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

Abstract

To date, molecular systematics of Myxogastria has been based primarily on small subunit riboso mal RNA (SSU rRNA) and elongation factor 1 alpha (EF 1α) genes. To establish a natural classification sys tem for the organisms, we examined phylogenetic relationships among myxogastrian species using cyto chrome c oxidase subunit I (COI) and SSU rRNA genes. Twenty new sequences were obtained, including 10 COI and 10 SSU rRNA sequences, were compared with sequences of related species from GenBank in order to construct phylogenic trees. The analysis of the two data sets supported the modern phylogeny of myxogastria: orders Liceida and Trichiida formed a sister group at the most basal clade, while orders Ste monitida and Physarida formed a close group, and order Echinostelida was a sister group to Stemonitida and Physarida. However, the partial COI sequences were too conserved to resolve of the branches in Stemonitida and Physarida. In addition, we also deemed the specific edited mRNA events of COI sequences in myxogas trian species.

Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing

“…The primers used were S1/SU19R or S3bF/S31R for SSU (Fiore-Donno et al, 2008Schnittler et al, 2017), PB1F/PB1R for EF1A (Novozhilov et al, 2014), COIF1/COIR1 or COMF/COMRs for COI (Feng & Schnittler, 2015;Liu et al, 2015;Novozhilov et al, 2019). Amplification protocols were as follows: denaturation for 5 min at 95°C, 39 cycles (30 s at 95°C, 30 s at 56°C, 1 min at 72°C) and 5 min at 72°C with S1/SU19R; denaturation for 5 min at 95°C, 34 cycles (30 s at 95°C, 30 s at 57.6°C, 48 s at 72°C) and 5 min at 72°C with S3bF/S31R; denaturation for 5 min at 95°C, 35 cycles (30 s at 95°C, 30 s at 65.4°C, 1 min at 72°C) and 10 min at 72°C with PB1F/PB1R; denaturation for 5 min at 95°C, 34 cycles (30 s at 95°C, 50 s at 50.7°C or 52.0°C, 1 min at 72°C) and 10 min at 72°C with COIF1/COIR1 or COMF/COMRs.…”