#ISEPpapers 28: January to June 2026

Your twenty-eighth digest of papers and preprints published by members of the International Society for Evolutionary Protistology is here. Do you like your #ISEPpapers as fresh as possible? Follow us on Mastodon or Bluesky. Enjoy!

The mitochondrial proteome of diplonemids: from conventional pathways to eccentric RNA editing and transcript processing. Michael W. Gray, Matus Valach, Matt Sarrasin, et al. Read.

Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid Proterozoic. Miguel M. Sandin, Phoebe Cohen, Hélène Morlon, Fabien Burki. Read.

Legacies of consecutive summer droughts on soil-borne plant parasitic protists (Oomycota: Stramenopila and Phytomyxea: Rhizaria) and protistan consumers (Cercozoa: Rhizaria) along an experimental plant diversity gradient. Marcel Dominik Solbach, Cynthia Albracht, Kenneth Dumack, Nico Eisenhauer, Anna Maria Fiore-Donno, Nils Heck, Anja Vogel, Cameron Wagg, Michael Bonkowski. Read.

A genetic transformation system for the heterotrophic diatom Nitzschia putrida (Bacillariophyceae). Longji Deng, Yixuan Li, Yasuhiro Tanizawa, Yasukazu Nakamura, Ryoma Kamikawa, Amanda Hopes, Thomas Mock. Read.

Single-cell phylogenomics identifies major groups of marine eugregarine endosymbionts (Apicomplexa). Eunji Park, Alana Closs, Kyle Hall, Tyrel Froese, Danja Currie-Olsen, et al. Read.

The photophobic response in the apusomonad Podomonas kaiyoae is mediated by coordination of cilia and actin filaments. Aika Shibata, Chiaki Yamamoto, Yuma Tani, Ryuji Yanase, Kogiku Shiba, et al. Read.

Single‐Cell Transcriptomes and Phylogenomic Analysis of Uncultivated Oxymonads. Morelia Trznadel, Gordon Lax, Vittorio Boscaro, Rudolf H. Scheffrahn, Christine A. Nalepa, Martin Kolisko, Patrick J. Keeling. Read.

Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta. Lukáš V. F. Novák, Sergio A. Muñoz-Gómez, Maria Ciobanu, Fabian van Beveren, Laura Eme, Purificación López-García, David Moreira. Read.

Re-evaluating the eukaryotic Tree of Life with independent phylogenomic data. Romain B. Leroy, Laura Eme, Purificación López-García, David Moreira. Read.

The genome sequence of the gastric gland parasite, Cryptosporidium proliferans. Monika M. Wiśniewska, Lenka Tůmová, Jeffrey D. Silberman, Eric D. Salomaki, Joseph Bielawski, Petr Táborský, Lenka Hlásková, Bohumil Sak, Martin Kváč, Martin Kolísko. Read.

Living together: evolutionary and ecological dimensions of protist endosymbiosis. Anna Karnkowska, Iván García-Cunchillos, Marta Sałek. Read.

Morphology, Ultrastructure, and Classification of Barthelonids (Metamonada Incertae Sedis): With Descriptions of Microbarthelona Gen. Nov., and Parabarthelona Gen. Nov. Takashi Shiratori, Yana Eglit, Euki Yazaki, Yuji Inagaki, Alastair G. B. Simpson. Read.

Dynamic stressor regimes drive shifts in biofilm-associated parasites. Annemie Doliwa, Ntambwe Albert Serge Mayombo, Iris Madge Pimentel, Philipp M. Rehsen, Anna-Maria Vermiert, Willem Kaijser, Lisa Voskuhl, Matthijs Vos, Bernd Sures, & Micah Dunthorn. Read.

Complete mitochondrial genomes of the Prototheca genus: comparative genomics and evolutionary insights. Daniel Wibberg, Zofia Bakuła, Iván García-Cunchillos, Jan Gawor, Robert Gromadka, Anna Karnkowska, Jacek Bielecki, & Tomasz Jagielski. Read.

Phylogenomics reveals multiple evolutionary lineages of marine crustacean-infecting gregarine apicomplexans. Ina Na, Victoria K. L. Jacko-Reynolds, Corey C. Holt, & Patrick J. Keeling. Read.

Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes. Zander Rainier Human, Martina Štursová, Iñaki Odriozola, Tomáš Větrovský, Adina Howe, Diana Navrátilová, Rubén López-Mondéjar, Lucia Žifčáková, Vendula Brabcová, et al. Read.

Capturing the extensive diversity of marine anaerobic scuticociliates (Oligohymenophorea, Ciliophora) through cultivation. Kateřina Koštířová, Johana Rotterová, William A. Bourland, & Ivan Čepička. Read.

A Revised Understanding of Petalomonad Diversity (Petalomonadida; Euglenida) Enabled by a Cultivation Approach, With Five New Species and Two New Genera. Won Je Lee, Gordon Lax, Elizabeth J. Weston, Julia A. Packer, Alexandra Hall, Sun Young Kim, Dong Hyuk Jeong, Alastair G. B. Simpson. Read.

Genome Sequence Data Reveal Complex and Variable Ploidy in the Amoebozoan Acanthamoeba castellanii. Morgan J. Colp, John M. Archibald. Read.

Colponemidia questions the ancestry of an ATG10-lacking ATG8–ATG12 conjugation system in Alveolata. Euki Yazaki, Ryu Isogai, Yuji Inagaki. Read.

Derlin-like proteins are essential for the function of Euglena gracilis chloroplasts. Anežka Konupková, Zoltán Füssy, Priscila Peña-Diaz, Masami Nakazawa, Vladimír Hampl. Read.

CSI-SSU: phylogenetic contamination screening of genomic datasets, demonstrated on The Protist 10,000 Genomes (P10K) Project. Alfredo L. Porfirio-Sousa, Robert E. Jones, Matthew W. Brown, Daniel J. G. Lahr & Alexander K. Tice. Read.

A billion-year-old bacterial machinery replicates plastid DNA and supports kleptoplastidy. Thibault Antoine, Fabien Burki, John M. Archibald, Eric Pelletier, Tom O. Delmont. Read.

Reversal to osmotrophy in eukaryotes. Purificación López-García & David Moreira. Read.

Diversity and evolution of DNA polymerase θ in eukaryotes and the origin of mitochondrion-localized DNA polymerase PolIA in euglenozoa. Ryu Isogai, Mingzhe Wei, Ryo Harada, Euki Yazaki, Takuro Nakayama, Ryan M. R. Gawryluk, Yuji Inagaki. Read.

The evolutionary transition from alga to parasite in the sister lineage of apicomplexans. Elizabeth C. Cooney, Alyssa-Lois Madden Gehman, Patrick J. Keeling. Read.

The spatial proteome of the Plasmodium falciparum schizont illuminates the composition and evolutionary trajectories of its organelles. Chisholm, S. A., Flores, V., Kemp, A., Breckels, L. M., Koreny, L., Dos Santos Pacheco, N., Barylyuk, K., Kuroshchenkova, A., Lilley, K. S., Rayner, J. C., & Waller, R. F. Read.