Computational protocol: Ardissonea crystallina has a type of sexual reproduction that is unusual for centric diatoms

Similar protocols

Protocol publication

[…] For the three gene based (SSU, rbcL, psbC) phylogenetic tree (Fig. ), a set of sequences from various species of diatoms (Supplementary Table , Supplementary Material) was downloaded from GenBank database (https://www.ncbi.nlm.nih.gov/genbank/). They were aligned with the corresponding sequences obtained from A. crystallina (SSU, rbcL, psbC, respectively deposited as MF555728, MF578744, MF578745) using Mega 6 software. After trimming, the same software was used for Maximum Likelihood phylogeny, which was conducted with 1000 bootstrap replications, a cut-off value of 50% and the tree was rooted with sequences from Bolidomonas pacifica.For the multigene phylogeny, the pre-existing alignment was downloaded from the deposit website http://datadryad.org/resource/doi:10.5061/dryad.610md/1. Concatenated sequences of the corresponding genes from A. crystallina were added (SSU, atpB, psaB, psaA, psbA, psbC, rbcL, respectively deposited as MF555728, MF578740, MF578741, MF578742, MF578743, MF578744, MF578745). Alignments were done using Clustal Omega and Maximum Likelihood phylogeny was conducted with RAxML 8 with 100 bootstrap replications. The resulting tree was rooted with B. pacifica, and a cut-off value of 50% was applied […]

Pipeline specifications

Software tools MEGA, Clustal Omega, RAxML
Application Phylogenetics