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Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene content evolution in the Viannia subgenus

View ORCID ProfileSimone Coughlan, Ali Shirley Taylor, Eoghan Feane, Mandy Sanders, Gabriele Schonian, View ORCID ProfileJames A Cotton, Tim Downing
doi: https://doi.org/10.1101/233148
Simone Coughlan
School of Mathematics, Applied Mathematics and Statistics, National University of Ireland, Galway.;
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Ali Shirley Taylor
School of Biotechnology, Dublin City University, Dublin, Ireland;
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Eoghan Feane
School of Biotechnology, Dublin City University, Dublin, Ireland;
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Mandy Sanders
Wellcome Trust Sanger Institute, Hinxton, UK;
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Gabriele Schonian
Charite University Medicine, Berlin, Germany
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James A Cotton
Wellcome Trust Sanger Institute, Hinxton, UK;
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Tim Downing
School of Biotechnology, Dublin City University, Dublin, Ireland;
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  • For correspondence: tim.downing@dcu.ie
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Abstract

The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America where the Viannia subgenus predominates, so far only L. (Viannia) braziliensis and L. (V.) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi and L. (V.) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with ten other Viannia genomes revealed four traits common to all Viannia: aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies, and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in most, L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from chromosome 34. This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.

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Posted December 14, 2017.
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Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene content evolution in the Viannia subgenus
Simone Coughlan, Ali Shirley Taylor, Eoghan Feane, Mandy Sanders, Gabriele Schonian, James A Cotton, Tim Downing
bioRxiv 233148; doi: https://doi.org/10.1101/233148
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Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene content evolution in the Viannia subgenus
Simone Coughlan, Ali Shirley Taylor, Eoghan Feane, Mandy Sanders, Gabriele Schonian, James A Cotton, Tim Downing
bioRxiv 233148; doi: https://doi.org/10.1101/233148

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