鳥類六種吸蟲的分子鑒定和線粒體基因組研究
發(fā)布時間：2021-07-12 12:19
分類學(xué)和系統(tǒng)學(xué)是學(xué)習(xí)生物多樣性的重要方法。采用分子數(shù)據(jù)挖掘與形態(tài)數(shù)據(jù)描述相結(jié)合的方法,可最大化地提供吸蟲分類及系統(tǒng)發(fā)育學(xué)的相關(guān)信息。核糖體DNA（rDNA）及線粒體（mt）基因組可提供豐富的遺傳標(biāo)記。部分或完整的rDNA序列已被廣泛用于吸蟲的物種鑒定及系統(tǒng)研究。然而,目前GenBank中僅有為數(shù)不多的吸蟲線粒體基因組數(shù)據(jù)。許多被忽略的或有分類及歸屬爭議的吸蟲需要通過解析其線粒體基因組序列來解決其分類爭議。盡管鳥類是最常見的吸蟲終末宿主之一,但對寄生于鳥類的吸蟲的分類及系統(tǒng)發(fā)育研究仍很有限。為了填補(bǔ)該空白,本論文解析了來自巴基斯坦不同食性鳥類的6種吸蟲的rDNA和mt基因組序列,研究了他們與其他吸蟲的系統(tǒng)發(fā)育關(guān)系。采用通用引物或者根據(jù)相對保守序列設(shè)計的引物,對寄生于不同鳥類的6種斜睪吸蟲,通過PCR擴(kuò)增獲得rDNA中的內(nèi)轉(zhuǎn)錄間隔區(qū)（ITS）及大亞基（LSU/28S）,以及完整或近乎完整的mt基因組序列。rDNA序列數(shù)據(jù)用于蟲種鑒定、遺傳變異以及部分物種科內(nèi)進(jìn)化樹構(gòu)建。注釋、描述了6種吸蟲的mt基因組的基因排列、12個蛋白編碼基因（PCGs）的堿基組成、堿基偏斜、密碼子使用、相對同義密碼子...
【文章來源】：中國農(nóng)業(yè)科學(xué)院北京市
【文章頁數(shù)】：104 頁
【學(xué)位級別】：博士
【文章目錄】：
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
本文編號：3279904
【文章來源】：中國農(nóng)業(yè)科學(xué)院北京市
【文章頁數(shù)】：104 頁
【學(xué)位級別】：博士
【文章目錄】：
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
本文編號：3279904
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