Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms.

Genome Biology and Evolution
Kasper U KjeldsenAndreas Schramm

Abstract

While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60-130 Myr) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it with the genomes of Verminephrobacter eiseniae and two nonsymbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in size and showed no A-T bias. We characterized the strength of purifying selection (ω = dN/dS) and codon usage bias in 876 orthologous genes. Symbiont genomes exhibited strong purifying selection (ω = 0.09 ± 0.07), although transition to symbiosis entailed relaxation of purifying selection as evidenced by 50% higher ω values and less codon usage bias in symbiont compared with reference genomes. Relaxation was not evenly distributed among functional gene categories but was overrepresented in genes involved in signal transduction and cell envelope biogenesis. The same gene categories also harbored instances of positive selection ...Continue Reading

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Citations

Feb 26, 2015·Proceedings of the National Academy of Sciences of the United States of America·Gordon M Bennett, Nancy A Moran
Sep 13, 2015·Genome Biology and Evolution·Amanda M V BrownDee R Denver
Mar 24, 2017·FEMS Microbiology Ecology·Laura-Carlota PazMarie Braad Lund
Nov 7, 2017·Molecular Biology and Evolution·Shelbi L Russell, Colleen M Cavanaugh
May 29, 2016·Applied and Environmental Microbiology·Vera TaiPatrick J Keeling
Feb 15, 2015·Applied and Environmental Microbiology·Gili HrusaLaura J Runyen-Janecky
Apr 21, 2018·Scientific Reports·Consuelo BadillaJoanne M Santini

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Datasets Mentioned

BETA
AFAL00000000

Methods Mentioned

BETA
454 sequencing
PCR

Software Mentioned

CLC Genomics Workbench
PhyML
InterPro
ENCprime
BlastP
COG
R
GLIMMER
codeml
Blast

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