#Genomics

DNA Zoo collaboration yields two new anteater chromosome-scale genomes

Frederic Delsuc

Jun 30, 2022
1 min

DNA Zoo collaboration yields two new anteater chromosome-scale genomes

By teaming up with the DNA Zoo team who generated HiC structural data to upgrade our high-quality hybrid genome assemblies, we are releasing two new chromosome-scale genome assemblies for the giant anteater (Myrmecophaga tridactyla) (https://www.dnazoo.org/post/on-the-shoulders-of-giants) and the southern tamandua (Tamandua tetradactyla) (https://www.dnazoo.org/post/the-ant-hunter). The new chromosome scale assemblies and annotations can be found here: - Giant anteater (https

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Frederic Delsuc

Jun 28, 2022
1 min

Congratulations Mariana!

Congratulations to Mariana Escobar Rodriguez for a successful oral defense of her Master project from the Erasmus Mundus Master Programme in Evolutionary Biology (MEME). Mariana's project was on the comparative genomics and transcriptomics of mucine genes in mammals. Good luck Mariana for your next MEME step at the University of Groningen (Netherlands). #Genomics #Master #Students #Bioinformatics #Transcriptomics

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Frédéric presented a talk on chitinase gene family evolution at the ALPHY/AIEM meeting

Frederic Delsuc

Mar 15, 2022
1 min

Frédéric presented a talk on chitinase gene family evolution at the ALPHY/AIEM meeting

After two years of virtual meetings, Frédéric was especially delighted to attend the ALPHY/AIEM annual meeting of the evolutionary genomics and bioinformatics French community in Rennes (France). Frédéric exposed our latest results on comparative genomics and transcriptomics of salivary glands to investigate the evolution of the chitinase gene family in placentals. Our results demonstrate that divergent molecular mechanisms underlie convergent adaptation to the ant-eating die

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First publication of the European Reference Genome Atlas (ERGA) consortium

Frederic Delsuc

Jan 23, 2022
1 min

First publication of the European Reference Genome Atlas (ERGA) consortium

As a member of the recently created European Reference Genome Atlas (ERGA), Frédéric participated to the first paper of the consortium published in Trends in Ecology and Evolution (doi:10.1016/j.tree.2021.11.008). The ERGA is a pan-European scientific initiative aimed at generating high-quality complete genome resources for eukaryote species of continental Europe. This first consortium paper highlights the usefulness of producing high-quality complete genome resources in larg

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Bye Rémi, so long, and thanks for all the fish!

Frederic Delsuc

Dec 31, 2021
1 min

Bye Rémi, so long, and thanks for all the fish!

After four years within the ConvergeAnt project as a PhD student, then a postdoc, Rémi is moving for new adventures. From the field in French Guiana and South Africa tracking roadkill and anything else alive, to the lab setting up Nanopore long read sequencing, to the computing cluster assembling complex genomes and building and analyzing giant phylogenomic datasets, you mastered it all! Thank you again for everything and congrats for securing a well-deserved permanent resear

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Chris' new paper on gene loss in the melatonin pathway published in Open Research Europe

Frederic Delsuc

Dec 12, 2021
2 min

Chris' new paper on gene loss in the melatonin pathway published in Open Research Europe

Chris' study on the molecular evolution and loss of function of the genes involved in the melatonin pathway in vertebrates has been published in Open Research Europe (doi:10.12688/openreseurope.13795.1) a new gold open access journal edited by the European Commission with a transparent process of peer-review. In this work, we studied the molecular evolution of genes involved in the synthesis (AANAT, ASMT) and signaling (MTNR1A, MTNR1B) of melatonin, a hormone secreted by the

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The DNA Zoo updated our bat-eared fox genome assembly to chromosome-scale

