PUBLICATIONS

Full list of publications


2023

179. Bougon, J., Kadijk, E.C., Gallot-Lavallée, L., Curtis, B.A., Landers, M., Archibald, J.M. & Khaperskyy, D. A. 2023. Influenza A virus NS1 effector domain is required for PA-X mediated host shutoff. bioRxiv preprint. 10.1101/2023.10.02.560421.

178. Jerlström-Hultqvist, J., Gallot-Lavallée, L., Salas-Leiva, D., Curtis, B. A., Pašuthová,K., Čepička, I., Stairs, C., Pipaliya, S., Dacks, J., Archibald, J. M., & Roger, A. J. 2023. A unique symbiosome in an anaerobic single-celled eukaryote. bioRxiv preprint. doi: 10.1101/2023.03.03.530753.

177. Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ari JB, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. 2023. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. bioRxiv preprint. doi: 10.1101/2023.01.31.526407

176. Gallot-Lavallée, L., Jerlström-Hultqvist, J., Stairs, C. W., Cepicka, I., Roger, A. J., & Archibald, J. M. 2023. Massive intein content in three Anaeramoeba genomes reveals new aspects of intein mobility in eukaryotes. Proc. Natl. Acad. Sci. USA. 120, 49: e2306381120.

175. Collier, J. L., Rest, J. S., Lavington, E., Gallot-Lavallée, L., Kuo, A., Jenkins, J., Pangilinan, J. Daum, C., Grigoriev, I. V., Filloramo, G. F., Curtis, B. A., Vanclova, A., & Archibald, J. M. 2023. The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Curr. Biol. 33, 5199-5207.

174. Rius, M., Rest, J. S., Filloramo, G., Vanclova, A., Archibald, J. M., & Collier, J.L. 2023. Horizontal gene transfer and fusion spread carotenogenesis among diverse heterotrophic protists. Genome. Biol. Evol. 15(3): evad029. doi.org/10.1093/gbe/evad029.

173. Zhang, X., Hu, Y., Cheng, Z. & Archibald, J. M. 2023. HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes. STAR Protocols. 24, 102014.


2022

172. Kim, J. I., Tanifuji, G., Minseok, J., Shin, W., & Archibald, J. M. 2022. Gene loss, pseudogenization and genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics. BMC Biol. 20:227.

171. Hess, S., Williams, S, Busch, A., Irisarri, I., Delwiche, C.F., de Vries, S., Darienko, T., Roger, A.J., Archibald, J. M., Buschmann, H., von Schwartzenberg, K., & de Vries, J. 2022. A phylogenomically informed five-order system for the closest relatives of land plants. Curr. Biol. 32, 1-10.

170. Matthey-Doret, C., Colp., M. J., Escoll Guerrero, P., Thierry, A., Curtis, B. A., Sarrain, M., Gray, M.W., Lang B.F., Archibald, J. M., Buchrieser, C., & Koszul, R. 2022. Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin re-organization. Genome Res. 32, 1698-1710.

169. Kim, J. I., Jo, B. Y., Park, M. G., Yoo, Y. D., Shin, W., & Archibald, J. M. 2022. Evolutionary dynamics and lateral gene transfer in raphidophycean plastid genomes. Frontiers Plant Sci. 13, doi:10.3389/fpls.2022. 896138.

168. Zhang, X., Hu, Y., Eme, L., Maruyama, S., Eveleigh, R. J. M., Curtis, B. A., Sibbald, S. J., Hopkins, J. F., Filloramo, G. V., van Wijk, K., & Archibald, J. M. 2022. Protocol for TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. STAR Protocols. 3, 101175.

167. Lawniczak, M. K. N., Durbin, R., Flicek, P., Lindblad-Toh, K., Wei, X., Archibald, J. M., Baker, W. J., Belov, K., Blaxter, M. L., Marques Bonet, T., Childers, A. K., Coddington, J. A., Crandall, K. A., Crawford, A. J., Davey, R. P., Di Palma, F., Fang, Q., Haerty, W., Hall, N., Hoff, K. J., Howe, K., Jarvis, E. D., Johnson W. E., Johnson, R. N., Kersey, P. J., Liu, X., Lopez, J. V., Myers, E. W., Pettersson, O. V., Phillippy, A. M., Poelchau, M. F., Pruitt, K. D., Rhie, A., Castilla-Rubio, J. C., Sahu, S. K., Salmon, N. A., Soltis, P. S., Swarbreck, D., Thibaud-Nissen, F., Wang, S., Wegrzyn, J. L., Zhang, G., Zhang, H., Lewin, H. A., Richards, S. 2022. Standards recommendations for the Earth BioGenome Project. Proc. Natl. Acad. Sci. USA. 119, 4 online-early e2115636118.

