Fig. 3: Phylogenetic history of the Chroococcidiopsidales order.

Phylogenetic trees of the Chroococcidiopsidales order based on 16S rRNA genes (A) and genome information (B). The two trees mirror and complement each other. In (A), it can be seen that the genus ‘Chroococcidiopsis’ is currently polyphyletic. Strains identified as such actually belong to multiple clades, some of which may be highly supported, but whose relationships with each other is sometimes unclear. Large, highly supported clades and/or clades with type species have been collapsed. Each color represents a genus-level taxon, some with associated genome information (B). These taxa include well-defined genera such as Chroococcidiopsis sensu stricto (I), Sinocapsa (IV), Aliterella (VI), Haliplanktos (VII) and Pseudocyanosarcina (VIII). They also encompass yet-undefined genera lacking a type species—Hot desert Chroococcidiopsidales (II) and ‘Additional desert clade’ (V). Moreover, ‘Gloeocapsa’ (III) represents a cluster of taxonomically ambiguous, closely related strains (Gloeocapsa, Gloeocapsopsis, Chroogloeocystis and Speleotes). Although showing low support in this tree, the Sinocapsa (IV) branch is stable across multiple tree-building methods. The related Nostocales are indicated by a gray rectangle (see “Materials and Methods”: Single-gene phylogenies and rooting). The tree was rooted with Pleurocapsa sp. PCC 7327, another FaRLiP strain, as an outgroup.