LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

Mobile DNA
Eric Disdero, Jonathan Filée


Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available. However, existing TE population genomic softwares were not designed to handle long reads and the development of new dedicated tools is needed. LoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against simulated and genuine Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tool to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences. LoRTE is an efficient and accurate tool to identify structural genomic variants caused by TE insertion or deletion. LoRTE is available for download at http://www.egce.cnrs-gif.fr/?p=6422.


Aug 20, 2005·PLoS Computational Biology·Hadi QuesnevilleDominique Anxolabehere
Apr 29, 2008·Nucleic Acids Research·Mark JohnsonThomas L Madden
Mar 19, 2011·Biology Direct·Aurélie Hua-VanPierre Capy
Feb 10, 2012·Nature·T F MackayRichard A Gibbs
Nov 7, 2012·Bioinformatics·Yukiteru OnoMichiaki Hamada
Jul 26, 2013·Molecular Biology and Evolution·Julie M CridlandKevin R Thornton
Mar 19, 2014·Nucleic Acids Research·Philipp KochBryan R Downie
Apr 23, 2014·Nucleic Acids Research·Jiali ZhuangZhiping Weng
Jun 5, 2014·Bioinformatics·Matthias ZytnickiHadi Quesneville
Jan 1, 2014·Scientific Data·Kristi E KimJane M Landolin
Nov 19, 2015·Nucleic Acids Research·Reazur RahmanNelson C Lau
Aug 16, 2016·Briefings in Bioinformatics·Lavanya RishishwarI King Jordan
Oct 18, 2016·Nature Methods·Chen-Shan ChinMichael C Schatz


Sep 21, 2018·Nature Reviews. Genetics·Patricia Goerner-Potvin, Guillaume Bourque
May 19, 2018·Frontiers in Plant Science·Jungnam Cho
Feb 18, 2021·Genome Biology and Evolution·Caiti Smukowski HeilMaitreya J Dunham

Methods Mentioned


Related Concepts

Trending Feeds


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.

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.

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.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Separation Anxiety

Separation anxiety is a type of anxiety disorder that involves excessive distress and anxiety with separation. This may include separation from places or people to which they have a strong emotional connection with. It often affects children more than adults. Here is the latest research on separation anxiety.

KIF1A Associated Neurological Disorder

KIF1A associated neurological disorder (KAND) is a rare neurodegenerative condition caused by mutations in the KIF1A gene. KAND may present with a wide range and severity of symptoms including stiff or weak leg muscles, low muscle tone, a lack of muscle coordination and balance, and intellectual disability. Find the latest research on KAND here.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.