© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Adapt to plants
Nat. Genet. 50, 138–150 (2018)
Plant–bacteria interactions are important
for agricultural production and plant
conservation due to their profound
effects on plant growth and productivity.
Plant-associated genes that evolved in
bacteria over hundreds of millions of
years of adaptation are important for such
interactions. However, these genes remain
poorly understood. Using a comparative
genomics approach, Asaf Levy, from the
US Department of Energy Joint Genome
Institute, Isai Salas Gonzalez, from the
University of North Carolina at Chapel
Hill, and their colleagues identified plant-
associated (and root-associated) genes and
tried to characterize their functions.
The researchers sequenced 484 genomes
of bacterial isolates from the roots of
Brassicaceae, poplar and maize; these
sequences were then combined with existing
publicly available bacterial genomes,
resulting in a data set of 3,837 genomes.
Of these, 1,160 genomes are plant-
associated. Compared with non-plant-
associated bacteria, plant-associated
bacteria displayed a genomic expansion of
carbohydrate metabolism and transport
genes, and shrinkage of mobile elements.
Thousands of putative plant-associated
gene clusters were identified by comparing
phylogenetically related genomes
isolated from different environments
and then validated by computational and
experimental approaches. For example,
two genes were experimentally shown to
control bacterial colonization. Some plant-
associated gene clusters captured known
plant-associated operons, such as those
related to root nodulation and gibberellin
biosynthesis, whereas others captured
novel putative plant-associated operons,
such as those that encode the novel type
VI effector Hyde protein that kills other
plant-associated bacteria and may mediate
competition among plant-associated
microorganisms. The co-occurrence of
many plant-associated gene clusters in
multiple distant taxa suggests inter-taxon
horizontal gene transfers have taken place.
Hundreds of plant-associated domains
were identified as being reproducibly
enriched in multiple bacterial taxa,
64 of which mimicked plant domains.
In many cases, these domains showed
a high homology with proteins from plant-
associated oomycetes and fungi, indicating
convergent evolution or horizontal gene
transfer between evolutionarily distant
microorganisms — probably driven by
similar selective forces.
Published online: 29 January 2018
Credit: Diekleinert / Alamy Stock Photo
NATuRE PLANTS | VOL 4 | FEBRUARY 2018 | 60 | www.nature.com/natureplants