Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers.

Reeve, Wayne; O’Hara, G.W.; Chain, Patrick; Ardley, Julie; Bräu, Lambert; Nandesena, Kemanthi; Tiwari, Ravi; Copeland, Alex; Nolan, Matt; Han, Cliff; Brettin, Thomas; Land, Miriam; Ovchinikova, Galina; Ivanova, Natalia; Mavromatis, Konstantinos; Markowitz, Victor; Kyrpides, Nikos C.; Melino, Vanessa; Denton, Matthew D.; Yates, Ron; Howieson, John

doi:10.4056/sigs.852027

Cited by 56 publications

(50 citation statements)

References 21 publications

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“…Bacterial genetic and post-genomic approaches have demonstrated the critical role played by genes involved in the synthesis of nodulation factors (that is, nod genes) and surface polysaccharides (for example, exo or rkp genes) in providing signals for the recognition of S. meliloti and S. medicae by their host (Jones et al, 2007). While most functional studies have used S. meliloti as a model bacterium because the genome of the strain 1021 was available (Galibert et al, 2001), more studies in future might be performed on S. medicae now that the genome sequence of the strain WSM 419 has been released (Reeve et al, 2010), because this bacterium, isolated in Sardinia, is a better symbiont than S. meliloti 1021 for the model legume M. truncatula (Terpolilli et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

et al. 2011

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We investigated the genomic diversity of a local population of the symbiotic bacterium Sinorhizobium medicae, isolated from the roots of wild Medicago lupulina plants, in order to assess genomic diversity, to identify genomic regions influenced by duplication, deletion or strong selection, and to explore the composition of the pan-genome. Partial genome sequences of 12 isolates were obtained by Roche 454 shotgun sequencing (average 5.3 Mb per isolate) and compared with the published sequence of S. medicae WSM 419. Homologous recombination appears to have less impact on the polymorphism patterns of the chromosome than on the chromid pSMED01 and megaplasmid pSMED02. Moreover, pSMED02 is a hot spot of insertions and deletions. The whole chromosome is characterized by low sequence polymorphism, consistent with the high density of housekeeping genes. Similarly, the level of polymorphism of symbiosis genes (low) and of genes involved in polysaccharide synthesis (high) may reflect different selection. Finally, some isolates carry genes that may confer adaptations that S. medicae WSM 419 lacks, including homologues of genes encoding rhizobitoxine synthesis, iron uptake, response to autoinducer-2, and synthesis of distinct polysaccharides. The presence or absence of these genes was confirmed by PCR in each of these 12 isolates and a further 27 isolates from the same population. All isolates had rhizobitoxine genes, while the other genes were co-distributed, suggesting that they may be on the same mobile element. These results are discussed in relation to the ecology of Medicago symbionts and in the perspective of population genomics studies.

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Section: Introductionmentioning

confidence: 99%

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

et al. 2011

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“…Deletion analyses of pRetCNF42e revealed the presence of genes, which are essential for growth in rich medium. The equivalents of pRetCNF42e are also found in other Rhizobium species, namely pRL11JI in Rlv 3841 [17], pRLG202 in Rlt WSM2304 [47], pRLG132502 in Rlt WSM1325 [46], and pRleTA1b in Rlt TA1 [30]. At least the latter one, similarly to pRetCNF42e, cannot be entirely eliminated from the cell by incompatibility purposes leading instead to its cointegration with other extrachromosomal replicons residing in the bacterium [30].…”

Section: The Impact Of Postgenomic Knowledge To Rhizobial Plasmid Rolmentioning

confidence: 93%

“…viciae (Rlv) and trifoli (Rlt) are closely related species differing in their host-specificity but displaying very similar genome organization: a single circular chromosome and several large plasmids. Each of them carries the majority of nod-nif-fix genes on the plasmid, named pSym [17,36,46,47,82], but the pSyms of Rhe, Rlv and Rlt belong to different incompatibility groups and have quite different genes content other than those related to symbiotic performance [14,30,83]. In contrast to Sme, several major cluster of genes engaged in the biosynthesis of various surface polysaccharides are chromosomal.…”

Section: Rhizobial Plasmids Structure Gene Content and Impact On Bacmentioning

confidence: 99%

“…viciae 3841 [17], R. etli CFN42 [36] and R. leguminosarum bv. trifolii WSM2304 and WSM1325 [46,47], containing multiple (4-6) plasmids have been obtained. In the context of the functional and especially evolutionary studies of plasmid and replication systems, such genomes are of great interest because each of them has several plasmids, all belonging to the repABC family.…”

