title: Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts.
abstract: Bacterial endosymbiosis is an important evolutionary process in insects, which can harbor both obligate and facultative symbionts. The evolution of these symbionts is driven by evolutionary convergence, and they exhibit among the tiniest genomes in prokaryotes. The large host spectrum of facultative symbionts and the high diversity of strategies they use to infect new hosts probably impact the evolution of their genome and explain why they undergo less severe genomic erosion than obligate symbionts. Candidatus Hamiltonella defensa is suitable for the investigation of the genomic evolution of facultative symbionts because the bacteria are engaged in specific relationships in two clades of insects. In aphids, H. defensa is found in several species with an intermediate prevalence and confers protection against parasitoids. In whiteflies, H. defensa is almost fixed in some species of Bemisia tabaci, which suggests an important role of and a transition toward obligate symbiosis. In this study, comparisons of the genome of H. defensa present in two B. tabaci species (Middle East Asia Minor 1 and Mediterranean) and in the aphid Acyrthosiphon pisum revealed that they belong to two distinct clades and underwent specific gene losses. In aphids, it contains highly virulent factors that could allow protection and horizontal transfers. In whiteflies, the genome lost these factors and seems to have a limited ability to acquire genes. However it contains genes that could be involved in the production of essential nutrients, which is consistent with a primordial role for this symbiont. In conclusion, although both lineages of H. defensa have mutualistic interactions with their hosts, their genomes follow distinct evolutionary trajectories that reflect their phenotype and could have important consequences on their evolvability.
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France.
authors.forename: Pierre-Antoine
authors.initials: PA
authors.lastname: Rollat-Farnier
authors.affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain.
authors.forename: Diego
authors.initials: D
authors.lastname: Santos-Garcia
authors.affiliation: Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China School of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Lin'an, Hangzhou, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Rao
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France.
authors.forename: Marie-France
authors.initials: MF
authors.lastname: Sagot
authors.affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Silva
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Henri
authors.affiliation: Department of Entomology, NeweYa'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel.
authors.forename: Einat
authors.initials: E
authors.lastname: Zchori-Fein
authors.affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain.
authors.forename: Amparo
authors.initials: A
authors.lastname: Latorre
authors.affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain.
authors.forename: Andrés
authors.initials: A
authors.lastname: Moya
authors.affiliation: CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, Evry, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.affiliation: Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Shu-Sheng
authors.initials: SS
authors.lastname: Liu
authors.affiliation: Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Xiao-Wei
authors.initials: XW
authors.lastname: Wang
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Vavre
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France laurence.mouton@univ-lyon1.fr.
authors.forename: Laurence
authors.initials: L
authors.lastname: Mouton
mesh_terms: D000818:Animals; D001042:Aphids / Q000382:microbiology*; D002473:Cell Wall / Q000737:chemistry; D004755:Enterobacteriaceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D019143:Evolution, Molecular; D017353:Gene Deletion; D016680:Genome, Bacterial; D023281:Genomics; D006430:Hemiptera / Q000382:microbiology*; D010802:Phylogeny; D013559:Symbiosis; D037521:Virulence Factors / Q000235:genetics
chemical_list: D037521:Virulence Factors
keywords: Bemisia tabaci; Hamiltonella defensa; aphids; comparative genomics