TABLE 2.

The 13 different pathways/processes examined in this study as determinants of the social behavior in model Myxococcota genomes, along with the number of genes in each module, and the percentage of genes identified in Zodletone genomes as well as the genomes of three Myxococcota type species known to exhibit nonsocial behavior^a,b

Major function in the social lifestyle	Process/pathway	No. of genes in module	Zodletone lineages (%)		Type species (nonsocial) (%)			Notes on homologues identified/missing in Zodletone genomes
			O__JAFGXQ01	F__JAFGIB01	Anaeromyxobacter dehalogenes	Labilithrix luteola	Vulgatibacter incomptus	Homologues identified	Homologues missing
Gene regulatory networks governing early events of aggregation and mound formation prior to sporulation	Enhancer-binding protein (EBP) module	9	88.9	88.9	88.9	100	88.9	8 total: 6 DNA-binding transcriptional response regulator domains of the NtrC family, 1 serine/threonine kinases, and 1 peptidase	ActC (one of the Act group of proteins)
	MrpC module	8	75	62.5	75	75	87.5	2 catalytic domains of serine/threonine kinases, 2 component system sensor histidine kinases, an oligopeptide transporter, and a DNA-binding transcriptional response regulator of the NtrC family	MrpC, a transcription factor that works cooperatively to control the start of sporulation
	Nla24 module	2	100	100	100	100	100	A DNA-binding transcriptional response regulator of the NtrC family and a diguanylate-cyclase (DGC) or GGDEF domain
	FruA module	1	0	0	0	0	0		FruA, a transcription factor that works cooperatively to control the start of sporulation
Exopolysaccharide production necessary for the formation of fruiting bodies	EPS production	8	12.5	12.5	50	100	62.5	1 homologue identified with a sugar transporter domain	7 out of 8 homologues missing
Extracellular signal production	C-signal	3	0	0	0	0	0		All proteins in this module: CsgA encoding the actual C-signal protein, the activating protease PopC, and its inhibitor PopD
	A-signal	8	25	25	75	75	75	2 DNA-binding transcriptional response regulators of the NtrC family	A-signal production-specific homologues
Gene regulatory networks governing sporulation	Aggregation, sporulation, fruiting body formation	35	11.4	11.4	40	22.9	42.7	1 sugar transporter and 3 transcriptional regulators	The majority of sporulation-specific genes The dev operon CRISPR-Cas genes The Exo and Nfs genes (both involved in forming the spore polysaccharide coat) The spore coat protein Tps The putative FAD-binding monooxygenase MXA2872 FruA-MrpC-regulated genes (Fmg) mcu operon encoding a chaperone/usher secretion system important for spore-coat assembly
Coordination of the two motility systems (Frz) and induction of Nla24 module (Dif)	Chemosensory pathways	17	35.3	35.3	40	25.7	31.4	1 Dif gene and 3 Frz genes identified, mainly due to their similarity to chemotaxis protein histidine kinases, chemotaxis methyltransferase, and methylesterase Two of the three cell-polarity regulatory proteins were identified, a small GTPase, and its cognate GTPase activator	5 of the 6 Dif chemosensory network homologues The cytoplasmic receptor for the Frz chemosensory network FrzCD, the 2 coupling proteins FrzA and FrzB, the dual response regulator protein FrzZ that localizes to the cell poles and interact with the 3 cell-polarity regulatory proteins 1 of the 3 cell-polarity regulatory proteins (RomR)
Fine tuning and optimizing the onset of aggregation and sporulation	Development timers	6	50	50	83.3	83.3	83.3	RodK and 2 of the RedCDEF, a 4-component system necessary for controlling aggregation timing Homologues are similar to sensor histidine kinase (n = 2), and a helix-turn-helix-containing response regulator	2 of the RedCDEF, a 4-component system necessary for controlling aggregation timing.
Motility	Adventurous (A) motility	18	33.3	27.8	77.8	38.9	88.9	3 Glt complex genes and 2 Agl complex genes (similarity to TolQR/ExbBD/MotAB-like channel)	AglZ that contributes to the assembly of the inner membrane complex CglB, the lipoprotein interacting with the substratum at focal adhesion sites GltA, B, H, K (outer membrane beta barrel structures that transport the lipoprotein CglB to the external surface) AglQS (inner membrane complex)
	Social (S) motility	14	57.1	57.1	71.4	64.3	64.3	S motility is mediated by type IV pili (T4P) The majority of T4P genes were identified	PilA (the major pilin), PilI, and PilO
Sharing of resources, kin-recognition for exclusion of cheaters	Outer membrane exchange (OME)	2	50	50	50	100	50	TraA partner, TraB, was identified mainly because it contains an outer membrane OmpA domain	TraA, the cell surface receptor, was not identified in Zodletone genomes.

^aMore details are in the supplementary text and Table S6.

^bThe cells with percentage of genes identified are color coded as follows: dark gray with white font, >50% of the pathway was identified in the genome; light gray, 25 to 50% of the pathway was identified in the genome; white, <25% of the pathway was identified in the genome.