166. Blaxter, M., Archibald, J. M., Childers, A. K., Coddington, J. A., Crandall, K. A., Di Palma, F., Durbin, R., Edwards, S. V., Graves, J. A. M., Hackett, K. J., Hall, N., Jarvis, E. D., Johnson, R. N., Karlsson, E. K., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Lindblad-Toh, K., Lopez, J. V., Moran, N.A., Robinson, G. E., Ryder, O. A., Shapiro, B., Soltis, P. S., Warnow, T., Zhang, G., & Lewin, H. A. 2022. Why sequence all eukaryotes? Proc. Natl. Acad. Sci. USA. 119, 4 online-early e2115636118.

165. Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, M.L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S. M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. T. P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J. H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O'Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. 2022. The Earth BioGenome Project 2020: starting the clock. Proc. Natl. Acad. Sci. USA. 119, 4 online-early e2115636118.

2021
164. Fürst-Jansen, J. M. R., de Vries, S. von Schwartzenberg, K. Archibald, J. M., & de Vries, J. 2021. Submergence of the filamentous Zygnematophyceae Mougeotia induces differential gene expression patterns associated with photosynthesis. Protoplasma. Online-early: doi: 10.1007/s00709-021-01730-1.

163. Wright, V., Archibald, J. M., Beinart, R., Dawson, M.N., Hentschel, U., Keeling, P.J., Lopez, J.V., Martín-Durán, J.M., Petersen, J.M., Sigwart, J.D., Simakov, O., Sutherland, K.R., Sweet, M., Talbot, N., Thompson, A.W., Bender, S., Harrison, P.W., Rajan, J., Cochrane, G., Berriman, M., Lawniczak, M. & Blaxter, M. 2021. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life. Wellcome Open Res. 6:254.

162. Salas-Leiva, D. E., Tromer, E. C., Curtis, B. A., Jerlstrom-Hultqvist, J., Kolisko, M., Yi, Z., Salas-Leiva, J. S., Gallot-Lavallée, L., Kops, J. J. P. L., Archibald, J. M., Simpson, A. G. B., & Roger, A. J. 2021. A free-living protist that apparently lacks canonical eukaryotic DNA replication and segregation systems. Nat. Comm. 12:6003.

161. Rowarth, N. M., Curtis, B. A., Einfeldt, A. L., Archibald, J. M., Lacroix, C. R., & Gunawardena, A. H. L. A. N. 2021. RNA-Seq analysis reveals potential regulators involved in program cell death and remodeling of lace plant leaves (Aponogeton madagascariensis). BMC Plant Biol. 21:375.

160. Filloramo, G. V., Blanche, E., Curtis, B. A., & Archibald, J. M. 2021. Re-examination of two diatom reference genomes using long-read sequencing. BMC Genomics 22:379.

159. Blais, C. & Archibald, J. M. 2021. The past, present and future of the Tree of Life. Curr. Biol. 31, R311-329.

158. Sibbald, S. J., Lawton, M. & Archibald, J. M. 2021. Mitochondrial genome evolution in pelagophyte algae. Genome Biol. Evol. 13(3) Doi: 10.1093/gbe/evab018.


2020
157. Gallot-Lavallee, L. & Archibald, J. M. 2020. Evolution: viral rhodopsins illuminate algal evolution. Curr. Biol. 30, R1469-1471.

156. Archibald, J. M. 2020. Quick Guide: Cryptomonads. Curr. Biol. 30, R1116-R1115.

155. Kim, J. I., Minseok, J., Archibald, J. M & Shin, W. 2020. Comparative plastid genomics of non-photosynthetic chrysophytes: genome reduction and compaction. Frontiers in Plant Science. 11:572703.

154. de Vries, S., de Vries, J., Archibald, J. M., & Slamovits, C. S. 2020. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol. Ecol. 96, 0000.

153. Sibbald, S. J., Eme, L., Archibald, J. M. & Roger, A. J. 2020. Lateral gene transfer mechanisms and pan-genomes in eukaryotes. Trends Parasitol. 36(11): 927-941.

152. de Vries, J., de Vries, S., Curtis, B.A., Zhou, H., Penny, S., Feussner, K., Pinto, D.M., Steinert, M., Cohen, A., von Schwartzenberg, K., & Archibald, J. M. 2020. Heat stress response in the closest algal relatives of land plants reveals conserved stress signalling circuits. Plant J. 103, 1025-1048.

151. Sibbald, S. J. & Archibald, J. M. 2020. Genomic insights into plastid evolution. Genome Biol. Evol. 12 (7), 978-990.

