#ISEPpapers 26: October 2024 to March 2025

Your twenty-sixth 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!

A unique symbiosome in an anaerobic single-celled eukaryote. Jon Jerlström-Hultqvist, Lucie Gallot-Lavallée, Dayana E. Salas-Leiva, Bruce A. Curtis, Kristína Záhonová, Ivan Čepička, Courtney W. Stairs, Shweta Pipaliya, Joel B. Dacks, John M. Archibald, & Andrew J. Roger. Read.

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. Harriet Alexander, Sarah K. Hu, Arianna I. Krinos, Maria Pachiadaki, Benjamin J. Tully, Christopher J. Neely, Taylor Reiter. Read.

Refurbishing the marine parasitoid order Pirsoniales with newly (re)described marine and freshwater free-living predators. Kristina I. Prokina, Naoji Yubuki, Denis V. Tikhonenkov, Maria Christina Ciobanu, Purificación López-García, David Moreira. Read.

Viral infection to the raphidophycean alga Heterosigma akashiwo affects both intracellular organic matter composition and dynamics of a coastal prokaryotic community. Hiroaki Takebe, Haruna Hiromoto, Tetsuhiro Watanabe, Keigo Yamamoto, Keizo Nagasaki, Ryoma Kamikawa, Takashi Yoshida. Read.

Hidden syndinian and perkinsid infections in dinoflagellate hosts revealed by single-cell transcriptomics. Elizabeth C. Cooney, Brian S. Leander, Patrick J. Keeling. Read.

Adaptations and metabolic evolution of myzozoan protists across diverse lifestyles and environments. Ross F. Waller & Vern B. Carruthers. Read.

Evolutionary origins of the lysosome-related organelle sorting machinery reveal ancient homology in post-endosome trafficking pathways. Kiran J. More, Jonathan G. G. Kaufman, Joel B. Dacks, and Paul T. Manna. Read.

Expanded gene and taxon sampling of diplomonads shows multiple switches to parasitic and free-living lifestyle. Monika M. Wiśniewska, Eric D. Salomaki, Jeffrey D. Silberman, Kristina X. Terpis, Eva Mazancová, Petr Táborský, Vasana Jinatham, Eleni Gentekaki, Ivan Čepička & Martin Kolisko. Read.

It's time to consider the Arcellinida shell as a weapon. Kenneth Dumack, Enrique Lara, Clément Duckert, Elizaveta Ermolaeva, Ferry Siemensma, David Singer, Valentyna Krashevska, Mariusz Lamentowicz, Edward A.D. Mitchell. Read.

The nature of ‘jaws’: a new predatory representative of Provora and the ultrastructure of nibbling protists. Artem O. Belyaev, Sergey A. Karpov, Patrick J. Keeling, and Denis V. Tikhonenkov. Read.

Reduced plastid genomes of colorless facultative pathogens Prototheca (Chlorophyta) are retained for membrane transport genes. Kacper Maciszewski, Gabriela Wilga, Tomasz Jagielski, Zofia Bakuła, Jan Gawor, Robert Gromadka, & Anna Karnkowska. Read.

Long-read DNA sequencing reveals the organization of the mitochondrial genome in the early-branching dinoflagellate Oxyrrhis marina. Ronie Haro, Nikita Walunjkar, Soham Jorapur, Claudio H. Slamovits. Read.

How marine are Marine Stramenopiles (MAST)? A cross-system evaluation. Aleix Obiol, Javier del Campo, Colomban de Vargas, Frédéric Mahé, Ramon Massana. Read.

An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group. Tomáš Pánek, Alexander K. Tice, Pia Corre, et al. Read.

Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics. Kristína Záhonová, Harpreet Kaur, Chantel C. Furgason, Angela V. Smirnova, Peter F. Dunfield, Joel B. Dacks. Read.

Hijacking and integration of algal plastids and mitochondria in a polar planktonic host. Ananya Kedige Rao, Daniel Yee, Fabien Chevalier, et al. Read.

Diplonemid protists possess exotic endomembrane machinery, impacting models of membrane trafficking in modern and ancient eukaryotes. Kristína Záhonová, Julius Lukeš, Joel B. Dacks. Read.

Phylogenomic resolution of marine to freshwater dinoflagellate transitions. Mahara Mtawali, Elizabeth C Cooney, Jayd Adams, Joshua Jin, Corey C Holt, Patrick J Keeling. Read.

