Gene transfer to the nucleus and the evolution of chloroplasts

William Martin (), Bettina Stoebe, Vadim Goremykin, Sabine Hansmann, Masami Hasegawa and Klaus V. Kowallik
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William Martin: Institut für Genetik, Technische Universität Braunschweig
Bettina Stoebe: Botanisches Institut, Heinrich-Heine-Universität Düsseldorf
Vadim Goremykin: Institut für Genetik, Technische Universität Braunschweig
Sabine Hansmann: Institut für Genetik, Technische Universität Braunschweig
Masami Hasegawa: The Institute of Statistical Mathematics
Klaus V. Kowallik: Botanisches Institut, Heinrich-Heine-Universität Düsseldorf

Nature, 1998, vol. 393, issue 6681, 162-165

Abstract: Abstract Photosynthetic eukaryotes, particularly unicellular forms, possess a fossil record that is either wrought with gaps or difficult to interpret, or both. Attempts to reconstruct their evolution have focused on plastid phylogeny, but were limited by the amount and type of phylogenetic information contained within single genes1,2,3,4,5. Among the 210 different protein-coding genes contained in the completely sequenced chloroplast genomes from a glaucocystophyte, a rhodophyte, a diatom, a euglenophyte and five land plants, we have now identified the set of 45 common to each and to a cyanobacterial outgroup genome. Phylogenetic inference with an alignment of 11,039 amino-acid positions per genome indicates that this information is sufficient — but just barely so — to identify the rooted nine-taxon topology. We mapped the process of gene loss from chloroplast genomes across the inferred tree and found that, surprisingly, independent parallel gene losses in multiple lineages outnumber phylogenetically unique losses by more than 4:1. We identified homologues of 44 different plastid-encoded proteins as functional nuclear genes of chloroplast origin, providing evidence for endosymbiotic gene transfer to the nucleus in plants.

Date: 1998
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DOI: 10.1038/30234

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