Table 4.

Similarities and differences of immune damage induced by MG infection on chicks and chicken embryos.

Feature	Pathological Changes/Enriched GO and KEGG Term	Affected Genes
Similarities	(1)decreased body weight	No
	(2)increased spleen and thymus organ indices	No
	(3)increased tracheal mucosal thickness and narrowed alveolus space with inflammatory infiltration in the trachea and lungs	No
	(4)Enrichment of GO and KEGG pathways involved in TLRs	Upregulation of genes for TLR6, TLR7, and TLR1A in lung tissues; up-regulation of genes for TLR6 in spleen, thymus, and bursa of Fabricius;
	(5)Enrichment of GO and KEGG pathways involved in cytokines and chemokines	Upregulation of genes for IL8L1, IL8L2, TNFRSF6B, IL20RA, CCR2, LOC100857191, IL1B, CCR5, CXCL13L2, CCL5, CXCL13, LOC395551, and CSF3R;
	(6)Enrichment of GO terms involved in antimicrobial peptide-mediated immune response	RNASE6, S100A9, RSFR, and LBP.
	(7)Enrichment of GO terms involved in neutrophil degranulation: dysregulation	IL1B, HBE1, RNASE6, S100A9, BST1, ADGRG5, RSFR, LBP, and CXCL13L2;
	(8)Enrichment of GO and KEGG pathways involved in neutrophil chemotaxis	IL8L1, CSF3R, IL8L2, SYK, CCL5, LOC100857191, CXCL13L2, CXCL13, CCL26;
Differences	(1)The number of DEGs related to TLRs in chicks was lower than that in chicken embryos	Upregulations of genes for MAP3K8, SPP1, TLR4, TLR2A, TLR15, CD88, FOS, CCL4, TLR6, TLR3, LY96, and IRF7 were observed in chicken embryos, but not chicks
	(2)The number of DEGs related to cytokines, chemokines, and their receptors in chicks was lower than that in chicken embryos	Upregulations of genes for CSF3, IL18RAP, CSF2RB, IL16, IL18R1, IL10RA, CCL20, CSF1R, IL18, IL13RA2, TNFRSF4, IL1R2, XCR1, IL2RA, CCL4, CX3CR1, CXCR1, CRCBL, IL2RG, CSF2RA, and LOC101747500 in were observed in chicken embryos, but not in chicks
	(3)The number of DEGs related to antimicrobial peptides in chicks was lower than that in chicken embryos	Upregulations of AVBD1, 3, 4, 5, 6, 7, and 8 and DEFB4A, CATH1, CATH2, and CATH3 were observed in chicken embryos only
	(4)Enrichment of GO and KEGG pathways involved in phagocytosis in chickens but not in chicks	Upregulations of C1R, NCF2, BLB1, NCF4, ITGB2, TUBA4AL, TLR1A, TAP1, NCF1C, CYBB, TUB4A, TLR2A, BF1, MMR1L3, LOC771876, MMR1L4, MARCO, DMA, DMB2, LOC420160, ATP6V1G3, ATP6V0D2, TLR4, LOC428421 were observed in chicken embryos only
	(5)Enrichment of GO and KEGG pathways involved in DNA replication and cell cycle in chicks, but not in chicken embryos	Upregulations of FEN1, RFC3, MCM3, MCM4, MCM5, DNA2, MCM2, BUB1B, CDK1, BUB1 were observed in chicks only

Notes: The similarities and differences between chick and chicken embryos listed in the table were mainly drawn based on GO and KEGG enrichment analysis results.