53 lines
1.4 KiB
Org Mode
53 lines
1.4 KiB
Org Mode
#+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
|
|
|
|
\vspace{1.3cm}
|
|
|
|
#+caption: Axolotl
|
|
#+attr_html: :width 50% :height :30%
|
|
[[./assets/axolotl.jpg]]
|
|
* Genome characteristics
|
|
- Large genome: *32 Gb*
|
|
- High number of repeats: ~65%
|
|
- Mostly long terminal repeats (LTR)
|
|
|
|
\vspace{2cm}
|
|
|
|
#+caption: Major repeat classes
|
|
#+attr_html: :width 50% :height :40%
|
|
[[./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
|
|
|
|
\vspace{1.5cm}
|
|
|
|
#+caption: Median intron sizes
|
|
#+attr_html: :width 50% :height :40%
|
|
[[./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
|
|
#+attr_html: :width 60% :height :50%
|
|
[[./assets/knock-out.png]]
|
|
* Conclusion
|
|
- Sequencing and annotation of a challenging organism
|
|
- Identification of limb regeneration transcripts
|
|
- Foundation to investigate gene regulation in regeneration
|