Frederic Delsuc

Jul 19, 2021
1 min

The DNA Zoo updated our bat-eared fox genome assembly to chromosome-scale

Thrilled to see that the DNA Zoo (www.dnazoo.org/post/i-m-all-ears) has upgraded our recently published (https://elifesciences.org/articles/63167) bat-eared fox hybrid genome assembly to the chromosome-scale with new Hi-C structural data. The new chromosome scale assembly and annotation can be found here (www.dnazoo.org/assemblies/Otocyon_megalotis). Great publicly available genomic resource for the community. #Bioinformatics #Genomics #Roadkill

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Two ConvergeAnt talks presented at the virtual Evolution 2021 meeting

Frederic Delsuc

Jun 25, 2021
2 min

Two ConvergeAnt talks presented at the virtual Evolution 2021 meeting

Chris and Frédéric presented talks at the Virtual Evolution 2021 meeting the annual meeting of the American Society of Naturalists, the Society for the Study of Evolution, and the Society of Systematic Biologists held online because of travel restrictions due to the ongoing COVID-19 pandemic. Chris presented his work on the molecular erosion of tooth-related genes in the xenarthran radiation (armadillos, anteaters, and sloths) showing that independent and distinct events of d

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Invited talk at the 2nd Virtual Meeting of Systematics, Biogeography, and Evolution

Frederic Delsuc

Jun 22, 2021
1 min

Invited talk at the 2nd Virtual Meeting of Systematics, Biogeography, and Evolution

Frédéric was invited to share his views on mammalian phylogenomics and genome-scale species delineation in the "Current methods and applications of big‐data phylogenetics" symposium at the 2nd Virtual Meeting of Systematics, Biogeography, and Evolution. It was a real pleasure to be part of this inclusive event that brings together researchers with different backgrounds from around the world and which is coordinated by young interdisciplinary Latinx scientists, supporting and

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Sampling six-banded armadillos at the Montpellier zoo

Frederic Delsuc

Apr 19, 2021
1 min

Sampling six-banded armadillos at the Montpellier zoo

Frédéric visited the Parc Zoologique de Montpellier to collect blood from their two hosted six-banded armadillos (Euphractus sexcinctus) on the occasion of a routine annual check-up. These samples will be used for genome sequencing using Nanopore long reads. Many thanks as always to Baptiste Chenet and Laurie Virolle for their kind help and collaboration. #Fieldwork #Transcriptomes #Zoo #Genomics #Armadillos

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Rémi's roadkill genomics paper published in eLife!

Frederic Delsuc

Mar 15, 2021
2 min

Rémi's roadkill genomics paper published in eLife!

Rémi's new study about genomics of carnivores based on roadkill samples is finally published in eLife after using their new pre-print review system. In this paper, we generated two reference genomes using hybrid Nanopore/Illumina sequencing to study the genetic differentiation between the allopatric populations of aardwolf (Proteles cristatus) and bat-eared fox (Otocyon megalotis). First, we estimated the genetic diversity among carnivores for the COX1 and CYTB mitochondrial

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Mathilde attended an online course on Speciation Genomics

Frederic Delsuc

Dec 11, 2020
1 min

Mathilde attended an online course on Speciation Genomics

Mathilde attended the 4th edition of the Speciation Genomics course organized by Physalia. This one-week online course run by run by Dr. Mark Ravinet (University of Nottingham, UK) an Dr. Joana Meier (University of Cambridge, UK) provides how-to-guide on the main bioinformatic tools to perform statistical analysis of speciation using population genomics data. Mathilde will use her improved skills to analyze the genome re-sequencing data to perform species delimitation in some

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Invited talk at the 1st Xenarthra International Conservation Congress

Frederic Delsuc

Nov 30, 2020
1 min

Invited talk at the 1st Xenarthra International Conservation Congress

Frédéric was invited to present the recent advances made on sequencing xenarthran genomes in the ConvergeAnt project at the 1st Xenarthra International Conservation Congress. This four-days online congress was followed by a virtual meeting of the IUCN/SSC Anteater, Sloth and Armadillo Specialist Group to discuss conservation priority actions on this evolutionary distinct placental group. Delsuc F. (2020). Recent Advances and Future Prospects in Xenarthran Phylogenomics. 1st

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Frederic Delsuc

Oct 14, 2020
1 min

Au revoir Amandine !

