The Closest Lineage of Archaeplastida is Revealed by Phylogenomics Analyses That Include

Overview

Journal Open Biol

Specialties Biology
Cell Biology
Molecular Biology

Date 2022 Apr 13

PMID 35414259

Authors

Euki Yazaki

Akinori Yabuki

Ayaka Imaizumi

Keitaro Kume

Tetsuo Hashimoto

Yuji Inagaki

Affiliations

Soon will be listed here.

Abstract

By clarifying the phylogenetic positions of 'orphan' protists (unicellular micro-eukaryotes with no affinity to extant lineages), we may uncover the novel affiliation between two (or more) major lineages in eukaryotes. was an orphan protist, which failed to be placed within the previously described lineages by pioneering phylogenetic analyses. In this study, we analysed a 319-gene alignment and demonstrated that represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name 'Pancryptista' for Cryptista plus . The 319-gene analyses also indicated that is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called 'CAM clade' here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of and Rhodelphidia) and the particular phylogenetic 'signal' most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies.

Citing Articles

Foraging mechanisms in excavate flagellates shed light on the functional ecology of early eukaryotes.

Suzuki-Tellier S, Miano F, Asadzadeh S, Simpson A, Kiorboe T Proc Natl Acad Sci U S A. 2024; 121(22):e2317264121.

PMID: 38781211 PMC: 11145212. DOI: 10.1073/pnas.2317264121.

Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion.

Harada R, Hirakawa Y, Yabuki A, Kim E, Yazaki E, Kamikawa R Mol Biol Evol. 2024; 41(2).

PMID: 38271287 PMC: 10877234. DOI: 10.1093/molbev/msae014.

Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction.

Lang B, Beck N, Prince S, Sarrasin M, Rioux P, Burger G Front Plant Sci. 2023; 14:1222186.

PMID: 37469769 PMC: 10352661. DOI: 10.3389/fpls.2023.1222186.

The complete mitochondrial genome of harbors a unique repeat structure and a specific -spliced gene.

Fang J, Xu X, Chen Q, Lin A, Lin S, Lei W Front Microbiol. 2022; 13:966219.

PMID: 36238593 PMC: 9551565. DOI: 10.3389/fmicb.2022.966219.

The closest lineage of Archaeplastida is revealed by phylogenomics analyses that include .

Yazaki E, Yabuki A, Imaizumi A, Kume K, Hashimoto T, Inagaki Y Open Biol. 2022; 12(4):210376.

PMID: 35414259 PMC: 9006020. DOI: 10.1098/rsob.210376.

References

Shalchian-Tabrizi K, Eikrem W, Klaveness D, Vaulot D, Minge M, Le Gall F . Telonemia, a new protist phylum with affinity to chromist lineages. Proc Biol Sci. 2006; 273(1595):1833-42. PMC: 1634789. DOI: 10.1098/rspb.2006.3515. View

Irisarri I, Strassert J, Burki F . Phylogenomic Insights into the Origin of Primary Plastids. Syst Biol. 2021; 71(1):105-120. DOI: 10.1093/sysbio/syab036. View

Katoh K, Misawa K, Kuma K, Miyata T . MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002; 30(14):3059-66. PMC: 135756. DOI: 10.1093/nar/gkf436. View

Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I . Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644-52. PMC: 3571712. DOI: 10.1038/nbt.1883. View

Heiss A, Kolisko M, Ekelund F, Brown M, Roger A, Simpson A . Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes. R Soc Open Sci. 2018; 5(4):171707. PMC: 5936906. DOI: 10.1098/rsos.171707. View

Hoppenrath M, Leander B . Ebriid phylogeny and the expansion of the Cercozoa. Protist. 2006; 157(3):279-90. DOI: 10.1016/j.protis.2006.03.002. View

Strassert J, Jamy M, Mylnikov A, Tikhonenkov D, Burki F . New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life. Mol Biol Evol. 2019; 36(4):757-765. PMC: 6844682. DOI: 10.1093/molbev/msz012. View

Lartillot N, Philippe H . A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 2004; 21(6):1095-109. DOI: 10.1093/molbev/msh112. View

Yazaki E, Kume K, Shiratori T, Eglit Y, Tanifuji G, Harada R . Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP. Proc Biol Sci. 2020; 287(1934):20201538. PMC: 7542792. DOI: 10.1098/rspb.2020.1538. View

10.

Cavalier-Smith T, Chao E, Lewis R . Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. Mol Phylogenet Evol. 2015; 93:331-62. DOI: 10.1016/j.ympev.2015.07.004. View

11.

Yang J, Harding T, Kamikawa R, Simpson A, Roger A . Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids. Genome Biol Evol. 2017; 9(5):1161-1174. PMC: 5421314. DOI: 10.1093/gbe/evx086. View

12.

Price M, Dehal P, Arkin A . FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010; 5(3):e9490. PMC: 2835736. DOI: 10.1371/journal.pone.0009490. View

13.

Haas B, Papanicolaou A, Yassour M, Grabherr M, Blood P, Bowden J . De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013; 8(8):1494-512. PMC: 3875132. DOI: 10.1038/nprot.2013.084. View

14.

Price M, Dehal P, Arkin A . FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009; 26(7):1641-50. PMC: 2693737. DOI: 10.1093/molbev/msp077. View

15.

Zhao S, Burki F, Brate J, Keeling P, Klaveness D, Shalchian-Tabrizi K . Collodictyon--an ancient lineage in the tree of eukaryotes. Mol Biol Evol. 2012; 29(6):1557-68. PMC: 3351787. DOI: 10.1093/molbev/mss001. View

16.

Shiratori T, Ishida K . A New Heterotrophic Cryptomonad: Hemiarma marina n. g., n. sp. J Eukaryot Microbiol. 2016; 63(6):804-812. DOI: 10.1111/jeu.12327. View

17.

Wang H, Minh B, Susko E, Roger A . Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation. Syst Biol. 2017; 67(2):216-235. DOI: 10.1093/sysbio/syx068. View

18.

Adl S, Bass D, Lane C, Lukes J, Schoch C, Smirnov A . Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J Eukaryot Microbiol. 2018; 66(1):4-119. PMC: 6492006. DOI: 10.1111/jeu.12691. View

19.

Yabuki A, Tame A . Phylogeny and Reclassification of Hemistasia phaeocysticola (Scherffel) Elbrächter & Schnepf, 1996. J Eukaryot Microbiol. 2014; 62(3):426-9. DOI: 10.1111/jeu.12191. View

20.

Yabuki A, Chao E, Ishida K, Cavalier-Smith T . Microheliella maris (Microhelida ord. n.), an ultrastructurally highly distinctive new axopodial protist species and genus, and the unity of phylum Heliozoa. Protist. 2011; 163(3):356-88. DOI: 10.1016/j.protis.2011.10.001. View