#+TITLE: The axolotl genome and the evolution of key tissue formation regulators
#+AUTHOR: Amin Kasrou Aouam
#+SUBTITLE: Genome Biology
#+PANDOC_OPTIONS: pdf-engine:xelatex
#+PANDOC_METADATA: theme:metropolis
* Introduction
- /Ambystoma mexicanum/
- No metaphormosis
- Extensive regeneration abilities

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#+caption: Axolotl
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[[./assets/axolotl.jpg]]
* Genome characteristics
- Large genome: *32 Gb*
- High number of repeats: ~65%
- Mostly long terminal repeats (LTR)

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#+caption: Major repeat classes
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[[./assets/repeats.png]]
* Methods
- PacBio + Illumina
- Development of a novel genome assembler (MARVEL)
- Thorough assessment of the genome assembly
* Genome annotation and analysis
- Protein-coding genes: ~23.000
- Large median intron size: x13 human
- Intron size varies in developmental genes
- Identification of 5 transcripts

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#+caption: Median intron sizes
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[[./assets/introns.png]]
* Comparative genomics analysis
- Analysis of homologs: *Pax* family
- Deletion of Pax3: functionality present in Pax7
- Mutation experiments: CRISPR and TALEN

#+caption: Effect of a Pax7 mutation
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[[./assets/knock-out.png]]
* Conclusion
- Sequencing and annotation of a challenging organism
- Identification of limb regeneration transcripts
- Foundation to investigate gene regulation in regeneration