Comparative analysis of spleen transcriptome detects differences in evolutionary adaptation of immune defense functions in bighead carp and silver carp

Li, Guoxi; Zhao, Yaping; Guo, Shuang; Liu, Bianzhi; Chen, Yi; Sun, Xiaolun; Feng, Jianxin

doi:10.1016/j.fsi.2018.09.077

Cited by 12 publications

(7 citation statements)

References 63 publications

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“…Among them, the genes encoding for phosphoinositide 3-kinase adapter protein 1, Ras-related protein Rap-1b, complement factor I, and probable ATP-dependent RNA helicase DHX58 were related to immune adaptation. Li et al (2019) found that B cell-mediated immunity, chemokine-mediated signaling pathway, and immunoglobulin mediated immune response were the positively selected biological processes in big head carp, whereas those in silver carp mainly included the antigen processing and presentation, defense response to fungus, and detection of bacteria. Chen et al (2008) revealed that TLR9 gene was positive selection in teleosts.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing

et al. 2020

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Spinibarbus caldwelli is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of S. caldwelli, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by de novo assembly. Additionally, we calculated that the divergence time between S. caldwelli and Sinocyclocheilus grahami is 23.14 million years ago (Mya). And both of them diverged from Ctenopharyngodon idellus 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as POLR3B, PIK3C3, TOPORS, FASTKD3, CYPLP1A1, and UACA. Our results throw light on the nature of the natural selection of S. caldwelli and contribute to future immunological and transcriptome studies.

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Section: Discussionmentioning

confidence: 99%

Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing

et al. 2020

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“…In this study, DEGs identified in the spleen between CRS and FRS significantly enriched the phenylalanine metabolic pathway. Moreover, transcriptome studies in human [ 31 ], chicken [ 32 ], fish [ 33 ], and white shrimp Litopenaeus vannamei [ 34 ] have also shown that the important role of phenylalanine metabolic pathway in the control of immune ability. Moreover, our results showed that all the DEGs (PAH, TAT, and AOC3) enriched in the phenylalanine metabolism pathway were significantly upregulated, indicating that the phenylalanine metabolism pathway was promoted in CRS geese.…”

Section: Discussionmentioning

confidence: 99%

Effects and Mechanisms of Cage versus Floor Rearing System on Goose Growth Performance and Immune Status

Tang,

Hu,

Zhang

et al. 2023

Animals

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Currently, FRS and CRS are the two predominant dryland rearing systems in the goose industry. However, the effects of these two systems on goose growth performance and health, as well as the underlying mechanisms, have not been fully clarified. Thus, this study aimed to compare growth performance and immune status, as well as investigate the genome-wide transcriptomic profiles of spleen in geese, between CRS and FRS at 270 d of age. Phenotypically, the body weight and body size traits were higher in geese under FRS, while the weight and organ index of spleen were higher in geese under CRS (p < 0.05). Noticeably, the bursa of Fabricius of geese under FRS was degenerated, while that under CRS was retained. At the serum level, the immune globulin-G (IgG) and interleukin-6 (IL-6) levels were higher in geese under CRS (p < 0.05). At the transcriptomic level, we identified 251 differentially expressed genes (DEGs) in the spleen between CRS and FRS, which were mainly enriched in scavenger receptor activity, inflammatory response, immune response, neuroactive ligand–receptor interaction, phenylalanine metabolism, ECM receptor interaction, calcium signaling pathway, phenylalanine, tyrosine, and tryptophan biosynthesis, regulation of actin cytoskeleton, and MAPK signaling pathways. Furthermore, through protein–protein interaction (PPI) network analysis, ten candidate genes were identified, namely, VEGFA, FGF2, NGF, GPC1, NKX2-5, FGFR1, FGF1, MEIS1, CD36, and PAH. Further analysis demonstrated that geese in CRS could improve their immune ability through the “phenylalanine metabolism” pathway. Our results revealed that the FRS improved growth performance, whereas the CRS improved goose immune function by increasing levels of IL-6 and IgG in serum. Moreover, the phenylalanine metabolism pathway could exert positive effects on immune function of geese under CRS. These results can provide reliable references for understanding how floor and cage rearing systems affect goose growth performance and immune capacity.

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“…In recent years, with the rapid development and application of high-throughput sequencing technologies, considerably more attention has been focused on elucidating the molecular mechanisms regulating spleen function. The primary goal is to identify genes involved in spleen function by transcriptome analysis in different species, such as the mouse [ 8 , 82 ] , goose [ 83 ] , pig [ 84 ] , giant panda [ 85 ] , common carp [ 86 ] as well as bighead carp and silver carp [ 87 ] . In addition, to elucidate epigenetic regulation of spleen function, non-coding RNAs such as miRNA, lncRNA or circRNA were identified by transcriptome sequencing in different species, such as the mouse [ 82 ] , pig [ 83 ] , giant panda [ 84 ] , Chinese giant salamander [ 88 ] , green-spotted puffer fish [ 89 ] , rainbow trout [ 90 ] , and common carp [ 19 ] .…”

Section: Discussionmentioning

confidence: 99%

Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella)

et al. 2022

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The spleen is an important immune organ in fish. MicroRNAs (miRNAs) have been shown to play an important role in the regulation of immune function. However, miRNA expression profiles and their interaction networks associated with the postnatal late development of spleen tissue are still poorly understood in fish. The grass carp (Ctenopharyngodon idella) is an important economic aquaculture species in China. Here, two small RNA libraries were constructed from the spleen tissue of healthy grass carp at one-year-old and three-year-old. A total of 324 known conserved miRNAs and 9 novel miRNAs were identified by using bioinformatic analysis. Family analysis showed that 23 families such as let-7, mir-1, mir-10, mir-124, mir-8, mir-7, mir-9, and mir-153 were highly conserved between vertebrates and invertebrates. In addition, 14 families such as mir-459, mir-430, mir-462, mir-7147, mir-2187, and mir-722 were present only in fish. Expression analysis showed that the expression patterns of miRNAs in the spleen of one-year-old and three-year-old grass carp were highly consistent, and the percentage of miRNAs with TPM > 100 was above 39%. Twenty significant differentially expressed (SDE) miRNAs were identified. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that these SDE miRNAs were primarily involved in erythrocyte differentiation, lymphoid organ development, immune response, lipid metabolic process, the B cell receptor signaling pathway, the T cell receptor signaling pathway, and the PPAR signaling pathway. In addition, the following miRNA-mRNA interaction networks were constructed: immune and hematopoietic, cell proliferation and differentiation, and lipid metabolism. This study determined the miRNA transcriptome as well as miRNA-mRNA interaction networks in normal spleen tissue during the late development stages of grass carp. The results expand the number of known miRNAs in grass carp and are a valuable resource for better understanding the molecular biology of the spleen development in grass carp.

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Comparative analysis of spleen transcriptome detects differences in evolutionary adaptation of immune defense functions in bighead carp and silver carp

Cited by 12 publications

References 63 publications

Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing

Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing

Effects and Mechanisms of Cage versus Floor Rearing System on Goose Growth Performance and Immune Status

Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella)

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