Research Article: The Dynamics of Lateral Gene Transfer in Genus Leishmania – A Route for Adaptation and Species Diversification

Date Published: January 5, 2016

Publisher: Public Library of Science

Author(s): Elisabet Vikeved, Anders Backlund, Cecilia Alsmark, Peter John Myler. http://doi.org/10.1371/journal.pntd.0004326

Abstract: BackgroundThe genome of Leishmania major harbours a comparably high proportion of genes of prokaryote origin, acquired by lateral gene transfer (LGT). Some of these are present in closely related trypanosomatids, while some are detected in Leishmania only. We have evaluated the impact and destiny of LGT in genus Leishmania.Methodology/Principal FindingsTo study the dynamics and fate of LGTs we have performed phylogenetic, as well as nucleotide and amino acid composition analyses within orthologous groups of LGTs detected in Leishmania. A set of universal trypanosomatid LGTs was added as a reference group. Both groups of LGTs have, to some extent, ameliorated to resemble the recipient genomes. However, while virtually all of the universal trypanosomatid LGTs are distributed and conserved in the entire genus Leishmania, the LGTs uniquely present in genus Leishmania are more prone to gene loss and display faster rates of evolution. Furthermore, a PCR based approach has been employed to ascertain the presence of a set of twenty LGTs uniquely present in genus Leishmania, and three universal trypanosomatid LGTs, in ten additional strains of Leishmania. Evolutionary rates and predicted expression levels of these LGTs have also been estimated. Ten of the twenty LGTs are distributed and conserved in all species investigated, while the remainder have been subjected to modifications, or undergone pseudogenization, degradation or loss in one or more species.Conclusions/SignificanceLGTs unique to the genus Leishmania have been acquired after the divergence of Leishmania from the other trypanosomatids, and are evolving faster than their recipient genomes. This implies that LGT in genus Leishmania is a continuous and dynamic process contributing to species differentiation and speciation. This study also highlights the importance of carefully evaluating these dynamic genes, e.g. as LGTs have been suggested as potential drug targets.

Partial Text: Trypanosomatids are single flagellated, kinetoplastid protozoa with parasitic lifestyles. Primary hosts are often insects [1], but secondary hosts may be vertebrates and some species, such as the sister genera Leishmania and Trypanosoma, cause major diseases in humans [2]. The kinetoplastids uniquely harbour the kinetoplast, a tubular network of interlocked circular mitochondrial DNA. Based on several molecular markers [3–7], genus Leishmania is divided into the three subgenera Leishmania, Viannia and Sauroleishmania. Fraga and co-workers (2010) further sub-divides these three subgenera into several informal complexes, in general congruence with most previous studies. The main advancements in the most recent classifications is the separation of the major- and tropica-complexes, and the erection of a guyanensis-complex encompassing strains previously included in the braziliensis-complex [3, 4].

In this study we contribute data to increase the understanding of the fate of genes acquired by LGT in eukaryote genomes. We have combined a PCR based screen and sequence determination of orthologues to previously detected LGTs in un-sequenced Leishmania genomes with thorough bioinformatics analyses of our unique dataset. Our aim was to determine the depth of the transfer of LGTs previously reported in L. major within genus Leishmania and to evaluate the fate of the Leishmania-specific transferome in comparison to the LGTs shared by all trypanosomatids.

Source:

http://doi.org/10.1371/journal.pntd.0004326

 

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