Abstract
Considerable discordance between morphologies and molecules, which can be caused by convergent morphologies, cryptic species or plastic phenotypes, has been frequently detected, especially in microbes. One of the best examples could be the well-known halteriid ciliates, whose systematic position remains highly unresolved, because it resembles oligotrichs in terms of morphology while associates with hypotrichs in phylogeny based on maker genes. In the present work, we report the deep sequencing and analyses of RNA-seq data from the representative halteriid, Halteria grandinella. The results indicate that: 1) the transcriptome includes 92,114 genes (aa >= 50) with the N50 of 957 bp, which is much better than the single-cell transcriptome; 2) H. grandinella shares more homologous genes in higher sequence identity with hypotrichous oxytrichids than with oligotrichs; 3) the codon usage bias of H. grandinella is much more similar with that of oligotrich Strombidium sulcatum, and UAA and UAG are reassigned to encode glutamine, which is a common feature of oligotrichs and hypotrichs; and 4) phylogenomic analyses based on 132 orthologs and 47,263 amino acid sites place H. grandinella as a sister to hypotrichs while other oligotrichs cluster together. Based on all the information so far available, we thus suggest that H. grandinella could be an extremely specialized "oligotrich-like" hypotrich. The similar morphology between halteriids and oligotrichs results from convergent evolution to adapt to the planktonic lifestyle. We hypothesize the evolutionary relationship of the core spirotrichs that halteriids and oxytrichids share the most common ancestor, followed successively by other hypotrichs, oligotrichs/choreotrichs, and euplotids.