Two-Gene Phylogeny of Bright-Spored Myxomycetes (Slime Moulds, Superorder Lucisporidia)

Abstract

Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ∼10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.

Perichaena longipes, a new myxomycete from the Neotropics

“…The third branch consists of T. decipiens and H. calyculata, both of which are defined by stalked cellulate sporocarps and a capillitium with spiral bands. This branching pattern within the Trichiaceae corresponds fully to the phylogeny based on full-length sequences of both 18S and EF1αin the bright-spored myxomycetes (Fiore-Donno et al 2013). This branching pattern indicates that among the main genera of the Trichiaceae only Arcyria seems to be monophyletic, with all other genera distributed among different branches and thus presumably characterized as para-or polyphyletic.…”

“…To this end we sequenced a 5′ region of the 18S gene, recently demonstrated as a useful barcode marker for myxomycetes (Fiore-Donno et al 2012, 2013. This same locus also was sequenced in two other morphologically distinct species, Perichaena pedata (a stipitate form) and P. chrysosperma (Curr.)…”

Occurrence and distribution of Perichaena (Trichiaceae, Myxomycetes) in the Brazilian Northeastern Region

“…For some authors, such as Eliasson (1977;, Keller & Eliasson (1992) and Novozhilov et al (2008), species with capillitium scanty or absent indicate a possible affinity between Perichaena and Licea; however, this relationship was not supported in recent molecular phylogenetic analyses that showed the genus Perichaena to be monophyletic (Fiore-Donno et al 2013). Hypothallus conspicuous.…”

Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes

“…The existence of two more advanced groups has also been proposed, one characterized by bright color spores and consisting of Trichiida and Liceida, and the other characterized by dark spores and com prising Physarida and Stemonitida [8,9]. More recent analyses based on the SSU rRNA gene [4,10,11] have defined the primary phylogenetic bifurcation within Class Myxogastria as a split between the dark spored superorder Columellidia (orders Trichiida and Liceida) and the bright spored superorder Lucispo ridia (orders Physarida and Stemonitida). In addition, Echinostelida was the basal group of the superorder Lucisporidia.…”

“…In addition, Echinostelida was the basal group of the superorder Lucisporidia. However, the sequences of 1α genes were too conserved to provide enough informative sites for resolution of the branches in superorder Col umellidia [4,11]. Hence, SSU rRNA can be used to analyze the higher order phylogeny of myxogastria, while other genes should be used to clarify the rela tionships of the Class Myxogastria.…”