After two years of hard bench (and some field) work, Amandine Magdeleine is leaving the ConvergeAnt project. Amandine has been instrumental in producing the ant-eating mammal genomes and transcriptomes of the project and hundreds of ant mitogenomes using Illumina sequencing, but she also processed the hundreds of fecal samples for microbiome sequencing using 16S rRNA and metagenomics with the MinION. Best wishes for your next endeavor Amandine! #Genomics #Microbiomes #Nanopor

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Talk at the Biodiversity Genomics 2020 meeting

Frederic Delsuc

Oct 7, 2020
1 min

Talk at the Biodiversity Genomics 2020 meeting

Rémi presented our results on genome-wide species delineation in aardwolf and bat-eared fox in the Conservation Genomics session of the Biodiversity Genomics 2020 meeting. This online meeting was organized by the Tree of Life programme at the Wellcome Sanger Institute to celebrate success, explore challenges and look to the future of sequencing all life on Earth. Rémi's talk can be watched from the congress' YouTube channel: Allio R.*, Tilak M.-K., Avenant N.L., Corre E., Nab

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Frederic Delsuc

Jun 4, 2020
1 min

Congratulations to Sophie!

Congratulations to Sophie Teullet who virtually, but successfully, defended her project from the Ecology and Evolution Master from the University of Toulouse (MEE). Sophie's M2 project dissected the molecular evolution of chitinase genes in mammals using genomic and transcriptomic data. Despite the lockdown consecutive to the COVID-19 epidemics, Sophie did a wonderful job while working remotely on her project and obtained her degree with highest honors. Congrats again! #Tran

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Invited talk at Montpellier Omics Days 2020

Frederic Delsuc

Feb 7, 2020
1 min

Invited talk at Montpellier Omics Days 2020

Frédéric has been invited to present our results on roadkill genomics using the MinION portable device from Oxford Nanopore Technologies at the 8th edition of the Montpellier Omics Days. Frédéric's talk (in French) can be watched from the congress' YouTube channel: Delsuc F. (2020). Rubrique des chiens écrasés : assemblage hybride de génomes de mammifères de qualité à partir de spécimens récoltés le long des routes. 8th Montpellier Omics Days (Montpellier, France). [Invited o

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Frederic Delsuc

Feb 4, 2020
1 min

Talk at ALPHY 2020

Rémi presented our results on using roadkill for genome-wide species delimitation in myrmecophagous carnivores at ALPHY 2020, a Bioinformatics and Evolutionary Genomics conference held this year in Lyon (France). He also gave a seminar on the same topic at the LEHNA lab at the University of Lyon the day before the conference. Allio R.*, Tilak M.-K., Avenant N.L., Corre E., Nabholz B. & Delsuc F. (2020). Roadkill genomics: high quality mammalian genomes from hybrid assembly of

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Frederic Delsuc

Jan 11, 2020
1 min

Talk at PAG meeting 2020

Frédéric presented our results on sequencing high quality genomes from roadkill for genome-wide species delimitation in ant-eating carnivorans at the Plant and Animal Genome conference in San Diego, CA, USA (PAG 2020). This annual conference is the "grand messe" of genomics and it was an honor to be selected for a talk this year. Thanks to Elinor Karlsson and Ellie Armstrong for organizing the "Feline and Canine Genomics Workshop". It was also the occasion for Frédéric to vis

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Protocol for sequencing mammalian roadkill tissues with the MinION shared on Protocols.io

Frederic Delsuc

Aug 8, 2019
1 min

Protocol for sequencing mammalian roadkill tissues with the MinION shared on Protocols.io

We are happy to share our optimized protocol for sequencing long reads from mammalian roadkill tissues with the Oxford Nanopore Technology (ONT). This protocol was specifically developed to optimize DNA extraction and sequencing roadkill tissues containing necrotized cells and impurities that result in DNA degradation. First, we observed that DNA preservation was generally better in RNAlater than in 95% EtOH preserved tissues. Second, we found that physically removing necroti

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