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  1. Article ; Online: Symbiotic revolutions at the interface of genomics and microbiology.

    Archibald, John M

    PLoS biology

    2024  Volume 22, Issue 4, Page(s) e3002581

    Abstract: Symbiosis is an old idea with a contentious history. New genomic technologies and research paradigms are fueling a shift in some of its central tenets; we need to be humble and open-minded about what the data are telling us. ...

    Abstract Symbiosis is an old idea with a contentious history. New genomic technologies and research paradigms are fueling a shift in some of its central tenets; we need to be humble and open-minded about what the data are telling us.
    MeSH term(s) Symbiosis/genetics ; Genomics
    Language English
    Publishing date 2024-04-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3002581
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  2. Article ; Online: Cryptomonads.

    Archibald, John M

    Current biology : CB

    2020  Volume 30, Issue 19, Page(s) R1114–R1116

    Abstract: John Archibald introduces cryptomonads, an important group of protists. ...

    Abstract John Archibald introduces cryptomonads, an important group of protists.
    MeSH term(s) Cryptophyta/physiology ; Evolution, Molecular ; Genetic Markers
    Chemical Substances Genetic Markers
    Language English
    Publishing date 2020-10-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2020.08.101
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  3. Article ; Online: Genomics reveals alga-associated cyanobacteria hiding in plain sight.

    Archibald, John M

    Proceedings of the National Academy of Sciences of the United States of America

    2019  Volume 116, Issue 32, Page(s) 15757–15759

    MeSH term(s) Cyanobacteria ; Dinoflagellida ; Genomics
    Language English
    Publishing date 2019-07-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1909788116
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  4. Article ; Online: Treasurer's Report for Financial Year (FY) 2019.

    Thorne, Jeffrey L / Archibald, John M

    Molecular biology and evolution

    2021  Volume 38, Issue 7, Page(s) 3028

    Language English
    Publishing date 2021-05-19
    Publishing country United States
    Document type Editorial
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msab012
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  5. Article ; Online: The past, present and future of the tree of life.

    Blais, Cédric / Archibald, John M

    Current biology : CB

    2021  Volume 31, Issue 7, Page(s) R314–R321

    Abstract: The advent of comparative genomics in the late 1990s led to the discovery of extensive lateral gene transfer in prokaryotes. The resulting debate over whether life as a whole is best represented as a tree or a network has since given way to a general ... ...

    Abstract The advent of comparative genomics in the late 1990s led to the discovery of extensive lateral gene transfer in prokaryotes. The resulting debate over whether life as a whole is best represented as a tree or a network has since given way to a general consensus in which trees and networks co-exist rather than stand in opposition. Embracing this consensus allows us to move beyond the question of which is true or false. The future of the tree of life debate lies in asking what trees and networks can, and should, do for science.
    MeSH term(s) Animals ; Gene Transfer, Horizontal/genetics ; Genomics/trends ; Phylogeny ; Prokaryotic Cells/metabolism
    Language English
    Publishing date 2021-04-13
    Publishing country England
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2021.02.052
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  6. Article ; Online: HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes.

    Zhang, Xi / Hu, Yining / Cheng, Zhenyu / Archibald, John M

    STAR protocols

    2023  Volume 4, Issue 1, Page(s) 102014

    Abstract: Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate ... ...

    Abstract Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene sets, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021)
    MeSH term(s) Eukaryota/genetics ; Genes, Duplicate/genetics ; Genome/genetics ; Eukaryotic Cells ; Genomics/methods
    Language English
    Publishing date 2023-01-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.102014
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  7. Article ; Online: Evolution: Protein Import in a Nascent Photosynthetic Organelle.

    Archibald, John M

    Current biology : CB

    2017  Volume 27, Issue 18, Page(s) R1004–R1006

    Abstract: An amoeba named Paulinella harbours 'chromatophores', cyanobacterium-derived photosynthetic bodies that evolved independent of plastids. Proteomics has shown that hundreds of nucleus-encoded proteins are targeted to the chromatophore, revealing the host ... ...

    Abstract An amoeba named Paulinella harbours 'chromatophores', cyanobacterium-derived photosynthetic bodies that evolved independent of plastids. Proteomics has shown that hundreds of nucleus-encoded proteins are targeted to the chromatophore, revealing the host cell's contributions to its recently established organelle.
    MeSH term(s) Amoeba ; Biological Evolution ; Cercozoa ; Photosynthesis ; Plastids ; Symbiosis
    Language English
    Publishing date 2017-09-23
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2017.08.013
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  8. Article ; Online: Genomic Insights into Plastid Evolution.

    Sibbald, Shannon J / Archibald, John M

    Genome biology and evolution

    2020  Volume 12, Issue 7, Page(s) 978–990

    Abstract: The origin of plastids (chloroplasts) by endosymbiosis stands as one of the most important events in the history of eukaryotic life. The genetic, biochemical, and cell biological integration of a cyanobacterial endosymbiont into a heterotrophic host ... ...

    Abstract The origin of plastids (chloroplasts) by endosymbiosis stands as one of the most important events in the history of eukaryotic life. The genetic, biochemical, and cell biological integration of a cyanobacterial endosymbiont into a heterotrophic host eukaryote approximately a billion years ago paved the way for the evolution of diverse algal groups in a wide range of aquatic and, eventually, terrestrial environments. Plastids have on multiple occasions also moved horizontally from eukaryote to eukaryote by secondary and tertiary endosymbiotic events. The overall picture of extant photosynthetic diversity can best be described as "patchy": Plastid-bearing lineages are spread far and wide across the eukaryotic tree of life, nested within heterotrophic groups. The algae do not constitute a monophyletic entity, and understanding how, and how often, plastids have moved from branch to branch on the eukaryotic tree remains one of the most fundamental unsolved problems in the field of cell evolution. In this review, we provide an overview of recent advances in our understanding of the origin and spread of plastids from the perspective of comparative genomics. Recent years have seen significant improvements in genomic sampling from photosynthetic and nonphotosynthetic lineages, both of which have added important pieces to the puzzle of plastid evolution. Comparative genomics has also allowed us to better understand how endosymbionts become organelles.
    Language English
    Publishing date 2020-05-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1759-6653
    ISSN (online) 1759-6653
    DOI 10.1093/gbe/evaa096
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  9. Article ; Online: Evolution: New Protist Predators under the Sun.

    Colp, Morgan J / Archibald, John M

    Current biology : CB

    2019  Volume 29, Issue 19, Page(s) R936–R938

    Abstract: A lineage of predatory, non-photosynthetic protists related to red algae has been discovered, changing the way we think about the biology of the first photosynthetic eukaryotes. ...

    Abstract A lineage of predatory, non-photosynthetic protists related to red algae has been discovered, changing the way we think about the biology of the first photosynthetic eukaryotes.
    MeSH term(s) Eukaryota ; Rhodophyta
    Language English
    Publishing date 2019-10-08
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2019.08.029
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  10. Article ; Online: Evolution: Gene transfer in complex cells.

    Archibald, John M

    Nature

    2015  Volume 524, Issue 7566, Page(s) 423–424

    MeSH term(s) Eukaryota/genetics ; Evolution, Molecular ; Models, Genetic ; Organelles/genetics ; Symbiosis/genetics
    Language English
    Publishing date 2015-08-27
    Publishing country England
    Document type Comment ; Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature15205
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