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Title: Genomes of three facultatively symbiotic Frankia sp. strainsreflect host plant biogeography

Abstract

Filamentous actinobacteria from the genus Frankia anddiverse woody trees and shrubs together form N2-fixing actinorhizal rootnodule symbioses that are a major source of new soil nitrogen in widelydiverse biomes 1. Three major clades of Frankia sp. strains are defined;each clade is associated with a defined subset of plants from among theeight actinorhizal plant families 2,3. The evolution arytrajectoriesfollowed by the ancestors of both symbionts leading to current patternsof symbiont compatibility are unknown. Here we show that the competingprocesses of genome expansion and contraction have operated in differentgroups of Frankia strains in a manner that can be related to thespeciation of the plant hosts and their geographic distribution. Wesequenced and compared the genomes from three Frankia sp. strains havingdifferent host plant specificities. The sizes of their genomes variedfrom 5.38 Mbp for a narrow host range strain (HFPCcI3) to 7.50Mbp for amedium host range strain (ACN14a) to 9.08 Mbp for a broad host rangestrain (EAN1pec.) This size divergence is the largest yet reported forsuch closely related bacteria. Since the order of divergence of thestrains is known, the extent of gene deletion, duplication andacquisition could be estimated and was found to be inconcert with thebiogeographic history of the symbioses. Host plant isolation favoredgenomemore » contraction, whereas host plant diversification favored genomeexpansion. The results support the idea that major genome reductions aswell as expansions can occur in facultatively symbiotic soil bacteria asthey respond to new environments in the context of theirsymbioses.« less

Authors:
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Publication Date:
Research Org.:
COLLABORATION - U. LyonI/France
Sponsoring Org.:
USDOE
OSTI Identifier:
919667
Report Number(s):
LBNL-59824
R&D Project: Y00023; BnR: 600305000; TRN: US200822%%464
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Journal Article
Resource Relation:
Journal Name: Genome Research; Journal Volume: 17; Journal Issue: 1; Related Information: Journal Publication Date: 01/2007
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; BACTERIA; COMPATIBILITY; CONTRACTION; DISTRIBUTION; DIVERSIFICATION; FRANKIA; GENES; NITROGEN; SHRUBS; SOILS; STRAINS; TRAJECTORIES; TREES

