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

Author:

Coughlan Simone1,Taylor Ali Shirley2,Feane Eoghan2,Sanders Mandy3,Schonian Gabriele4,Cotton James A.3,Downing Tim12ORCID

Affiliation:

1. School of Mathematics, Applied Mathematics and Statistics, National University of Ireland, Galway, Republic of Ireland

2. School of Biotechnology, Dublin City University, Dublin, Republic of Ireland

3. Wellcome Trust Sanger Institute, Hinxton, UK

4. Charité University Medicine, Berlin, Germany

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 10 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 all bar L. lainsoni , L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3’ end of 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.

Funder

Wellcome Trust

National University of Ireland, Galway

Publisher

The Royal Society

Subject

Multidisciplinary

Reference94 articles.

1. Pan American Health Organization. 2017 Leishmaniases: epidemiological report in the Americas. See http://www2.paho.org/hq/index.php?option=com_docman&task=doc_view&Itemid=270&gid=39646&lang=en.

2. World Health Organization. 2010 Control of the leishmaniases. World Health Organization Technical Report Series 949.

3. The current status of zoonotic leishmaniases and approaches to disease control

4. The biology and control of Phlebotomine sand flies

5. Phlebotomine sandflies and the spreading of leishmaniases and other diseases of public health concern

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3