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Draft genome assemblies of 380 rhizobia isolates (Bradyrhizobia) from Southwestern Australia

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About this Collection

Draft genome assemblies of 380 rhizobia isolates (Bradyrhizobia) from Southwestern Australia


Draft genome assemblies of 380 Bradyrhizobium isolates collected from soil samples at the base of Acacia acuminata trees in Southwest Australia


Genomics Microbial Ecology Microbial Genetics


https://doi.org/10.25919/5c36dd4f30b5c


01 Aug 2016


30 Sep 2017


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CSIROEnquiries@csiro.au
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Bradyrhizobium rhizobia genome symbiont soil bacteria Acacia legume


CSIRO_datacollection_metadata.xlsx


Soil samples were collected across 20 sites in Southwest Australia at the base of Acacia acuminata trees. Acacia acuminata seedlings were grown in the soil under glasshouse conditions in order to trap rhizobia in seedling root nodules. Rhizobia cells were first cultured from Acacia nodules on yeast-mannitol agar media plates. DNA was extracted from cell cultures and the DNA was used to create 380 indexed paired-end 150bp Illumina libraries. Illumina libraries were sequenced on two Illumina2000 lanes. Sequence data from each sequencing lane were separated into individual sequence sample files. Poor quality reads were removed from each sample sequence file using Trmmomatic. Reads from each sample were assembled in SPades using settings at k=33,55,77. Contigs within each draft assembly with a coverage lower than 5 and 200 base pairs were removed from each draft assembly.


Funding and support for this project was provided by Office of the Chief Executive Postdoctoral Fellowship and the Biodiversity Ecosystems Knowledge & Service Program


Creative Commons Attribution 4.0 International Licence


CSIRO (Australia)


Simonsen, Anna; Prober, Suzanne; Barrett, Luke; Edwards, Owain; Thrall, Pete (2017): Draft genome assemblies of 380 rhizobia isolates (Bradyrhizobia) from Southwestern Australia. v1. CSIRO. Data Collection. 102.100.100/44182 https://doi.org/10.25919/5c36dd4f30b5c


All Rights (including copyright) CSIRO 2017.


Access to this collection's metadata and/or files (if any) are restricted until 25 Sep 2020. Although the associated metadata is public, the files (if any) have not been approved for general release. Please phone or email the contact person for this collection to discuss access to the files.

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Location Details

27°33′56.16″ S


34°24′25.92″ S


121°37′38.28″ E


114°37′13.08″ E


WGS84


More about this Collection

Bradyrhizobium japonicum


Rhizobia


Bacteria


Proteobacteria


Alphaproteobacteria


Rhizobiales


Bradyrhizobiaceae


Bradyrhizobium


japonicum


Closest taxon assignment, based on a BLAST search using 16S rrna gene markers, suggest that these strains are most closely related to B. japonicum but taxonomic assignment at the species level is not absolute.


About this Project

Biodiversity Eco Know & Serv - Awards &


Rhizobia are critical for growth and establishment of Acacia species in Australia. The purpose of this study is to investigate the role of climate adaptation in rhizobia by identifying how rhizobia genotypes respond to an existing climate gradient in Southwest Australia. The draft genome assembly provides sequence information that can be used to de... more


Suzanne Prober


Survey of rhizobia in soils of South-West Australia


Rhizobia are critical for growth and establishment of Acacia species in Australia. The purpose of this study was to investigate the role of climate adaptation in rhizobia by identifying how rhizobia genotypes respond to an existing climate gradient in South-West Australia. The draft genome assembly information provides sequence information that can... more


Survey


Illumina2000 Sequencer


Anna Simonsen


Suzanne Prober


Luke Barrett


Owain Edwards


Pete Thrall


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