Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions.
We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.
Agricultural Research Service, US Department of Agriculture, Corvallis, Oregon, United States of America. Joyce.Loper@ars.usda.gov
Joyce E
JE
Loper
Karl A
KA
Hassan
Dmitri V
DV
Mavrodi
Edward W
EW
Davis
Chee Kent
CK
Lim
Brenda T
BT
Shaffer
Liam D H
LD
Elbourne
Virginia O
VO
Stockwell
Sierra L
SL
Hartney
Katy
K
Breakwell
Marcella D
MD
Henkels
Sasha G
SG
Tetu
Lorena I
LI
Rangel
Teresa A
TA
Kidarsa
Neil L
NL
Wilson
Judith E
JE
van de Mortel
Chunxu
C
Song
Rachel
R
Blumhagen
Diana
D
Radune
Jessica B
JB
Hostetler
Lauren M
LM
Brinkac
A Scott
AS
Durkin
Daniel A
DA
Kluepfel
W Patrick
WP
Wechter
Anne J
AJ
Anderson
Young Cheol
YC
Kim
Leland S
LS
Pierson
Elizabeth A
EA
Pierson
Steven E
SE
Lindow
Donald Y
DY
Kobayashi
Jos M
JM
Raaijmakers
David M
DM
Weller
Linda S
LS
Thomashow
Andrew E
AE
Allen
Ian T
IT
Paulsen
D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D001427:Bacterial Toxins / Q000235:genetics; D001430:Bacteriocins / Q000235:genetics; D018740:Genetic Heterogeneity; D014644:Genetic Variation; D016680:Genome, Bacterial; D054884:Host-Pathogen Interactions / Q000235:genetics; D007313:Insecta / Q000235:genetics; D005810:Multigene Family; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D010944:Plants / Q000235:genetics / Q000382:microbiology; D011551:Pseudomonas fluorescens / Q000235:genetics* / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012118:Resorcinols / Q000378:metabolism; D017422:Sequence Analysis, DNA
D001426:Bacterial Proteins; D001427:Bacterial Toxins; D001430:Bacteriocins; D012118:Resorcinols