Characterization of Allobodo yubaba sp. nov. and Novijibodo darinka gen. et sp. nov., cultivable free‐living species of the phylogenetically enigmatic kinetoplastid taxon Allobodonidae. Julia A Packer, Daryna Zavadska, Elizabeth J. Weston, Yana Eglit, Daniel J. Richter, Alastair G. B. Simpson. Read.

Where Is Cryptosporidium Population Genomics Going Next: The Challenge and the Promise. Randi Turner, Rodrigo de Paula Baptista, Benjamin M. Rosenthal, Jessica C. Kissinger, & Asis Khan. Read.

Drastic genome reduction driven by parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate. Takuro Nakayama, Ryo Harada, Akinori Yabuki, Mami Nomura, Kogiku Shiba, Kazuo Inaba, Yuji Inagaki. Read.

On the possibility of yet a third kinetochore system in the protist phylum Euglenozoa. Corinna Benz, Maximilian W. D. Raas, Pragya Tripathi, Drahomíra Faktorová, Eelco C. Tromer, Bungo Akiyoshi, Julius Lukeš. Read.

Reconstructing the last common ancestor of all eukaryotes. Thomas A. Richards, Laura Eme, John M. Archibald, et al. Read.

Methanogenic symbionts of anaerobic ciliates are host and habitat specific. Daniel Méndez-Sánchez, Anna Schrecengost, Johana Rotterová, Kateřina Koštířová, Roxanne A Beinart, Ivan Čepička. Read.

Far-red light acclimation in Phaeophila dendroides (Ulvales, Ulvophyceae) isolated from a coral skeleton. Chieko Onami, Yohei Nishibori, Shoichiro Suda, Ryoma Kamikawa, Hideaki Miyashita. Read.

Morphology, behavior, and phylogenomics of Oxytoxum lohmannii, Dinoflagellata. Elizabeth C. Cooney, Dean M. Jacobson, Gordon V. Wolfe, Kelley J. Bright, Juan F. Saldarriaga, Patrick J. Keeling, Brian S. Leander, Suzanne L. Strom. Read.

Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life. Guifré Torruella, Luis Javier Galindo, David Moreira, Purificación López-García. Read.

Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data. Dandan Zhao, Dayana E. Salas-Leiva, Shelby K. Williams, Katherine A. Dunn, Jason D. Shao, Andrew J. Roger. Read.

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. Thomas K. F. Wong, Nhan Ly-Trong, Huaiyan Ren, et al. Read.

Complete mitochondrial genomes of ancyromonads provide clues for the gene content and genome structures of ancestral mitochondria. Ryo Harada, Takashi Shiratori, Akinori Yabuki, Yuji Inagaki, Andrew J. Roger, Ryoma Kamikawa. Read.

The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics. Romana Vargová, Roxanne Chevreau, Marine Alves, Camille Courbin, Kara Terry, Pierre Legrand, Marek Eliáš, Julie Ménétrey, Joel B. Dacks, & Catherine L. Jackson. Read.

The retromer and retriever systems are conserved and differentially expanded in parabasalids. Abhishek Prakash Shinde, Jitka Kučerová, Joel Bryan Dacks, Jan Tachezy. Read.

Positive selection of a starch synthesis gene and phenotypic differentiation of starch accumulation in symbiotic and free-living coral symbiont dinoflagellate species. Yuu Ishii, Shunsuke Kanamori, Ryusaku Deguchi, Masakado Kawata, Shinichiro Maruyama, Takashi Yoshida, Ryoma Kamikawa. Read.

A new type of photoacclimation to far-red light found in a newly isolated Neochloris sp. (Chlorophyceae, Chlorophyta) from Lake Biwa, Japan. Fei Wang, Yohei Nishibori, Sho Kitazaki, Ryoma Kamikawa, Hideaki Miyashita. Read.

Viral infection to the raphidophycean alga Heterosigma akashiwo affects both intracellular organic matter composition and dynamics of a coastal prokaryotic communit. Hiroaki Takebe, Haruna Hiromoto, Tetsuhiro Watanabe, Keigo Yamamoto, Keizo Nagasaki, Ryoma Kamikawa, Takashi Yoshida. Read.

