| 摘要 | 第7-14页 |
| ABSTRACT | 第14-18页 |
| 1. INTRODUCTION | 第26-56页 |
| 1.1 BACKGROUND | 第26-28页 |
| 1.2 INTRODUCTION OF CATFISH | 第28-31页 |
| 1.3 TELEOST SWIMBLADDER | 第31-33页 |
| 1.4 RNA-SEQ ANALYSIS AND ITS APPLICATION IN AQUACULTURE SPECIES | 第33-37页 |
| 1.4.1 Transcriptome and RNA-sequencing | 第33页 |
| 1.4.2 RNA-seq pipline | 第33-34页 |
| 1.4.3 RNA-seq bioinformatics tools | 第34-36页 |
| 1.4.4 Application of RNA-seq in aquaculture species | 第36-37页 |
| 1.5 WHOLE GENOME SEQUENCING AND ITS APPLICATION IN AQUACULTURE SPECIES | 第37-42页 |
| 1.5.1 Whole genome sequencing | 第37-38页 |
| 1.5.2 Workflow of whole genome sequencing | 第38-39页 |
| 1.5.3 Current status of whole genome sequencing in aquaculture species | 第39-42页 |
| 1.6 CHEMOKINES AND THEIR RECEPTORS | 第42-53页 |
| 1.6.1 Introduction of chemokine superfamily | 第42-43页 |
| 1.6.2 Nomenclature classification and structures of chemokines and their receptors | 第43-50页 |
| 1.6.3 Chemokines and their receptors in teleosts | 第50-53页 |
| 1.7 MAJOR QUESTIONS OF THIS THESIS | 第53-54页 |
| 1.8 OUTLINE OF THIS THESIS | 第54-56页 |
| 2. COMPARATIVE TRANSCRIPTOME ANALYSIS OF CHANNEL, BLUE AND INTERSPECIFIC HYBRID CATFISH SWIMBLADDER BY RNA-SEQ | 第56-82页 |
| 2.1 INTRODUCTION | 第56-58页 |
| 2.2 MATERIALS AND METHODS | 第58-62页 |
| 2.2.1 Ethic statement | 第58页 |
| 2.2.2 Tissue collection, RNA isolation, library construction and sequencing | 第58-59页 |
| 2.2.3 Generating genome indexes and reads mapping | 第59页 |
| 2.2.4 Differential expression analysis and Gene Ontology (GO) enrichment | 第59-60页 |
| 2.2.5 Experimental validation by RT-qPCR | 第60-62页 |
| 2.3 RESULTS | 第62-75页 |
| 2.3.1 Sequencing and mapping of short expressed reads from catfish swimbladder | 第62-63页 |
| 2.3.2 Analysis of differentially expressed genes | 第63-64页 |
| 2.3.3 Clustering and GO analysis | 第64-69页 |
| 2.3.4 Validation of RNA-seq results by RT qPCR | 第69-75页 |
| 2.4 DISCUSSION | 第75-80页 |
| 2.5 CONCLUSION | 第80-82页 |
| 3. RNA-SEQ ANALYSIS OF THE SWIMBLADDER REVEALS EXPRESSION SIGNATURES IN RESPONSE TO HYPOXIA IN CHANNEL CATFISH | 第82-114页 |
| 3.1 INTRODUCTION | 第82-83页 |
| 3.2 MATERIALS AND METHODS | 第83-88页 |
| 3.2.1 Experimental animals and tissue collection | 第83-84页 |
| 3.2.2 RNA extraction, library construction and sequencing | 第84页 |
| 3.2.3 Reads mapping and differential expression analysis | 第84-86页 |
| 3.2.4 Gene Ontology and enrichment analysis | 第86页 |
| 3.2.5 Identification of swimbladder-enriched genes | 第86-87页 |
| 3.2.6 Experimental validation by RT-qPCR | 第87-88页 |
| 3.3 RESULTS | 第88-108页 |
| 3.3.1 Sequencing and mapping of short expressed reads | 第88-90页 |
| 3.3.2 Analysis of differentially expressed genes | 第90-92页 |
| 3.3.3 Analysis of expression signatures and gene pathways | 第92-105页 |
| 3.3.4 Enriched genes in swimbladder transcriptomes | 第105-107页 |
| 3.3.5 Validation of RNA-seq results by RT-qPCR | 第107-108页 |
| 3.4 DISCUSSION | 第108-113页 |
| 3.5 CONCLUSION | 第113-114页 |
| 4. CXC CHEMOKINES IN CHANNEL CATFISH AND THETR INVOLVEMENT IN HYPOXIA AND DISEASE RESPONSES | 第114-137页 |
| 4.1 INTRODUCTION | 第114-116页 |
| 4.2 MATERIALS AND METHODS | 第116-122页 |
| 4.2.1 Gene identification and sequence analysis | 第116-117页 |
| 4.2.2 Phylogenetic analysis | 第117-118页 |
| 4.2.3 Synteny and schematic genomic organization analysis | 第118-119页 |
| 4.2.4 Bacterial infecitons and sample collecion | 第119-121页 |
| 4.2.5 Hypoxia challenge and sample collecion | 第121页 |
| 4.2.6 Expression analysis of catfish CXC chemokines using RNA-Seq datasets | 第121-122页 |
