Transcriptome Analysis Of Four Kinds Of Domestic Pigeons

The pigeons have excellent flying ability and navigation and positioning ability.In the past,researchers have conducted a lot of experimental studies on the superior flight and positioning performance of pigeons,but there are few studies on the genetic factors of pigeon flight performance from the transcriptome level.Therefore,this study uses racing pigeons and ornamental pigeons as test subjects.By comparing the transcriptomes of the pectoral muscles,brain and blood tissue of the two,the molecular mechanism of the pigeons' flying and positioning capabilities is revealed.The specific research results are as follows:1.477 differentially expressed genes were obtained by screening the breast muscles of racing pigeons and ornamental pigeons.GO annotation and KEGG functional enrichment analysis were performed on these differentially expressed genes.The results showed that genes highly expressed in the breast muscles of racing pigeons were significantly enriched in PPAR signaling pathway 18 signal pathways such as metabolism,pyruvate metabolism and glycolysis/gluconeogenesis;highly expressed genes in the breast muscle of ornamental pigeons are significantly enriched in arginine and proline metabolism,eukaryotic ribose biosynthesis and myocardial contraction7 Pathways.Through the analysis of 477 differential gene weighted co-expression networks and protein interaction networks,three(brown,yellow and blue)gene modules that are significantly related to traits are obtained,and the brown and yellow modules are significantly positively related to the pigeon breast muscles;The blue module was significantly positively correlated with the breast muscles of ornamental pigeons,and then the three gene modules were functionally enriched.The results showed that the brown module was significantly enriched in pyruvate metabolism,PPAR signaling pathway,fatty acid metabolism,peroxisomes,metabolic pathways and There are 11 signal pathways such as antibiotic biosynthesis;the yellow module is significantly enriched into the peroxisome and metabolic pathways;the blue module is significantly enriched into the ribosome pathway.By performing differential alternative splicing and Wien analysis on the breast muscle transcriptome of racing pigeons and ornamental pigeons,the results showed that there were 4535 genes with differential alternative splicing between the two groups,and then according to the standard significance of | IncLevel Difference |? 0.05 and FDR ?0.1 According to the analysis,there are 161 genes with significant difference in alternative splicing between the two groups.Among them,DTNA,PDLIM3 and LIAS are simultaneously highly expressed genes in the pigeon breast muscles,and P4HA2,PRKAG3 and ANKHD1 are highly expressed genes in the ornamental pig breast muscles.2.By screening brain tissues of racing pigeons and ornamental pigeons,167 differentially expressed genes were obtained,and these differential genes were functionally enriched using the KOBAS online enrichment website.The results showed that a total of 4 pathways were significantly enriched,which are neuroactive ligands-Receptor interaction,RNA polymerase pathway and ribosome and eukaryotic ribosome biogenesis.By performing differential alternative splicing analysis on the brain transcriptomes of racing pigeons and ornamental pigeons,the results showed that there were 7649 genes with differential alternative splicing between the two groups,and then according to the standard significance analysis of | IncLevelDifference |? 0.05 and FDR ?0.1.It is known that there are 318 genes with significant difference in alternative splicing between the two groups.Among them,the MRPS18A gene is also a highly expressed gene in the pigeon brain tissue and this gene regulates the pigeon brain through two splicing methods:SE and MXE.3.Three batches of 21 retinal transcription components of cattle,human,macaques,long-tailed macaque,domestic rats,pigeons and chickens were assembled by Trinity.The 7071 shared genes in the three batches were analyzed by weighted co-expression network analysis and divided 17 gene modules significantly related to traits,of which blue and lightyellow modules were significantly correlated with cattle vision;cyan and midnightblue modules were significantly correlated with human vision;royalblue modules were significantly positively correlated with macaque vision;greenyellow,grey60 and salmon modules and food The visual abilities of cynomolgus monkeys are significantly correlated,the brown,mangeta and red modules are significantly correlated with the eyesight of rats;the pink,tan and yellow modules are significantly correlated with the vision of pigeons;the black,green and purple modules are significantly correlated with the vision of chickens,and then Enriched the function of gene modules with significant positive correlation.The results showed that the genes in the module are mainly involved in the synthesis and metabolism of substances,immune response and other aspects.By estimating the MM and GS values of the genes of each module member,then the Top5 core genes were selected from the significant related modules of cattle,pigeons and other species,and finally the core genes of the retinas of these 7 species were strictly screened,and cattle(RBFOX2,ATF1)were found),humans(GRB10,NBR1),domestic rats(CCND1),pigeons(RERE,SOD1,GPX4 and CDK1)and chickens(BBS4,ACAT1)are likely to be important genes that affect the visual ability of the corresponding species.4.Single cell transcriptome sequencing analysis was performed on the cells in pigeon blood,and 4197 high-quality cells were obtained after filtering the original data.According to the t-SNE clustering algorithm,the 4197 cells were divided into 7 subgroups,and then GO and KEGG functional enrichment analysis was performed on each cell subgroup.The GO analysis results showed that in terms of cell composition,the cell subgroup 6 The genes of and 7 are significantly enriched in the ribosome entry;the genes of the cell subpopulations 2,1 and 4 are significantly enriched in the(viral)nucleocapsid and the nuclear ribonucleoprotein complex entry;in terms of molecular function,Cell subsets 3,2,1 and 4 are significantly enriched into nucleotide binding entries.The results of KEGG pathway enrichment showed enrichment into ribosomes,oxidative phosphorylation,proteasome,RNA transport,and myocardial contraction.Then integratedly analyze the KEGG pathway and the genes enriched in the 7 cell subpopulations respectively,and speculate from multiple angles of cell subpopulation 6 to cell subpopulation 4(6-7-5-3-2-1-4)It may be the aging process of cells.We also analyzed the hemoglobin genes(LOC102090851 and LOC102090541)and FTH1 genes in 7 cell subpopulations and speculated that as the pigeon red blood cells aging,the hemoglobin in the cells was gradually degraded and the degraded iron ions were sent to their own via transferrin Store in ferritin library.By comparing the expression of mitochondrial genes in pigeons and chickens in single red blood cells,we know that the expression level of mitochondrial genes in single red blood cells of pigeons is significantly higher than that of chickens(approximately 3 to 30 times),indicating that the number of mitochondria in pigeon red blood cells is more than that in chicken red blood cells.Through further analysis of single-cell data,it is found that SOD1,SOD2,TLR3,TLR4,IL15,IL16 and other immune genes exist in red blood cells,indicating that pigeon red blood cells have immune functions in addition to oxygen transport functions.