Phylogenetic position of the marine biflagellate Palpitomonas bilix is intriguing, since several ultrastructural characteristics implied its evolutionary connection to Archaeplastida or Hacrobia. The origin and early evolution of these two eukaryotic assemblages have yet to be fully elucidated, and P. bilix may be a key lineage in tracing those groups' early evolution. In the present study, we analyzed a 'phylogenomic' alignment of 157 genes to clarify the position of P. bilix in eukaryotic phylogeny. In the 157-gene phylogeny, P. bilix was found to be basal to a clade of cryptophytes, goniomonads and kathablepharids, collectively known as Cryptista, which is proposed to be a part of the larger taxonomic assemblage Hacrobia. We here discuss the taxonomic assignment of P. bilix, and character evolution in Cryptista.
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We are grateful to Dr. Andrew J. Roger (Dalhousie University, Canada) for his technical helps and suggestions. We also thank Dr. Aaron Heiss (University of Tsukuba, Japan) for critical comments and English-language corrections. A.Y., R. K., and S. A. I. were supported by Research Fellowships from the Japanese Society for the Promotion of Science (JSPS) for Young Scientists (Nos. 201242 and 236484 for A.Y., 210528 for R.K., and 24007 for S.A.I.). M.K. was supported by a Discovery grant (227085-2011) from the Natural Sciences and Engineering Research Council of Canada awarded to Andrew J. Roger. This work was supported by grants from the JSPS awarded to Y.I. (Nos. 21370031, 22657025, and 23117006). Maximum-likelihood phylogenetic analyses conducted in the present work have been carried out under the ‘‘Interdisciplinary Computational Science Program’’ in Center for Computational Sciences, University of Tsukuba.
The roll-shaped ejective organelle, i.e., ejectisome (occasionally called as ‘trichocysts’), is identified in cryptomonads, kathablephar-ids and a few prasinophytes20. Major proteins, which comprise cylindrical coiled ribbons in the ejectisomes of the cryptophyte Pyrenomonas helgolandii, were found to be encoded by tri1, tri2, tri3-1, and tri3-221. We here surveyed tri genes/transcripts in the complete genome of the cryptophyte Guillardia theta, and transcrip-tomic data from the goniomonad Goniomonas sp. and the kathable-pharid R. truncata (PRJNA7379315). The Gu. theta genome was found to possess four tri1, eight tri2/3-1, and four tri3-2 genes (Fig. 2: Note that tri2 and tri3-1 are not distinguishable at the amino acid sequence level). We found four tri2/3-1 and three tri3-2 sequences in the transcriptomic data from Goniomonas sp. Two tri2/3-1 and one of tri3-2 sequences were additionally detected from the transcriptome data of another goniomonad species (Goniomonas avonlea; these data were recently generated as a part of the Marine Microbial Eukaryote Transcriptome Sequencing Project funded by the National Center for Genome Resources and the Gordon and Betty Moor Foundation’s Marine Microbiololgy Initiative: http:// marinemicroeukaryotes.org/). Likewise, the transcriptomic data from R. truncata contained three tri2/3-1 and two tri3-2 sequences. No tri1 sequence was detected in the data from Goniomonas sp., Go. avonlea or R. truncata even by a sensitive amino acid sequence similarity search using probabilistic methods (HMMER22; data not shown).