Table 2 Differential gene expression in Acrasis kona

category	Gro vs Agg		Agg vs Germ		full proteome
category	Aggup	Aggdn	Germup	Germdn	full proteome
A. general
Ako annotated accs	370	260	1188	1641	10881
Ako novel (unannotated) accs	100 (22.3%)	193 (42.6%)	461 (28.0%)	371 (18.4%)	4987 (31.4%)
Ako total Accs	448	453	1649	2012	15868
Ddi AX4 SDE accs*	2595 (1859–2078)	1898 (2069–2375)	–	–	11440
B. orthology groups (OGs)
Ako accs belonging to OGs	190	198	880	948	6817
Ako OGs	(162 OGs)	(176 OGs)	(558 OGs)	(657 OGs)	(2728 OGs)
OGs shared with Ngr	(35 OGs)	(18 OGs)	(104 OGs)	(133 OGs)	(360 OGs)
OGs shared with Disc	(75 OGs)	(35 OGs)	(162 OGs)	(232 OGs)	(605 OGs)
OGs unique to Ako	(52 OGs)	(123 OGs)	(292 OGs)	(292 OGs)	(1763 OGs)
Ako single copy accs	258	255	769	1064	9051
C. transmembrane (TM) or signal peptides (SP)
Ako accs with TM domains	67	83	371	371	3202
Ako accs with SPs	42	57	215	17	1712
Ako accs with TM and SP	9	15	62	62	439
Ako accs without TM or SP	349	328	11255	1686	11393

(A) Numbers of substantially differentially expressed accessions (accs) are shown for the transition from asocial feeding to social development (growth to aggregation - Gro vs Agg: Aggup/Aggdn) and from development back to asocial growth (aggregation to germination - Agg vs Germ: Germup/Germdn) (Supplementary Data 6). (B) Orthology groups (OGs) and their presence/absence in Naegleria gruber (Ngr) and Discoba as a whole (Dis) were determined using OrthoMCL (Table S5 and Supplementary Data 2)⁸⁹. Transmembrane domains and signal peptides were predicted using Phobius (Supplementary Data 1)⁹⁵.
abbreviations: accs (accessions), w/ (with), Ako (Acrasis kona), Ddi (Dictyostelium discoideum AX4), Ngr (Naegleria gruberi), Disc (Discoba), Gro (growth), Agg (aggregation), Germ (germination), Aggup/Aggdn (SDE increased/decreased from 0 h to 5 h aggregation), Germup/Germdn (SDE increased/decreased from 5 h aggregation to germination) (Supplementary Data 6). *Numbers of Ddi AX4 SDE accs averaged across two replicates (r1 + r2) each for 0 h vs 5 h starvation¹¹. SDE acc numbers calculated for sing qle replicates (0h_vs_5h_r1 and 0h_vs_5h _r2) are shown in parentheses (GFold v1.1.4)¹⁵.
Total numbers for individual categories in sections A and B are shown in bold.

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