150. Colp, M. & Archibald, J. M. 2020. The language of symbiosis: insights from protist biology. Cellular dialogs in the holobiont. Bosch, T. and Hadfield, M. (eds.). CRC Press.

149. Tanifuji, G., Kamikawa, R., Moore, C. E., Mills, T., Onodera, N. T., Kashiyama, Y., Archibald, J. M., Inagaki, Y, & Hahimoto, T. 2020. Comparative plastid genomics of photosynthetic and non-photosynthetic Cryptomonas species reveals loss of photosynthesis. Genome Biol. Evol.12, 3926-3937.

148. Gallot-Lavallee, L. & Archibald, J. M. 2020. Spotlight: Phagocytosis in a shape-shifting bacterium. Trends Microbiol.28, 429-430.


2019
147. Asman, A., Curtis, B. A. & Archibald, J. M. 2019. Nucleomorph small RNAs in cryptophyte and chlorarachniophyte algae. Genome Biol. Evol. 11, 1117-1134.

146. Grisdale, C. J., Smith, D. R., and Archibald, J. M. 2019. Relative mutation rates in nucleomorph-bearing algae. Genome Biol. Evol. 11, 1045-1053.

145. Sibbald, S. J., Hopkins, J. F., Filloramo, G. V., & Archibald, J. M. 2019. Ubiquitin fusion proteins in complex algae: implications for the spread of eukaryotic photosynthesis. BMC Genomics 20: 38.

144. Kim, J. I., Shin, H., Skaloud, P., Jung, J., Yoon, H.S., Archibald, J. M & Shin, W. 2019. Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation. BMC Evol. Biol. 19: 20.

143. Colp, M. J. & Archibald, J. M. 2019. Evolution: New protist predators under the sun. Curr. Biol. 29, R936-R-938.

142. Archibald, J. M. 2019. Genomics reveals alga-associated cyanobacteria hiding in plain sight. Proc. Natl. Acad. Sci. USA. 116, 15757-15759.


2018
141. Cenci, U., Sibbald, S. J., Curtis, B. A., Eme, L., Moog, D., Henrissat, B., Maréchal, E., Chabi, M., Djemiel, C., Roger, A. J., Kim, E., & Archibald, J. M. 2018. Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids. BMC Biology. 16, 137.

140. Lukeš, J., Jirsová, D., David, V., Wheeler, R. & Archibald, J. M. 2018. Massive mitochondrial DNA content in diplonemid and kinetoplastid protists. IUBMB Life. 70, 1267-1274.

139. Kim, J. I., Yoon, H. S., Gangman, Y., Shin, W., & Archibald, J. M. 2018. Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements. BMC Genomics. 19, 275.

138. de Vries, J., Curtis, B. A., Gould, S. B. & Archibald, J. M. 2018. Embryophyte stress signaling evolved in the algal progenitors of land plants. Proc. Natl. Acad. Sci. USA. 115, E3471-3480.

137. de Vries, S., de Vries, J., von Dahlen, J. K., Gould, S. B. & Archibald, J. M. 2018. On plant defense signaling networks and early land plant evolution. Commun. Integr. Biol. 11: e1486168.

136. de Vries, J. & Archibald, J. M. 2018. Plastid evolution: autonomy versus nuclear control. In: Advances in Botanical Research, Volume 85 (Plastid Genome Evolution). Chaw, S.-M. & Jansen, R. (eds.). Pp. 1-28.

135. Nowak, B. & Archibald, J. M. 2018. Opportunistic but lethal: the mystery of paramoebae. Trends Parasitol. 34, 404-419.

134. de Vries, J. & Archibald, J. M. 2018. Plant evolution: landmarks on the path to terrestrial life. New Phytol. 217, 1428-1434.

133. Archibald, J. M. 2018. Evolution: scaling life’s tree. Nature 560, 26-27.

132. de Vries, J. & Archibald J. M. 2018. Quick guide: plastid genomes. Curr. Biol. 28, R336-R337.

131. Raina, J.-B., Eme, L., Pollock, F.J., Spang, A., Archibald, J.M., & Williams, T.A. 2018. Symbiosis in the microbial world: from ecology to genome evolution. Biol. Open. 7, bio032524. doi:10.1242/bio.032524.

130. Cheng, S., Melkonian, M., Smith, S. A., Brockington, S., Archibald, J. M., Delaux, P.-M., Li, F.-W., Melkonian, B., Mavrodiev, E. V., Sun, W., Fu, Y., Yang, H., Soltis, D. E., Graham, S. W., Soltis, P. S., Liu, Z., Xu, X., and Wong, G. K.-S. 2018. 10KP: a phylodiverse genome sequencing plan. GigaScience. 7, 1-9.


