爪哇特有種Microhyla achatina粒線基因體完整序列及其親緣遣傳演化

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論文名稱

爪哇特有種Microhyla achatina粒線基因體完整序列及其親緣遣傳演化
(Complete mitochondrial genome sequence of Indonesian endemic frog Microhyla achatina and genetic evolution)

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至系統瀏覽論文 (2026-1-1以後開放)

摘要(中)

利用Sanger定序的技術完成印尼爪哇的特有種Microhyla achatina的全粒線基因體之序列，並將此資料存放在NCBI的GenBank中，登錄號為MW233587。其序列之總長度為16,725 bp，包含13個protein-coding genes、22個tRNA genes及兩個rRNA genes和兩個control regions（L-strand replication origin和D-loop）。親緣關係的分析是利用M. achatina和其他同科（Microhylidae科）中的物種之全粒線基因體序列，以Neighbor-joining、Maximum likelihood 及Bayesian inferences之運算方法所建立而成；其結果支持M. achatina和M. heymonsi是姊妹種，以及兩個單系屬Kaloula和Microhyla。另外因注意到ND5和ND6 DNA序列的變異性非常高，進而進行其親緣演化的分析，結果有顯著不同的結果；因此，ND5和ND6基因不適用於親緣演化的分析。此外，亦發現在密碼子中存在高度的核苷酸使用偏差，第二密碼子的T鹼基數量顯著較高（40.3 – 41.4%），而第三密碼子的G鹼基數量極低（6.6 – 8.6%）。本研究提供Microhyla achatina完整的粒線基因體序列，可供未來對Microhyla屬及Microhylidae家族遺傳演化之探討。

摘要(英)

The complete mitochondrial genome sequence of Microhyla achatina from Java, Indonesia was obtained by Sanger-sequencing technique and deposited in GenBank on NCBI with accession number of MW233587. The total length was 16,725 bp and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two control regions (L-strand replication origin and D-loop). Phylogenetic relationships were constructed based on the complete mitogenome data of M. achatina and others in family Microhylidae by using Neighbor-joining, Maximum likelihood and Bayesian inferences. The phylogeny suggested M. achatina as a sister taxon of M. heymonsi and two monophyletic genera Kaloula and Microhyla. Additionally, due to observing high variation of ND5 and ND6 genes, we further investigated phylogenies from these two genes, and revealed they evolved strikingly different from the mitogenome. Thus, ND5 and ND6 genes were not suitable for anuran phylogeny and evolution. Moreover, there were strong codon usage bias toward significantly high T at second codons (40.3 – 41.4%) and extremely low G at third codons (6.6 – 8.6%). The complete mitochondrial genome sequence generated in this study provides a valuable source for further phylogenetic or genetic evolutionary researches on genus Microhyla or family Microhylidae.

關鍵字(中)

★ Microhylidae
★ Microhyla achatina
★ 粒線體DNA
★ 分子系統發生學

關鍵字(英)

★ Microhylidae
★ Microhyla achatina
★ mitochondrial DNA
★ molecular phylogeny

論文目次

摘要 i
ABSTRACT ii
ACKNOWLEDGEMENT iii
Table of Contents iv
List of Figures vi
List of Tables vii
Explanation of Symbols viii
Chapter I. Introduction 1
1.1 Microhyla achatina 1
1.1.1. Taxonomy 1
1.1.2. Morphological characteristics of M. achatina 2
1.1.3. Ecological characteristics 3
1.2 Mitochondrial genome 5
1.3 Overview of phylogenetic analysis methods 6
1.3.1. Neighbor-joining 6
1.3.2. Maximum-likelihood 6
1.3.3. Bayesian inference 7
1.3.4. Substitution model of evolution 7
1.3.5. Bootstrap analysis in phylogenetic research 8
1.4 Previous studies on mitochondrial genome of genus Microhyla & purpose of this study 10
Chapter II. Material & methods 14
2.1 Taxon sampling 14
2.2 DNA extraction 15
2.3 Polymerase chain reaction (PCR) amplification 16
2.4 Sample assembly and analysis 18
2.5 Molecular and phylogenetic analyses 18
Chapter III. Results 21
3.1 Microhyla achatina complete mitochondrial genome sequence 21
3.2 Protein-coding genes (PCGs) 24
3.3 Non-coding genes 30
3.4 Non-coding regions 35
3.5 Phylogenetic analyses of 18 members in subfamily Microhylinae and Kalophryninae 39
Chapter IV. Discussion 47
4.1 Microhyla achatina mitochondrial genome structure 47
4.2 Genetic phylogeny of Microhyla achatina and subfamily Microhylinae 47
4.3 ND5 and ND6 genes could be inappropriate to use in phylogenetic analyses 48
Chapter V. Conclusion 50
Bibliography 51

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指導教授

劉阜果(Liu Fu-Guo Robert)

審核日期

2021-1-27

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