ArticleJournal of integrative bioinformatics2019
Ancestral Reconstruction and Investigations of Genomic Recombination on some Pentapetalae Chloroplasts.
Article in Journal of integrative bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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5 authors at 1 institution in 2 countries.
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Abstract
In this article, we propose a semi-automated method to rebuild genome ancestors of chloroplasts by taking into account gene duplication. Two methods have been used in order to achieve this work: a naked eye investigation using homemade scripts, whose results are considered as a basis of knowledge, and a dynamic programming based approach similar to Needleman-Wunsch. The latter fundamentally uses the Gestalt pattern matching method of sequence matcher to evaluate the occurrences probability of each gene in the last common ancestor of two given genomes. The two approaches have been applied on chloroplastic genomes from Apiales, Asterales, and Fabids orders, the latter belonging to Pentapetalae group. We found that Apiales species do not undergo indels, while they occur in the Asterales and Fabids orders. A series of experiments was then carried out to extensively verify our findings by comparing the obtained ancestral reconstruction results with the latest released approach called MLGO (Maximum Likelihood for Gene-Order analysis).
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