Section: Rhizobial Plasmid Maintenance Systemsmentioning

confidence: 99%

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Rhizobial plasmids — replication, structure and biological role

Mazur

Koper

2012

Open Life Sciences

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AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

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“…RL has a multi-partite genome, in the form of one large, circular chromosome (4-5Mb) and a variable number (1-6) of large or very large plasmids ( Figure I.4) (Young et al, 2006, Reeve et al, 2010a, Reeve et al, 2010b, Reeve et al, 2015. Some of these resemble chromosomes in their size and functional complexity, and are known as "chromids" .…”

mentioning

confidence: 99%

Genomics of Specificity in the Symbiotic Interaction between Rhizobium leguminosarum and Legumes

Rubio¹

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. Para el desarrollo de esta Tesis he contado con una beca UPM homologada financiada por el proyecto MICROGEN: Genómica Comparada Microbiana (Programa Consolider), que ha sido también el proyecto financiador del trabajo experimental.Quisiera reconocer la labor de aquellas personas que han contribuido al desarrollo y consecución de esta Tesis.Dr. Juan Imperial, por la dirección y supervisión de esta Tesis. Por ser un gran mentor y por enseñarme todo lo que sé.Dr. Manuel González Guerrero, por enseñarme los entresijos de la Ciencia y del trabajo en el laboratorio.Dra. Gisèle Laguerre, por su participación en el inicio de este proyecto y por facilitarnos el suelo P1 de Dijon.Dr. Paulo Arruda, por la formación que obtuve durante mi estancia en el laboratorio de Estudio de la Regulación y de la Expresión génica de la Universidad Estatal de Campinas.Dra. Belén Brito, por su gran ayuda en la primera fase de este proyecto y por recomendarme, sin ella nunca hubiera empezado esta Tesis.Rosabel Prieto, por su inestimable ayuda para la obtención de los Pool-Seqs y por enseñarme muchas de las técnicas que he necesitado durante la Tesis.Santiago de la Peña, por su valiosa ayuda en el análisis bioinformático de los genomas individuales.Dra. Julia Quintana, por enseñarme los conceptos de genética de poblaciones y por las largas discusiones científicas que tanto me han aportado.Dra. Viviana Escudero, por enseñarme a cuidar las plantas y valorar las cosas realmente importantes. Dra. Carmen Sánchez, por enseñarme las técnicas básicas de microbiología y genética molecular durante mi periodo como estudiante de máster.Dr. David Durán, por enseñarme los conceptos básicos de filogenia. XIII AGRADECIMIENTOSEscribir los agradecimientos es la parte más difícil de una tesis, no porque sea complicado, si no porque es la única parte que se lee todo el mundo y supone una gran presión añadida. Siempre me imaginaba escribir esta parte como algo extremadamente emotivo, pero después de escribir más de 200 páginas me he quedado sin palabras.La ciencia siempre fue lo que quise hacer, pero nunca pensé que pudiera hacerlo, pero… here I am! Ha sido un camino largo y duro, pero no lo cambiaría por nada, me he convertido en lo que quería y he conocido a los mejores. Desde que tengo 13 años sabía que quería estudiar esto, gracias a la inspiración de mi profesora de biología Marisa Alonso. Cuando llegué a la carrera, las cosas no fueron como esperaba, pero aún así descubrí mi pasión por la micro, la genética y las plantas… Y sobre todo conocí a grandes personas. Desde luego la mejor decisión que tomé fue hacer el máster, este fue el punto de inflexión, descubrí que era hacer ciencia… y eso me enganchó. Quiero agradecer a Pepe Palacios por acogerme en su laboratorio durante este periodo, ya que sin duda, mi paso por allí marcó mi vuelta. Por ello también quiero agradecer a todos los Rizobios y Levaduros, y en especial a Carmen Sánchez, por ser mi supervisora en los inicios y enseñarme muchas de las técnicas básicas de micro y genética molecular que he apre...

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Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers.

Cited by 56 publications

References 21 publications

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

Rhizobial plasmids — replication, structure and biological role

Genomics of Specificity in the Symbiotic Interaction between Rhizobium leguminosarum and Legumes

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