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The Feschotte Lab
Department of Biology
Life Science Building
Box 19498
Arlington, TX 76019

Office: ERB 433
Wet Lab: ERB 473-474
Dry lab: ERB 479

Office: 817-272-2426
Lab:817-272-5574
Fax: 817-272-2855

What's new

The Beauty of Reptilian Genomes

This magnificient creature on the left is a copperhead.

Copperheads are very common around Arlington. I found this fortunate, but not everybody agrees. Anyhow, this month we co-authored three papers that illustrate how fascinating these and other reptiles are when it comes to their genomes too. On this I hope everybody will agree.

The first paper, spearheaded by Todd Castoe and David Pollock at the University of Colorado Health Sciences Center, uses next-gen sequencing to carry out a comparative analysis of the repetitive DNA landscape of two celebrated snakes, the copperhead and the Burmese python. The two species display striking differences in repeat content, with the copperhead genome having two-fold higher density of TEs and much higher levels of TE-derived transcripts, despite having a smaller genome. How this might relate to differences in morphology and physiology between these two group of snakes is an interesting question awaiting further investigation.

The second paper reports the result of a large-scale screen to detect SPIN transposons in non-avian reptiles conducted by postdoc Clement Gilbert and a bunch of talented undergrads. We found that SPIN was introduced horizontally no less than 15 times in various lineages of squamates (lizards, snakes, including copperhead). In contrast, we found no traces of SPIN in crocodiles and turtles. These data triples the number of SPIN horizontal transfers known in animals and confirms a previously hypothesized transoceanic movement of the transposon.

The third paper summarizes the effort of the recently established Snake Genomics Consortium to produce a whole genome sequence for the Burmese python, led by Todd and David. A first draft of the genome assembly was released earlier this year. We are glad to participate in this exciting endeavor and look forward to getting involved in more genomic explorations of the reptile world.

 

Welcome Aurelie!

Welcome to our newest addition, Dr. Aurelie Kapusta, now a postdoc in the lab.

Aurelie did her graduate work in the lab of Mireille Betermier at the CNRS unit CGM in Gif-sur-Yvette, France. She worked on the crazy and fascinating genome gymnastics of the ciliate Paramecium (note the species is called Paramecium tetraurelia, though I am not sure it was named after Aurelie). Check out her latest paper here.

And watch out as Aurelie is also an avid Aikido fighter!

 

Fairwell to Clement and Sarah

Kudos to Clement Gilbert (left on pic) and Sarah Schaack (right), two superb ex-postdocs in the lab, who have now secured faculty positions.

Clement will join the CNRS unit 'Ecology, Evolution, Symbiosis' at the University of Poitiers, France (his hometown!) where he will work closely with Richard Cordaux, another excellent past collaborator.

Sarah will be an Assistant Professor in the Biology Department at Reed College in Portland, Oregon, one of the premier liberal arts colleges in the country.

Congrats to both et bonne chance pour la suite!

 

We moved!

Earlier this year the lab moved to the Engineering and Research Building. The ERB is a brand new state-of-the-art building housing research labs from the College of Engineering and the College of Science.

Our lab and offices are located on the 4th floor of the building alongside several of our close colleagues in the Genome Biology Group, including Pritham, Demuth, Betran labs on the 4th floor and Christensen, Roner and Hurdle labs on the 3rd floor.

Note: while office and lab locations are new, our mailing address remains the same.

Take a tour!

 

Genomic fossils of Hepatitis B-like virus in finch genome

Clement's latest paleovirology effort is published on September 28 in PLoS Biology.

Some highlights from the press:

Science/AAAS: Ancient Virus Found Hiding Out in Finch Genome (by Cassandra Wilyard)

MSNBC/LiveScience: Ancient viruses lurk in songbird's DNA (by Wynne Parry)

Scientific American: Ancient "Fossil" Virus Shows Infection to Be Millions of Years Old (by Katherine Harmon)

The Guardian (Science Blog Punctuated Equilibrium): Fossil virus leaves evolutionary footprints in songbird DNA (by Grrlscientist)

UTA Press Release (by Traci Peterson)

 

Welcome Xiaoyu!

The newest addition to the lab is Xiaoyu Zhuo.

