The Difference Of Spleen Transcriptome In Pig Different Developmental Stages And Comparative Transcriptome Analysis Across Species

With its location in the circulatory system and with the unusual structure of its lymphoid compartments,the spleen is a unique lymphoid organ.It is not only the largest immune organ in mammals,but also the largest blood filter in the body.It plays an important role in maintaining the body’s immune homeostasis,as well as the recovery of aging red blood cells and iron ion transport.LncRNAs are known to participate in regulatory networks for an array of biological processes.At present,there is absence of research on protein-coding genes and lncRNAs in different growth stages and different species in spleen.In this study,we constructed 39 strand-specific lncRNA libraries from five developmental stages in domestic pigs,three samples from Wild Boar,and the samples from other 9 mammals.We adopted a series of bioinformatics methods to study functional transcriptome and regulatory transcriptome of spleen.The main results are described as follows:（1）A total of 15,040 lncRNA transcripts were identified among the 18 samples from pig,including 12,967 lncNRA genes.Among of them,6,898 lncRNAs expressed in all 18samples,which accounted for 45.86%of all lncRNAs in pig developmental stages.（2）Compared with protein-coding genes,lncRNAs are shorter in transcript length,have fewer exons,and express at lower levels.（3）In the developmental samples of pig,the genes whose antisense intron overlapped with lncRNAs were enriched in T cell activation,B cell proliferation and differentiation,adaptive immune response,and metal ion binding were significantly enriched,which implied that the functional relationship of lncRNAs with their neighboring genes.（4）Based on the results of expression profiles of transcripts in the developmental samples of pig,both protein-coding genes and lncRNAs could separate samples into different developmental stages.Based on the results of Pearson correlation coefficient,both protein-coding genes and lncRNAs could separate samples into three broad classes:the embryonic development stage,the suckling period,and the sexual maturity period.The results of alternative splicing level（PSI value）of exons in protein-coding genes could separated samples as different developmental stages.（5）According to the results of short time-series research（STEM）,protein-coding genes and lncRNAs have the similar expression patterns during developmental stages.Genes in up-regulated modules were mainly enriched in innate immune response,adaptive immune response,and positive regulation of T cell proliferation.Genes in down-regulated modules were mainly enriched in cell division,DNA replication and cell proliferation.（6）The results of co-expression network indicated that the protein-coding genes and lncRNAs,who related to the factor of time,were enriched in the biological processes of adaptive immune response,B cell receptor signaling pathway and T cell activation.（7）According to the results of differential expression,CP,encodes ceruloplasmin precursor was differentially expressed in all five developmental stages.It has ferroxidase activity to oxidize Fe²⁺to Fe³⁺without releasing radical oxygen species,and it also involved in iron transport across the cell membrane,which is consistent with the main biological function of spleen.（8）We identified 4,783 1:1 orthologous genes in ten species.Among of them,2,780（58.12%）orthologous genes expressed in the spleen of all ten species.We also identified1,407 orthologous lncRNAs in the spleen of ten species.（9）Based on the expression profiles in ten species,both orthologous protein-coding genes and orthologous lncRNAs could separate samples as species.The expression pattern of orthologous lncRNAs have poor conservation between species.Based on the results of alternative splicing level of orthologous exons,samples could be separated as species,and have poor conservation between species.（10）Functional categories of genes which were not only specifically expressed in species,but also expression selection in species indicated that,the term of response to drug was existed in agriculture animals.In summary,spleen transcriptome had specific function change during the development process of pig,and had different function among species.These will provide reference for future studies,and have important significance in theory and practice.