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Probabilistic reconstruction of ancestral gene orders with insertions and deletions

Content Provider	ACM Digital Library
Author	Zhou, Jun Hu, Fei Tang, Jijun Zhou, Lingxi
Copyright Year	2014
Abstract	Changes of gene orderings have been extensively used as a signal to reconstruct phylogenies and ancestral genomes. Inferring the gene order of an extinct species has a wide range of applications, including the potential to reveal more detailed evolutionary histories, to determine gene content and ordering, and to understand the consequences of structural changes for organismal function and species divergence. In this study, we propose a new adjacency-based method, PMAG+, to infer ancestral genomes under a more general model of gene evolution involving gene insertions and deletions (indels), in addition to gene rearrangements. PMAG+ improves on our previous method PMAG by developing a new approach to infer ancestral gene contents and reducing the adjacency assembly problem to an instance of TSP. We designed a series of experiments to extensively validate PMAG+ and compared the results with the most recent and comparable method GapAdj. According to the results, ancestral gene contents predicted by PMAG+ coincides highly with the actual contents with error rates less than 1 percent. Under various degrees of indels, PMAG+ consistently achieves more accurate prediction of ancestral gene orders and at the same time, produces contigs very close to the actual chromosomes.
Starting Page	667
Ending Page	672
Page Count	6
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2014.2309602
Volume Number	11
Issue Number	4
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-07-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Ancestral genome Gene deletion Gene insertion Gene order Genome rearrangement
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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