2017
129. Tanifuji, G., Cenci, U., Moog, D., Dean, S., Nakayama, T., David, V., Fiala, I., Curtis, B. A., Sibbald, S.J., Onodera, N.T., Colp, M., Flegontov, P., Johnson-MacKinnon, J., McPhee, M., Inagaki, Y., Hashimoto, T., Kelly, S., Gull, K., Lukeš, J., and Archibald, J. M. 2017. Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. Scientific Rep. 7, 11688. doi:10.1038/s41598-017-11866-x.

128. Eleni Gentekaki, Bruce A. Curtis, Courtney Stairs, Vladimír Klimeš, Marek Eliáš, Dayana Salas, Emily K. Herman, Laura Eme, Maria C. Arias, Bernard Henrissat, Frédérique Hilliou, Mary Klute, Hiroshi Suga, Shehre- Banoo Malik, Arthur W. Pightling, Martin Kolisko, Richard A. Rachubinski, Alexander Schlacht, Darren M. Soanes, Anastasios D. Tsaousis, John M. Archibald, Steven G. Ball, Joel B. Dacks, C. Graham Clark, Mark van der Giezen, Andrew J. Roger. 2017. Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol. 15, e2003769.

127. Kim, J. I., Moore, C. E., Archibald, J. M., Bhattacharya, D., Gangman, Y., Yoon, H. S., & Shin, W. 2017. Evolutionary dynamics of cryptophyte plastid genomes. Genome Biol. Evol. 9, 1859-1872.

126. Kamikawa, R., Moog, D., Zauner, S., Tanifuji, G., Ishida, K.-I., Miyashita, H., Mayama, S, Hashimoto, T, Maier, U.-G., Archibald, J. M., and Inagaki, Y. 2017. A non-photosynthetic diatom reveals early steps of reductive evolution in plastids. Mol. Biol. Evol. 34, 2355-2366.

125. Muñoz-Gómez, S. A., Mejía-Franco, F. G., Durnin, K., Colp, M., Grisdale, C. J., Archibald, J. M., Slamovits, C. H. 2017. The new red algal subphylum Proteorhodophytina comprises the largest and most divergent plastid genomes known. Curr. Biol. 27, 1677-1684.

124. de Vries, J., de Vries, S., Slamovits, C. H., Rose, L. E., and Archibald, J. M. 2017.How embryophytic is the biosynthesis of phenylpropanoids and their derivatives in streptophyte algae? Plant and Cell Physiol. 58, 934-935. doi: 10.1093/pcp/pcx037.

123. de Vries, J., Archibald, J. M., and Gould, S. B. 2017. The carboxy terminus of YCF1 contains a motif conserved throughout >500 million years of streptophyte evolution. Genome Biol. Evol. 9, 473-479. doi: 10.1093/gbe/evx013.

122. Sibbald, S., Cenci, U., Colp, M., Eglit, Y., O’Kelly, C.J., & Archibald, J. M. 2017. Diversity and evolution of Paramoeba sp. and their kinetoplastid endosymbionts. J. Eukaryot. Microbiol. 4: 598-607.

121. Eme, L., Gentekaki, E., Curtis, B., Archibald, J. M., and Roger, A. J. 2017. Lateral gene transfer in adaptation of the anaerobic parasite Blastocystis to the gut. Curr. Biol. 27, 807-820.

120. Simpson, A. G. B., Slamovits, C. H. & Archibald, J. M. 2017. Protist diversity and eukaryote phylogeny. In: Handbook of the Protists (2nd edition of the Handbook of Protoctista by Margulis et al.). Archibald, J.M., Simpson, A.G.B, & Slamovits, C. (eds.). Springer. (Introductory chapter).

119. Hoef-Emden, K. & Archibald, J. M. 2017. Cryptophyta (Cryptomonads). In: Handbook of the Protists (2nd edition of the Handbook of Protoctista by Margulis et al.). Archibald, J.M., Simpson, A.G.B, & Slamovits, C. (eds.). Springer. (Invited book chapter).

118. Grisdale, C., & Archibald, J. M. 2017. Secondary and tertiary endosymbiosis. In: Reference Module in Life Sciences. Elsevier Publishing. ISBN: 978-0-12-809633-8.

117. Archibald J. M. 2017. Evolution: Protein import into a nascent photosynthetic organelle. Curr. Biol. 27, R1004-1006.

116. Sibbald, S. J. & Archibald J. M. 2017. More protist genomes needed. Nature Ecol. Evol. 1, 145. doi:10.1038/s41559-017-0145.

115. de Vries, J. & Archibald J. M. 2017. Endosymbiosis: did plastids evolve from a freshwater cyanobacterium? Curr. Biol. 27, R103-105.