The genome of the Gulf pipefish enables understanding of evolutionary innovations

Table 3 List of the top 15 pregnancy-depressed pouch tissue genes

Gene ID	Fold change	CPM	p value	Gene description	KO ID
SSCG00000006879	27.36	56.49	7.91E-43	Serine/threonine-protein kinase WNK2	K08867
SSCG00000018539	12.37	15.96	2.04E-26	FXYD domain-containing ion transport regulator 12
SSCG00000007973	4.73	53.34	1.66E-24	A disintegrin and metalloproteinase with thrombospondin motifs 6, partial	K08621
SSCG00000013585	10.78	19.10	1.07E-23	Tetratricopeptide repeat protein 18
SSCG00000005985	214.58	652.27	7.29E-23	patristacin, partial	K08076
SSCG00000008728	14.12	6.03	2.22E-22	Uridine-cytidine kinase-like 1	K00876
SSCG00000000969	4.32	19.82	1.25E-17	ras-like protein family member 11A	K07852
SSCG00000017729	6.14	359.52	1.71E-17	nidogen-2-like isoform X5	K06826
SSCG00000004506	6.00	12.98	4.08E-17	syntaxin-2-like isoform X1	K08486
SSCG00000010275	14.47	3.28	1.00E-16	acid-sensing ion channel 1
SSCG00000016046	6.75	8.51	1.51E-16	leucine-rich repeat-containing protein 4-like	K16351
SSCG00000014649	10.15	7.67	1.77E-16	homeobox protein MSX-2-like	K09341
SSCG00000019217	66.66	3.26	1.82E-16	leucine-rich repeat-containing protein 3-like
SSCG00000007661	5.19	24.20	2.23E-16	cytochrome P450 27C1-like	K17951
SSCG00000005388	19.81	1.44	5.60E-16	glutamate receptor ionotropic, delta-2 isoform X5	K05207

Included are the fold change (non-pregnant/pregnant), average expression level across 12 pouch libraries in copies per million (CPM), edgeR negative binomial exact test p value, gene description from top BLASTP hit, and the assigned KEGG orthology ID for each pipefish gene. See Additional file 2 SH2 for the full list

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