Article

 

Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis Public Deposited

Analytics
https://ir.library.oregonstate.edu/concern/articles/3484zj64f

To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. The published article can be found at:  http://gbe.oxfordjournals.org/content/7/9/2727

Descriptions

Attribute NameValues
Creator
Abstract
  • Bacterial mutualists can modulate the biochemical capacity of animals. Highly coevolved nutritional mutualists do this by synthesizing nutrients missing from the host’s diet. Genomics tools have advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (phylum Verrucomicrobia) from the dagger nematode Xiphinema americanum, a migratory ectoparasite of numerous crops that also vectors nepovirus. Previously, this endosymbiont was identified in the gut, ovaries, and eggs, but its role was unknown. We explored the potential role of this symbiont using fluorescence in situ hybridization, genome sequencing, and comparative functional genomics. We report the first genome of an intracellular Verrucomicrobium and the first exclusively intracellular non-Wolbachia nematode symbiont. Results revealed that Xiphinematobacter had a small 0.916-Mb genome with only 817 predicted proteins, resembling genomes of other mutualist endosymbionts. Compared with free-living relatives, conserved proteins were shorter on average, and there was large-scale loss of regulatory pathways. Despite massive gene loss, more genes were retained for biosynthesis of amino acids predicted to be essential to the host. Gene ontology enrichment tests showed enrichment for biosynthesis of arginine, histidine, and aromatic amino acids, as well as thiamine and coenzyme A, diverging from the profiles of relatives Akkermansia muciniphilia (in the human colon), Methylacidiphilum infernorum, and the mutualist Wolbachia from filarial nematodes. Together, these features and the location in the gut suggest that Xiphinematobacter functions as a nutritional mutualist, supplementing essential nutrients that are depleted in the nematode diet. This pattern points to evolutionary convergence with endosymbionts found in sap-feeding insects.
Resource Type
DOI
Date Available
Date Issued
Citation
  • Brown, A. M., Howe, D. K., Wasala, S. K., Peetz, A. B., Zasada, I. A., & Denver, D. R. (2015). Comparative genomics of a plant-parasitic nematode endosymbiont suggest a role in nutritional symbiosis. Genome Biology and Evolution, 7(9), 2727-2746. doi:10.1093/gbe/evv176
Journal Title
Journal Volume
  • 7
Journal Issue/Number
  • 9
Keyword
Rights Statement
Funding Statement (additional comments about funding)
  • This work was supported by the United States Department of Agriculture (grant SCA 58-5358-3-026).
Publisher
Peer Reviewed
Language
Replaces
Additional Information
  • description.provenance : Submitted by Patricia Black (patricia.black@oregonstate.edu) on 2015-11-06T15:23:50Z No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) BrownAmandaIntegrativeBiologyComparativeGenomicsPlant.pdf: 2239333 bytes, checksum: fdf697dc94acd083bac41342bbf9ce8e (MD5) BrownAmandaIntegrativeBiologyComparativeGenomicsPlantSuppData.zip: 5356464 bytes, checksum: fff13ba780c0e34e63bf5f64e5f0f6c2 (MD5)
  • description.provenance : Made available in DSpace on 2015-11-06T15:25:25Z (GMT). No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) BrownAmandaIntegrativeBiologyComparativeGenomicsPlant.pdf: 2239333 bytes, checksum: fdf697dc94acd083bac41342bbf9ce8e (MD5) BrownAmandaIntegrativeBiologyComparativeGenomicsPlantSuppData.zip: 5356464 bytes, checksum: fff13ba780c0e34e63bf5f64e5f0f6c2 (MD5) Previous issue date: 2015-09
  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2015-11-06T15:25:25Z (GMT) No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) BrownAmandaIntegrativeBiologyComparativeGenomicsPlant.pdf: 2239333 bytes, checksum: fdf697dc94acd083bac41342bbf9ce8e (MD5) BrownAmandaIntegrativeBiologyComparativeGenomicsPlantSuppData.zip: 5356464 bytes, checksum: fff13ba780c0e34e63bf5f64e5f0f6c2 (MD5)

Relationships

Parents:

This work has no parents.

Items

Thumbnail Title Date Uploaded Visibility Actions
BrownAmandaIntegrativeBiologyComparativeGenomicsPlant.pdf 07/25/2017 Public
BrownAmandaIntegrativeBiologyComparativeGenomicsPlantSuppData.zip 07/25/2017 Public