Xiaoyu grew up in Southern China and obtained his B.S. and M.S from Wuhan University. There he studied RNA splicing under the mentorship of Dr. Yi Zhang and Dr. Xiang-Dong Fu. He then worked for a pharmaceutical company for 3 years in the field of drug discovery.

So Xiaoyu is already an accomplished scientist and we are delighted to have him join the lab as a PhD student!

 

 

Promiscuous DNA

Review article 'Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution' published in the September issue of Trends in Ecology and Evolution.

Read it

Congrats to Sarah and Clement!

 

 

 

Our Nature paper evaluated as 'must read' by Faculty of 1000 - twice!

Read evaluation by Joachim Kurtz from the University of Muenster, Germany

Read evaluation by Andrea Schorn and Rob Martienssen from Cold Spring Harbor Laboratory, NY, USA

 

 

 

Bloodsucking parasites and mammalian hosts share transposons! Space Invaders strike again.

In a paper published in Nature on April 28, we report evidence for the horizontal transfer of transposons between invertebrate parasites and some of their vertebrate hosts.

The parasites include the triatomine Rhodnius prolixus or kissing bug (pic on the left by Erwin Huebner), an insect that feeds on the blood of a variety of mammals, including humans, and is responsible for the transmission of trypanosomes causing Chagas disease. We found that the bug genome harbors four families of DNA transposons that are nearly identical to those found in several vertebrates and include the particularly promiscuous transposon that we previously baptised 'Space Invaders' or SPIN.

We also detected the SPIN transposons in the genome of the great pond snail Lymnaea stagnalis, a species that act as an intermediate host for a number of trematodes or flukes that must complete their cycle in vertebrates, including some of those invaded by SPIN.

We conclude that host-parasite interactions must have facilitated the horizontal transfer of transposons across these widely diverged animals. Given the tremendous impact that transposon invasions can have on the structure and function of genomes, we argue that the passage of transposons across species boundaries has been a previously underappreciated force influencing animal evolution.

Congrats to Clement and Sarah for their outstanding contribution to this work!

Nature Editor's summary

Press release

 

 

Paleovirology: the past (and future) of viruses buried in the genome

A collection of clips and articles from the general press featuring work from our lab and many others, in the emerging area of 'paleovirology'. This is the study of the ancient history of viruses through the analysis of viral DNA sequences fossilized in the genome of their host species.

Such viral fossils are deposited in the genome when virus DNA integrates into the chromosome of the host reproductive germ cells and becomes subsequenty inherited from parent to offspring, becoming what scientists call 'endogenous viruses'.

Read more about what these fossils can tell us about the past and perhaps also the future of viruses, including some of our deadliest enemies:

Hunting fossil viruses in human DNA, by Carl Zimmer. The New York Times - January 11, 2010

A new breed of viral invasion, by Bob Grant. The Scientist - January 6, 2010

Bornavirus genes found in human DNA, by Tina Saey. Science News - January 6, 2010

Meet your viral ancestors, by Ed Yong. Not Exactly Rocket Science - January 6, 2010

Un nouvel ancetre viral de l'homme, by Stephane Foucart. Le Monde - January 8, 2010

Un nouvel heritage viral dans le genome de l'homme et d'autres mammiferes, by Les Echos via Agence France Presse - January 6, 2010

Genomic fossils in lemurs shed light on origin and evolution of HIV, Science Daily - March 24, 2009

Darwin's surprise, by Michael Specter, The New Yorker - December 3, 2007 (oldies but goodies)

Genomic fossils reveal germline infiltrations of lentivirus in lemurs

In a paper to appear in PLoS Genetics on March 20, we report that a retrovirus called pSIV, related to HIV and primate lentiviruses, has become stably integrated into the genome of several lemurs around 4.2 Million years ago. These are the first endogenous lentiviruses discovered in primates.

The gray mouse lemur Microcebus murinus represents one of two prosimian lineages infected by pSIV.

(Photo credit: David Haring, Duke Lemur Center)

 

We show that the germline infiltration of pSIV occurred in parallel in two different lineages of lemurs endemic to Madagascar. Based on ‘fossil’ sequences collected from different lemur species, we reconstructed computationally an apparently intact and complete DNA sequence for an ancestral prosimian lentivirus. These findings should allow future functional analysis of the extinct virus and advance our understanding of the biology and origin of lentiviruses, including HIV.

 

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