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

Royal Society Open Science
Simone CoughlanTim Downing

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 arch...Continue Reading

References

Mar 11, 1992·Transactions of the Royal Society of Tropical Medicine and Hygiene·R Bonfante-GarridoG Grimaldi
Jul 1, 1991·Memórias do Instituto Oswaldo Cruz·R D NaiffG Grimaldi Júnior
Mar 1, 1990·British Journal of Urology·P HenrikssonK Carlström
Sep 1, 1989·Transactions of the Royal Society of Tropical Medicine and Hygiene·J P DedetG Chatenay
Jan 1, 1989·Annales De Parasitologie Humaine Et Comparée·R Lainson, J J Shaw
Jan 1, 1981·Transactions of the Royal Society of Tropical Medicine and Hygiene·J R AriasA A de Souza
Dec 1, 1993·Molecular and Biochemical Parasitology·H B SteinkrausP J Langer
Mar 1, 1994·The American Journal of Tropical Medicine and Hygiene·E CupolilloH Momen
Jan 1, 1993·Parasitology·J F WalshM H Birley
Jul 1, 1995·Molecular and Biochemical Parasitology·E CupolilloS M Beverley
Jun 29, 1999·Clinics in Dermatology·R Killick-Kendrick
Dec 10, 1999·The American Journal of Tropical Medicine and Hygiene·A L BañulsM Tibayrenc
Feb 15, 2001·Cadernos de saúde pública·C R DaviesN Rodriguez
Feb 19, 2002·Molecular and Biochemical Parasitology·Phalgun B JoshiW Robert McMaster
Mar 11, 2003·Annals of Tropical Medicine and Parasitology·F PratlongJ P Dedet
Sep 4, 2003·Genome Research·Li LiDavid S Roos
Jun 25, 2005·Bioinformatics·Tim J CarverJulian Parkhill
Sep 16, 2005·International Journal for Parasitology·Marina Gramiccia, Luigi Gradoni
Oct 14, 2005·Molecular Biology and Evolution·Daniel H Huson, David Bryant
Feb 4, 2006·Journal of Clinical Microbiology·Brice RotureauBernard Carme
Jun 27, 2006·Medical Hypotheses·Brice Rotureau
Aug 26, 2006·Tropical Medicine & International Health : TM & IH·Anna Christina Tojal da SilvaGustavo Adolfo Sierra Romero
Sep 23, 2006·The Journal of Infectious Diseases·Nathalie AcestorNicolas Fasel
Jun 19, 2007·Nature Genetics·Christopher S PeacockMatthew Berriman
Sep 4, 2007·Molecular and Biochemical Parasitology·Christine Clayton, Michal Shapira
Oct 20, 2007·Transactions of the Royal Society of Tropical Medicine and Hygiene·Ana Lineth GarciaJean-Claude Dujardin
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Jun 6, 2009·Bioinformatics·Samuel AssefaMatthew Berriman
Sep 15, 2009·Molecular Biology and Evolution·Andrew P Jackson
Oct 20, 2009·Parasitology·R J Quinnell, O Courtenay
Nov 17, 2009·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Jorge FragaGert Van der Auwera
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 9, 2010·Clinical and Experimental Dermatology·E M van der SnoekC A J J Jaspers
Mar 30, 2010·The American Journal of Tropical Medicine and Hygiene·Pieter-Paul A M van ThielAldert Bart

❮ Previous
Next ❯

Citations

Dec 13, 2018·Memórias do Instituto Oswaldo Cruz·Sandra González-de la FuenteJose M Requena
Jun 15, 2019·Yeast·Ciaran Gilchrist, Rike Stelkens
Nov 28, 2018·Scientific Reports·Daniel Alfonso UrreaOmar Triana-Chavez
Aug 18, 2020·PLoS Neglected Tropical Diseases·Nathalia PinhoPatricia Cuervo
Dec 24, 2018·Microbiology Resource Announcements·Dhwani BatraMarcos de Almeida
Oct 12, 2019·BMC Genomics·Anzhelika ButenkoVyacheslav Yurchenko

❮ Previous
Next ❯

Datasets Mentioned

BETA
ERX005631
CP009404
ERX556165
ERX556164
ERX180458

Methods Mentioned

BETA
electrophoresis
PCR

Software Mentioned

Illumina Genome Analyzer II
BLASTn
MLEE
MLSA
Bcftools
SplitsTree
Clustal Omega
Velvet
SSPACE
Vcftools

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.