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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus
BMC Genomics, Volume 11, No. 1, Article 374, Year 2010
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Description
Background: The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence fiscally and technically problematic. To selectively obtain gene-enriched regions of this tick's genome, Cot filtration was performed, and Cot-filtered DNA was sequenced via 454 FLX pyrosequencing.Results: The sequenced Cot-filtered genomic DNA was assembled with an EST-based gene index of 14,586 unique entries where each EST served as a potential "seed" for scaffold formation. The new sequence assembly extended the lengths of 3,913 of the 14,586 gene index entries. Over half of the extensions corresponded to extensions of over 30 amino acids. To survey the repetitive elements in the tick genome, the complete sequences of five BAC clones were determined. Both Class I and II transposable elements were found. Comparison of the BAC and Cot filtration data indicates that Cot filtration was highly successful in filtering repetitive DNA out of the genomic DNA used in 454 sequencing.Conclusion: Cot filtration is a very useful strategy to incorporate into genome sequencing projects on organisms with large genome sizes and which contain high percentages of repetitive, difficult to assemble, genomic DNA. Combining the Cot selection approach with 454 sequencing and assembly with a pre-existing EST database as seeds resulted in extensions of 27% of the members of the EST database. © 2010 Guerrero et al; licensee BioMed Central Ltd.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC2893602/bin/1471-2164-11-374-S1.XLS
https://efashare.b-cdn.net/share/pmc/articles/PMC2893602/bin/1471-2164-11-374-S2.PNG
https://efashare.b-cdn.net/share/pmc/articles/PMC2893602/bin/1471-2164-11-374-S3.XLSX
https://efashare.b-cdn.net/share/pmc/articles/PMC2893602/bin/1471-2164-11-374-S4.DOC
https://efashare.b-cdn.net/share/pmc/articles/PMC2893602/bin/1471-2164-11-374-S5.DOC
Authors & Co-Authors
Guerrero, Felix David
United States, Washington, D.c.
Usda Agricultural Research Service
Moolhuijzen, Paula M.
Australia, Perth
Murdoch University
Peterson, Daniel G.
United States, Mississippi State
College of Agriculture and Life Sciences
Bidwell, Shelby L.
United States, Rockville
J. Craig Venter Institute
Caler, Elisabet V.
United States, Rockville
J. Craig Venter Institute
Bellgard, Matthew
Australia, Perth
Murdoch University
Nene, Vishvanath M.
Kenya, Nairobi
Biosciences Eastern and Central Africa - International Livestock Research Institute
Djikeng, Appolinaire
Kenya, Nairobi
Biosciences Eastern and Central Africa - International Livestock Research Institute
Statistics
Citations: 36
Authors: 8
Affiliations: 5
Identifiers
Doi:
10.1186/1471-2164-11-374
e-ISSN:
14712164
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study
Study Approach
Quantitative