53 lines
1.4 KiB
Org Mode
53 lines
1.4 KiB
Org Mode
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#+TITLE: The axolotl genome and the evolution of key tissue formation regulators
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#+AUTHOR: Amin Kasrou Aouam
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#+SUBTITLE: Genome Biology
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#+PANDOC_OPTIONS: pdf-engine:xelatex
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#+PANDOC_METADATA: theme:metropolis
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* Introduction
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- /Ambystoma mexicanum/
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- No metaphormosis
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- Extensive regeneration abilities
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\vspace{1.3cm}
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#+caption: Axolotl
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#+attr_html: :width 50% :height :30%
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[[./assets/axolotl.jpg]]
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* Genome characteristics
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- Large genome: *32 Gb*
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- High number of repeats: ~65%
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- Mostly long terminal repeats (LTR)
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\vspace{2cm}
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#+caption: Major repeat classes
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#+attr_html: :width 50% :height :40%
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[[./assets/repeats.png]]
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* Methods
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- PacBio + Illumina
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- Development of a novel genome assembler (MARVEL)
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- Thorough assessment of the genome assembly
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* Genome annotation and analysis
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- Protein-coding genes: ~23.000
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- Large median intron size: x13 human
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- Intron size varies in developmental genes
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- Identification of 5 transcripts
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\vspace{1.5cm}
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#+caption: Median intron sizes
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#+attr_html: :width 50% :height :40%
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[[./assets/introns.png]]
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* Comparative genomics analysis
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- Analysis of homologs: *Pax* family
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- Deletion of Pax3: functionality present in Pax7
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- Mutation experiments: CRISPR and TALEN
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#+caption: Effect of a Pax7 mutation
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#+attr_html: :width 60% :height :50%
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[[./assets/knock-out.png]]
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* Conclusion
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- Sequencing and annotation of a challenging organism
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- Identification of limb regeneration transcripts
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- Foundation to investigate gene regulation in regeneration
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