Citation Formats

Normand, Philippe, Lapierre, Pascal, Tisa, Louis S., Gogarten, J.Peter, Alloisio, Nicole, Bagnarol, Emilie, Bassi, Carla A., Berry,Alison, Bickhart, Derek M., Choisne, Nathalie, Couloux, Arnaud, Cournoyer, Benoit, Cruveiller, Stephane, Daubin, Vincent, Demange, Nadia, Francino, M. Pilar, Ggoltsman, Eugene, Huang, Ying, Kopp, Olga, Labarre,Laurent, Lapidus, Alla, Lavire, Celine, Marechal, Joelle, Martinez,Michele, Mastronunzio, Juliana E., Mullin, Beth, Niemann, James, Pujic,Pierre, Rawnsley, Tania, Rouy, Zoe, Schenowitz, Chantal, Sellstedt,Anita, Tavares, Fernando, Tomkins, Jeffrey P., Vallenet, David, Valverde,Claudio, Wall, Luis, Wang, Ying, Medigue, Claudine, and Benson, David R.. Genomes of three facultatively symbiotic Frankia sp. strainsreflect host plant biogeography. United States: N. p., 2006. Web. doi:10.1101/gr.5798407.
Normand, Philippe, Lapierre, Pascal, Tisa, Louis S., Gogarten, J.Peter, Alloisio, Nicole, Bagnarol, Emilie, Bassi, Carla A., Berry,Alison, Bickhart, Derek M., Choisne, Nathalie, Couloux, Arnaud, Cournoyer, Benoit, Cruveiller, Stephane, Daubin, Vincent, Demange, Nadia, Francino, M. Pilar, Ggoltsman, Eugene, Huang, Ying, Kopp, Olga, Labarre,Laurent, Lapidus, Alla, Lavire, Celine, Marechal, Joelle, Martinez,Michele, Mastronunzio, Juliana E., Mullin, Beth, Niemann, James, Pujic,Pierre, Rawnsley, Tania, Rouy, Zoe, Schenowitz, Chantal, Sellstedt,Anita, Tavares, Fernando, Tomkins, Jeffrey P., Vallenet, David, Valverde,Claudio, Wall, Luis, Wang, Ying, Medigue, Claudine, & Benson, David R.. Genomes of three facultatively symbiotic Frankia sp. strainsreflect host plant biogeography. United States. doi:10.1101/gr.5798407.
Normand, Philippe, Lapierre, Pascal, Tisa, Louis S., Gogarten, J.Peter, Alloisio, Nicole, Bagnarol, Emilie, Bassi, Carla A., Berry,Alison, Bickhart, Derek M., Choisne, Nathalie, Couloux, Arnaud, Cournoyer, Benoit, Cruveiller, Stephane, Daubin, Vincent, Demange, Nadia, Francino, M. Pilar, Ggoltsman, Eugene, Huang, Ying, Kopp, Olga, Labarre,Laurent, Lapidus, Alla, Lavire, Celine, Marechal, Joelle, Martinez,Michele, Mastronunzio, Juliana E., Mullin, Beth, Niemann, James, Pujic,Pierre, Rawnsley, Tania, Rouy, Zoe, Schenowitz, Chantal, Sellstedt,Anita, Tavares, Fernando, Tomkins, Jeffrey P., Vallenet, David, Valverde,Claudio, Wall, Luis, Wang, Ying, Medigue, Claudine, and Benson, David R.. Wed . "Genomes of three facultatively symbiotic Frankia sp. strainsreflect host plant biogeography". United States. doi:10.1101/gr.5798407. https://www.osti.gov/servlets/purl/919667.
@article{osti_919667,
title = {Genomes of three facultatively symbiotic Frankia sp. strainsreflect host plant biogeography},
author = {Normand, Philippe and Lapierre, Pascal and Tisa, Louis S. and Gogarten, J.Peter and Alloisio, Nicole and Bagnarol, Emilie and Bassi, Carla A. and Berry,Alison and Bickhart, Derek M. and Choisne, Nathalie and Couloux, Arnaud and Cournoyer, Benoit and Cruveiller, Stephane and Daubin, Vincent and Demange, Nadia and Francino, M. Pilar and Ggoltsman, Eugene and Huang, Ying and Kopp, Olga and Labarre,Laurent and Lapidus, Alla and Lavire, Celine and Marechal, Joelle and Martinez,Michele and Mastronunzio, Juliana E. and Mullin, Beth and Niemann, James and Pujic,Pierre and Rawnsley, Tania and Rouy, Zoe and Schenowitz, Chantal and Sellstedt,Anita and Tavares, Fernando and Tomkins, Jeffrey P. and Vallenet, David and Valverde,Claudio and Wall, Luis and Wang, Ying and Medigue, Claudine and Benson, David R.},
abstractNote = {Filamentous actinobacteria from the genus Frankia anddiverse woody trees and shrubs together form N2-fixing actinorhizal rootnodule symbioses that are a major source of new soil nitrogen in widelydiverse biomes 1. Three major clades of Frankia sp. strains are defined;each clade is associated with a defined subset of plants from among theeight actinorhizal plant families 2,3. The evolution arytrajectoriesfollowed by the ancestors of both symbionts leading to current patternsof symbiont compatibility are unknown. Here we show that the competingprocesses of genome expansion and contraction have operated in differentgroups of Frankia strains in a manner that can be related to thespeciation of the plant hosts and their geographic distribution. Wesequenced and compared the genomes from three Frankia sp. strains havingdifferent host plant specificities. The sizes of their genomes variedfrom 5.38 Mbp for a narrow host range strain (HFPCcI3) to 7.50Mbp for amedium host range strain (ACN14a) to 9.08 Mbp for a broad host rangestrain (EAN1pec.) This size divergence is the largest yet reported forsuch closely related bacteria. Since the order of divergence of thestrains is known, the extent of gene deletion, duplication andacquisition could be estimated and was found to be inconcert with thebiogeographic history of the symbioses. Host plant isolation favoredgenome contraction, whereas host plant diversification favored genomeexpansion. The results support the idea that major genome reductions aswell as expansions can occur in facultatively symbiotic soil bacteria asthey respond to new environments in the context of theirsymbioses.},
doi = {10.1101/gr.5798407},
journal = {Genome Research},
number = 1,
volume = 17,
place = {United States},
year = {Wed Feb 01 00:00:00 EST 2006},
month = {Wed Feb 01 00:00:00 EST 2006}
}
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