Title |
Simultaneous genome sequencing of symbionts and their hosts
|
---|---|
Published in |
Symbiosis, February 2012
|
DOI | 10.1007/s13199-012-0154-6 |
Pubmed ID | |
Authors |
Sujai Kumar, Mark L. Blaxter |
Abstract |
Second-generation sequencing has made possible the sequencing of genomes of interest for even small research groups. However, obtaining separate clean cultures and clonal or inbred samples of metazoan hosts and their bacterial symbionts is often difficult. We present a computational pipeline for separating metazoan and bacterial DNA in silico rather than at the bench. The method relies on the generation of deep coverage of all the genomes in a mixed sample using Illumina short-read sequencing technology, and using aggregate properties of the different genomes to identify read sets belonging to each. This inexpensive and rapid approach has been used to sequence several nematode genomes and their bacterial endosymbionts in the last year in our laboratory and can also be used to visualize and identify unexpected contaminants (or possible symbionts) in genomic DNA samples. We hope that this method will enable researchers studying symbiotic systems to move from gene-centric to genome-centric approaches. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United Kingdom | 2 | 50% |
Sweden | 1 | 25% |
Unknown | 1 | 25% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 2 | 50% |
Scientists | 2 | 50% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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United States | 5 | 4% |
United Kingdom | 5 | 4% |
Austria | 2 | 2% |
Germany | 2 | 2% |
New Zealand | 2 | 2% |
Portugal | 1 | <1% |
Brazil | 1 | <1% |
Czechia | 1 | <1% |
Canada | 1 | <1% |
Other | 0 | 0% |
Unknown | 99 | 83% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 35 | 29% |
Researcher | 31 | 26% |
Student > Master | 13 | 11% |
Student > Bachelor | 9 | 8% |
Student > Doctoral Student | 6 | 5% |
Other | 14 | 12% |
Unknown | 11 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 73 | 61% |
Biochemistry, Genetics and Molecular Biology | 18 | 15% |
Immunology and Microbiology | 4 | 3% |
Environmental Science | 3 | 3% |
Business, Management and Accounting | 1 | <1% |
Other | 6 | 5% |
Unknown | 14 | 12% |