| 4.3 RESULTS | 第122-131页 |
| 4.3.1 Identification of CXC chemokine genes in channel catfish | 第122-123页 |
| 4.3.2. Phylogenetic and syntenic analysis of catfish CXC chemokine genes | 第123-125页 |
| 4.3.3. Comparative analysis of copy numbers of CXC chemokine genes | 第125-127页 |
| 4.3.4 Genomic clusters of channel catfish CXC chemokines | 第127-128页 |
| 4.3.5. Expression of CXC chemokine genes following bacterial infection | 第128-129页 |
| 4.3.6. Comparison of CXC chemokine expression in resistant and susceptible fish | 第129-131页 |
| 4.3.7. Expression profile of CXC chemokine genes following hypoxia stress | 第131页 |
| 4.4 DISCUSSION | 第131-135页 |
| 4.5 CONCLUSION | 第135-137页 |
| 5. CC CHEMOKINES IN CHANNEL CATFISH AND THEIR INVOLVEMENT IN HYPOXIA AND DISEASE RESPONSES | 第137-161页 |
| 5.1 INTRODUCTION | 第137-139页 |
| 5.2 MATERIAL AND METHODS | 第139-143页 |
| 5.2.1 Gene identification and sequence analysis | 第139-140页 |
| 5.2.2 Phylogenetic analysis | 第140页 |
| 5.2.3 Synteny and schematic genomic organization analysis | 第140-141页 |
| 5.2.4 Bacterial infections and sample collection | 第141页 |
| 5.2.5 Hypoxia challenge and sample collection | 第141-142页 |
| 5.2.6 Expression analysis of catfish CC chemokines using RNA-Seq datasets | 第142-143页 |
| 5.3 RESULTS | 第143-154页 |
| 5.3.1 Identification of CC chemokine genes in channel catfish | 第143-145页 |
| 5.3.2 Phylogenetic and syntenic analysis of channel catfish CC chemokine genes | 第145-148页 |
| 5.3.3 Comparative analysis of copy numbers of CC chemokine genes | 第148-150页 |
| 5.3.4 Genomic clusters of channel catfish CC chemokine genes | 第150-151页 |
| 5.3.5 Expression of CC chemokine genes following bacterial infection | 第151-152页 |
| 5.3.6 Expression of CC chemokine in resistant and susceptible fish after ESC infection | 第152-153页 |
| 5.3.7 Expression profile of CC chemokine genes following hypoxia stress | 第153-154页 |
| 5.4 DISCUSSION | 第154-159页 |
| 5.5 CONCLUSION | 第159-161页 |
| 6. CC AND CXC CHEMOKINE RECEPTORS IN CHANNEL CATFISH AND THEIR INVOLVEMENT IN DISEASE AND HYPOXIA RESPONSES | 第161-183页 |
| 6.1 INTRODUCTION | 第161-163页 |
| 6.2 MATERIALS AND METHODS | 第163-166页 |
| 6.2.1 Gene identification and sequence analysis | 第163页 |
| 6.2.2 Phylogenetic analysis | 第163-164页 |
| 6.2.3 Synteny and schematic genomic organization analysis | 第164-165页 |
| 6.2.4 Bacterial infecions and sample collection | 第165页 |
| 6.2.5 Hypoxia challenge and sample collection | 第165页 |
| 6.2.6 Expression analysis of catfish CC and CXC chemokine receptors | 第165-166页 |
| 6.3 RESULTS | 第166-177页 |
| 6.3.1. Identification of CC and CXC chemokine receptors in channel catfish | 第166页 |
| 6.3.2. Phylogenetic and syntenic analysis of channel catfish CC and CXC chemokine receptors | 第166-168页 |
| 6.3.3 Comparison of copy numbers of CC and CXC chemokine receptors | 第168-172页 |
| 6.3.4. Genomic clusters of channel catfish CC and CXC chemokine receptors | 第172-174页 |
| 6.3.5. Expression of CCR and CXCR genes following bacterial infection | 第174-175页 |
| 6.3.6 Expression of chemokine receptors in resistant and susceptible catfish after ESC infection | 第175-176页 |
| 6.3.7 Expression profile of CC and CXC chemokine receptors following hypoxia stress | 第176-177页 |
| 6.4 DISCUSSION | 第177-182页 |
| 6.5 CONCLUSION | 第182-183页 |
| 7. CONLUSIONS AND PROSPECTS | 第183-186页 |
| 7.1 CONCLUSIONS | 第183-184页 |
| 7.2 PROSPECTS ABOUT FUTURE WORK | 第184-186页 |
| REFERENCE | 第186-210页 |
| 作者简历 | 第210-211页 |
| 攻读博士学位期间科研成果 | 第211-215页 |
| 致谢 | 第215-216页 |
