The Pangenome of the Plant-Selected Rhizobium leguminosarum bv viciae Sub-popuations

Jorrin, Beatriz and Imperial Ródenas, Juan (2014). The Pangenome of the Plant-Selected Rhizobium leguminosarum bv viciae Sub-popuations. In: "Workshop “Genomic of prokaryotes, handling the data analysis bottleneck. Glimpses at Pan-Genomes”", 05/11/2014-07/11/2014, Valencia, España. p. 1.

Description

Title: The Pangenome of the Plant-Selected Rhizobium leguminosarum bv viciae Sub-popuations
Author/s:
  • Jorrin, Beatriz
  • Imperial Ródenas, Juan
Item Type: Presentation at Congress or Conference (Article)
Event Title: Workshop “Genomic of prokaryotes, handling the data analysis bottleneck. Glimpses at Pan-Genomes”
Event Dates: 05/11/2014-07/11/2014
Event Location: Valencia, España
Title of Book: Genomic of prokaryotes, handling the data analysis bottleneck. Glimpses at Pan-Genomes
Date: 2014
Subjects:
Faculty: Centro de Investigación en Biotecnología y Genómica de Plantas (CBGP) (UPM)
Department: Biotecnologia [hasta 2014]
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

Rhizobium leguminosarum bv viciae (Rlv) is a bacterium able to establish effective symbioses with four different legume genera: Pisum, Lens, Lathyrus and Vicia. Classic studies using trap plants have previously shown that, given a choice, different plants prefer specific genotypes of rhizobia, which are adapted to the host (1, 2). In previous work we have performed a Pool-Seq analysis bases on pooled DNA samples from Rlv nodule isolates obtained from Pisum sativum, Lens culinaris, Vicia fava and V. sativa plants, used as rhizobial traps. This experiment allowed us to test the host preference hypothesis: different plant hosts select specific sub-populations of rhizobia from the available population present in a given soil. We have observed that plant-selected sub-populations are different at the single nucleotide polymorphism (SNP) level. We have selected individual isolates from each sub-population (9 fava-bean isolates, 14 pea isolates 9 vetch isolates and 9 lentil isolates) and sequenced their genomes at draft level (ca. 30x, 90 contigs). Genomic analyses have been carried out using J-species and CMG-Biotools. All the isolates had similar genome size (7.5 Mb) and number of genes (7,300). The resulting Average Nucleotide Identity (ANIm) tree showed that Rhizobium leguminosarum bv viciae is a highly diverse group. Each plant-selected subpopulation showed a closed pangenome and core genomes of similar size (11,500 and 4,800 genes, respectively). The addition of all four sub-population results in a larger, closed pangenome of 19,040 genes and a core genome of similar size (4,392 genes). Each sub-population contains a characteristic set of genes but no universal, plant-specific genes were found. The core genome obtained from all four sub-populations is probably a representative core genome for Rhizobium leguminosarum, given that the reference genome (Rhizobium leguminosarum bv. viciae strain 3841) contains most of the core genome. We have also analyzed the symbiotic cluster (nod), and different nod cluster genotypes were found in each sub-population. Supported by MINECO (Consolider-Ingenio 2010, MICROGEN Project, CSD2009-00006).

More information

Item ID: 39276
DC Identifier: http://oa.upm.es/39276/
OAI Identifier: oai:oa.upm.es:39276
Official URL: http://www.vitsalud.es/?eventos=workshop-genomics-of-prokaryotes-handling-the-data-analysis-bottleneck-glimpses-at-pan-genomes
Deposited by: Memoria Investigacion
Deposited on: 12 May 2016 16:57
Last Modified: 12 May 2016 16:57
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