鸟类六种吸虫的分子鉴定和线粒体基因组研究
发布时间：2021-07-12 12:19
分类学和系统学是学习生物多样性的重要方法。采用分子数据挖掘与形态数据描述相结合的方法,可最大化地提供吸虫分类及系统发育学的相关信息。核糖体DNA（rDNA）及线粒体（mt）基因组可提供丰富的遗传标记。部分或完整的rDNA序列已被广泛用于吸虫的物种鉴定及系统研究。然而,目前GenBank中仅有为数不多的吸虫线粒体基因组数据。许多被忽略的或有分类及归属争议的吸虫需要通过解析其线粒体基因组序列来解决其分类争议。尽管鸟类是最常见的吸虫终末宿主之一,但对寄生于鸟类的吸虫的分类及系统发育研究仍很有限。为了填补该空白,本论文解析了来自巴基斯坦不同食性鸟类的6种吸虫的rDNA和mt基因组序列,研究了他们与其他吸虫的系统发育关系。采用通用引物或者根据相对保守序列设计的引物,对寄生于不同鸟类的6种斜睾吸虫,通过PCR扩增获得rDNA中的内转录间隔区（ITS）及大亚基（LSU/28S）,以及完整或近乎完整的mt基因组序列。rDNA序列数据用于虫种鉴定、遗传变异以及部分物种科内进化树构建。注释、描述了6种吸虫的mt基因组的基因排列、12个蛋白编码基因（PCGs）的碱基组成、碱基偏斜、密码子使用、相对同义密码子...
【文章来源】：中国农业科学院北京市
【文章页数】：104 页
【学位级别】：博士
【文章目录】：
摘要
ABSTRACT
LIST OF ABBREVIATIONS
CHAPTER1 INTRODUCTION
1.1 Background
1.1.1 Use of nuclear rDNA for trematode identification and systematics
1.1.2 Significance of mtDNA in trematode taxonomy and phylogeny
1.2 Mitochondrial genomes of trematodes
1.2.1 Structure and gene organization
1.2.2 Genetic code,nucleotide composition and length of genes
1.2.3 Leucine zipper
1.2.4 Transfer and ribosomal RNA genes
1.2.5 Overlaps between mt genes
1.2.6 Non-coding regions
1.3 Conclusion
1.4 Purpose and significance of the study
CHAPTER2 Characterization of the complete mitochondrial genome of Plagiorchis maculosus(Digenea,Plagiorchiidae):representative of a taxonomically complex digenean family
2.1 Summary
2.2 Introduction
2.3 Materials and methods
2.3.1 Trematode specimens and DNA extraction
2.3.2 Amplification of ITS and28S rDNA
2.3.3 PCR-based sequencing of complete mitogenome
2.3.4 Mitogenome annotation and data analyses
2.3.5 Phylogenetic analyses
2.4 Results and discussion
2.4.1 Molecular identification of specimens
2.4.2 Mitochondrial genome arrangement and nucleotide usage
2.4.3 Protein-coding genes and codon usage
2.4.4 Transfer and ribosomal RNA genes
2.4.5 Non-coding region
2.4.6 Molecular phylogeny
2.5 Conclusion
CHAPTER3 Molecular phylogenetics and mitogenomics of three avian dicrocoeliids(Digenea:Dicrocoeliidae)and comparison between mitogenomes of avian and mammalian dicrocoeliids
3.1 Summary
3.2 Introduction
3.3 Materials and Methods
3.3.1 Parasites collection and genomic DNA isolation
3.3.2 Amplification and analysis of nuclear28S rDNA
3.3.3 Long-PCR-based sequencing of mt genom
3.3.4 mtDNA sequence assembly,annotation and analyses
3.3.5 Genetic relationship of Dicrocoeliidae with other digenean
3.4 Results and discussion
3.4.1 Molecular phylogeny within Dicrocoeliidae
3.4.2 Gene organization,size and nucleotide content of mitogenomes
3.4.3 Protein-coding genes and codon usage
3.4.4 Transfer and ribosomal RNA genes
3.4.5 Non-coding regions
3.4.6 Diversity and mutation rate rate among dicrocoeliid mitogenomes
3.4.7 Phylogeny of the Dicrocoeliidae
3.5 Conclusion
Chapter4 Characterization of the complete mitochondrial genome of Uvitellina sp.,representative of the family Cyclocoelidae and phylogenetic implications
4.1 Summary
4.2 Introduction
4.3 Materials and Methods
4.3.1 Sampling,identification and DNA extraction
4.3.2 ITS rDNA sequencing and comparison with European cyclocoelids
4.3.3 Long-PCR and mt genome sequencing
4.3.4 Sequence assembly and mitogenome characterization
4.3.5 Phylogenetic analyses
4.4 Results and discussion
4.4.1 Identification and differences in ITS rDNA with European cyclocoelids
4.4.2 Mitochondrial genome features and gene content
4.4.3 Genetic relationships
4.5 Conclusion
Chapter5 Mitochondrial and nuclear ribosomal DNA dataset suggests that Hepatiarius sudarikovi Feizullaev1961 is a member of the genus Opisthorchis Blanchard,1895(Digenea:Opisthorchiidae)
5.1 Summary
5.2 Introduction
5.3 Materials and methods
5.3.1 Parasites and DNA extraction
5.3.2 The acquisition of H.sudarikovi ITS rDNA
5.3.3 PCR-based sequencing of H.sudarikovi mt genome
5.3.4 Genome assembly,annotation,and bioinformatics analysis
5.3.5 Phylogenetic analysis
5.4 Results and discussion
