found 31 coding genes, including 19 protein-coding genes (7 have complete ORF and the other 12 contain only partial gene sequences) and 12 tRNA genes. Among the 21 tRNA genes in mtDNA, 9 are mitochondrial origin and 12 are plastid origin. Analysis of the codons conferred by tRNA genes revealed that 21 tRNA genes may only recognize 45 of the 61 codons, which it is not sufficient for translation. Therefore, for translation in the mitochondria of Phalaenopsis, tRNA imported from the nucleus may be needed.

In mitochondrial transcripts, we identified a total of 1032 RNA editing sites, including 1,020 C-to-U and 12 U-to-C conversions, on average representing 0.18% of detected nucleotides. In all editing sites, 978 and 898 edits were found in the leaf and floral tissues, respectively. A total of 844 edits were commonly identified both in the two tissues, while the leaf or floral tissues have 33 and 53 specific edits, respectively. The leaf and floral tissues contained 894 and 837 edits, respectively, with a total of 790 edits in common .

CONCLUSION
By high-throughput sequencing, 137 and 1,032 RNA edits were identified in plastid and mitochondrial transcriptomes of P. aphrodite, respectively, the highest number reported so far in monocots. In intron, IGS, 3’ and 5’ UTR, we identified several RNA editing sites, and the secondary structure might change after RNA editing in plastid and mitochondrial transcripts. These results suggested that editing in some cis-elements of primary transcripts might be important for splicing in moth orchid. Additionally, RNA editing occurs in trnM in plastid plays an important role in formation of standard clover-leaf tRNA structure.
論文目次 Chinese Abstract (中文摘要) .......................................................................... I
Abstract ........................................................................................................... II
Acknowledgements ....................................................................................... VI
Table of Contents ........................................................................................ VII
Contents of Tables .......................................................................................... X
Contents of Figures ..................................................................................... XII
Contents of Appendices ............................................................................. XIV
Abbreviation List ........................................................................................ XV
Chapter 1 Research Background ................................................................... 1
1-1 RNA editing in land plants ...................................................................... 1
1-2 RNA editing affects tRNA maturation and RNA splicing in plant ......... 3
1-3 RNA editing factors in plant organelles .................................................. 4
1-4 Purpose of this study ............................................................................. 15
Chapter 2 Materials and Methods ............................................................... 18
2-1 Plant material ......................................................................................... 18
2-2 Plastid and mitochondrion isolation from leaf and flower .................... 18
2-3 Purification of genomic DNA from mitochondrion .............................. 20
2-3 Purification of genomic DNA from mitochondrion .............................. 20
2-4 Genomic sequencing and assembly of mitochondrion .......................... 20
2-5 Gene annotation of mitochondrial genes ............................................... 23
2-6 Prediction of RNA editing site .............................................................. 24
2-7 RNA purification ................................................................................... 24
2-8 RNA sequencing ................................................................................... 25
2-9 RNA edits determination and gene expression profile .......................... 26
2-10 Prediction of RNA structure ................................................................ 27
Chapter 3 RNA Editing in Plastid ............................................................... 28
3-1 Introduction ........................................................................................... 28
3-2 Results ................................................................................................... 30
3-3 Discussion ............................................................................................. 40
Chapter 4 RNA Editing in Mitochondrion ................................................. 49
4-1 Introduction ........................................................................................... 49
4-2 Results ................................................................................................... 51
4-3 Discussion ............................................................................................. 64
References ...................................................................................................... 78
Tables ............................................................................................................. 98
Figures .......................................................................................................... 184
Appendix ...................................................................................................... 240
Related Paper Publication .......................................................................... 245
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