A new member of the dynamin superfamily modulates mitochondrial membrane branching in Trypanosoma brucei. Chloé Alexandra Morel, Corinne Asencio, David Moreira, Corinne Blancard, Bénédicte Salin, Etienne Gontier, Stéphane Duvezin-Caubet, Manuel Rojo, Frédéric Bringaud, Emmanuel Tetaud. Read.

Molecular phylogeny of the SELMA translocation machinery recounts the evolution of complex photosynthetic eukaryotes. Rafael Isaac Ponce-Toledo, David Moreira, Purificación López-Garcia, Philippe Deschamps. Read.

Functional SUF system facilitated mitochondrial loss. Maggie Lawton & Ryan M. R. Gawryluk. Read.

Novel Foraging Mechanisms in Atypical Excavate Flagellates. Sei Suzuki‐Tellier, Alastair GB Simpson, Thomas Kiørboe. Read.

Cultivation of Ancyromonas melba, and Reclassification as the Type Species of Divimonas gen. nov., a Phylogenetically Important Ancyromonad Lineage. Kate M. Barkhouse, Yana Eglit, Elizabeth J. Weston, Adriana B. A. Jenkins, Alastair G. B. Simpson. Read.

The enigmatic genus Malacophrys Kahl, 1926 (Ciliophora: Intramacronucleata) belongs to the class Oligohymenophorea. William Bourland, Ivan Čepička. Read.

Phylogenomics of coral-infecting corallicolids reveal multiple independent losses of chlorophyll biosynthesis in apicomplexan parasites. Victoria KL Jacko-Reynolds, Waldan K Kwong, Samuel J Livingston, Morelia Trznadel, Anthony M Bonacolta, Gordon Lax, Jade Shivak, Nicholas AT Irwin, Mark JA Vermeij, Javier Del Campo, Patrick J Keeling. Read.

Untangling the mix of plastid endosymbiosis events. Patrick J. Keeling, Fabien Burki. Read.

Phylogenetic position and mitochondrial genome evolution of ‘orphan’ eukaryotic lineages. Vasily Zlatogursky, Vittorio Boscaro, Gordon Lax, Matias Wanntorp, Nina Pohl, Fabien Burki, Patrick J. Keeling. Read.

Single-cell phylogenomics identifies major groups of marine eugregarine parasites (Apicomplexa). Eunji Park, Ina Na, Alana Closs, Kyle Hall, Tyrel Froese, Danja Currie-Olsen, Ondine Pontier, Niels Van Steenkiste, Patrick J. Keeling, Brian S. Leander. Read.

The morphology and small subunit rDNA gene phylogeny of the novel goniomonad genus Ebisugoniomonas and two novel Poseidogoniomonas species. Daryna Zavadska, Maria Sachs, Hartmut Arndt, Daniel J. Richter. Read.

Metacollinia emscheri n. sp., a novel sanguicolous apostome ciliate of freshwater amphipods (Gammarus spp.) Sebastian Prati, Sonja Rückert, Daniel S Grabner, Bernd Sures, Jamie Bojko. Read.

The expanded genome of Hexamita inflata, a free-living diplomonad. Zeynep Akdeniz, Michal Havelka, Michal Stoklasa, Alejandro Jiménez-González, Vojtěch Žárský, Feifei Xu, Courtney W Stairs, Jon Jerlström-Hultqvist, Martin Kolísko, Jan Provazník, Staffan Svärd, Jan O Andersson, Jan Tachezy. Read.

Anaerobic protist survival in microcosms is dependent on microbiome metabolic function. Karla Iveth Aguilera-Campos, Julie Boisard, Viktor Törnblom, Jon Jerlström-Hultqvist, Ada Behncké-Serra, Elena A Cotillas, Courtney Stairs. Read.

Ultrastructure of Olkasia polycarbonata (Euglenozoa, Euglenida) demonstrates cytoskeletal innovations associated with the feeding and flagellar apparatuses. Maia V. Palka, Regine Claire Manglicmot, Gordon Lax, Kevin C. Wakeman, Brian S. Leander. Read.

A pilot study of intestinal protist detection in humans, animals, and the environment in a slum area in Mymensingh, Bangladesh. Sadiya Maxamhud, Md Shahiduzzaman, ARM Beni Amin, Md Zawad Hossain, Eleni Gentekaki, Anastasios D Tsaousis. Read.