5.4.1 Morphological identification
5.4.2 ITS sequence comparison with other flukes within Opisthorchiidae
5.4.3 Characterization of the H.sudarikovi mt genome
5.4.4 Phylogenetic analysis
5.5 Conclusion
Conclusion
References
Acknowledgement
Resume
本文编号：3279904
【文章来源】：中国农业科学院北京市
【文章页数】：104 页
【学位级别】：博士
【文章目录】：
摘要
ABSTRACT
LIST OF ABBREVIATIONS
CHAPTER1 INTRODUCTION
1.1 Background
1.1.1 Use of nuclear rDNA for trematode identification and systematics
1.1.2 Significance of mtDNA in trematode taxonomy and phylogeny
1.2 Mitochondrial genomes of trematodes
1.2.1 Structure and gene organization
1.2.2 Genetic code,nucleotide composition and length of genes
1.2.3 Leucine zipper
1.2.4 Transfer and ribosomal RNA genes
1.2.5 Overlaps between mt genes
1.2.6 Non-coding regions
1.3 Conclusion
1.4 Purpose and significance of the study
CHAPTER2 Characterization of the complete mitochondrial genome of Plagiorchis maculosus(Digenea,Plagiorchiidae):representative of a taxonomically complex digenean family
2.1 Summary
2.2 Introduction
2.3 Materials and methods
2.3.1 Trematode specimens and DNA extraction
2.3.2 Amplification of ITS and28S rDNA
2.3.3 PCR-based sequencing of complete mitogenome
2.3.4 Mitogenome annotation and data analyses
2.3.5 Phylogenetic analyses
2.4 Results and discussion
2.4.1 Molecular identification of specimens
2.4.2 Mitochondrial genome arrangement and nucleotide usage
2.4.3 Protein-coding genes and codon usage
2.4.4 Transfer and ribosomal RNA genes
2.4.5 Non-coding region
2.4.6 Molecular phylogeny
2.5 Conclusion
CHAPTER3 Molecular phylogenetics and mitogenomics of three avian dicrocoeliids(Digenea:Dicrocoeliidae)and comparison between mitogenomes of avian and mammalian dicrocoeliids
3.1 Summary
3.2 Introduction
3.3 Materials and Methods
3.3.1 Parasites collection and genomic DNA isolation
3.3.2 Amplification and analysis of nuclear28S rDNA
3.3.3 Long-PCR-based sequencing of mt genom
3.3.4 mtDNA sequence assembly,annotation and analyses
3.3.5 Genetic relationship of Dicrocoeliidae with other digenean
3.4 Results and discussion
3.4.1 Molecular phylogeny within Dicrocoeliidae
3.4.2 Gene organization,size and nucleotide content of mitogenomes
3.4.3 Protein-coding genes and codon usage
3.4.4 Transfer and ribosomal RNA genes
3.4.5 Non-coding regions
3.4.6 Diversity and mutation rate rate among dicrocoeliid mitogenomes
3.4.7 Phylogeny of the Dicrocoeliidae
3.5 Conclusion
Chapter4 Characterization of the complete mitochondrial genome of Uvitellina sp.,representative of the family Cyclocoelidae and phylogenetic implications
4.1 Summary
4.2 Introduction
4.3 Materials and Methods
4.3.1 Sampling,identification and DNA extraction
4.3.2 ITS rDNA sequencing and comparison with European cyclocoelids
4.3.3 Long-PCR and mt genome sequencing
4.3.4 Sequence assembly and mitogenome characterization
4.3.5 Phylogenetic analyses
4.4 Results and discussion
4.4.1 Identification and differences in ITS rDNA with European cyclocoelids
4.4.2 Mitochondrial genome features and gene content
4.4.3 Genetic relationships
4.5 Conclusion
Chapter5 Mitochondrial and nuclear ribosomal DNA dataset suggests that Hepatiarius sudarikovi Feizullaev1961 is a member of the genus Opisthorchis Blanchard,1895(Digenea:Opisthorchiidae)
5.1 Summary
5.2 Introduction
5.3 Materials and methods
5.3.1 Parasites and DNA extraction
5.3.2 The acquisition of H.sudarikovi ITS rDNA
5.3.3 PCR-based sequencing of H.sudarikovi mt genome
5.3.4 Genome assembly,annotation,and bioinformatics analysis
5.3.5 Phylogenetic analysis
5.4 Results and discussion
5.4.1 Morphological identification
5.4.2 ITS sequence comparison with other flukes within Opisthorchiidae
5.4.3 Characterization of the H.sudarikovi mt genome
5.4.4 Phylogenetic analysis
5.5 Conclusion
Conclusion
References
Acknowledgement
Resume
本文编号：3279904
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