HomeoWorms

Analysis Of The Distribution Of Developmental Gene Transcripts In The Intact Body Of The Annelids Pygospio elegans, Platynereis dumerilii And Arenicola marina

This repository is contain the results of a project conducted at the Bioinformatics Institute, aimed to determine the distribution of transcripts coding developmental genes in three annelid species with different regenerative abilities.

General workflow

• Finding sequences containing homeobox domain(blastp)
• Annotation of selected sequences functionally and finding possible orthologs (eggnog mapper v.2.0.0)
• Conducting an phylogenetic analysis of possible orthologs (MAFFT v.7.526)
• Performing transcript distribution analysis (Python)

Content description

Notebooks

• Phylo.ipynb - the notebook contains code for constructing phylogenetic trees
• main.ipynb - the notebook contains steps of transcript distribution analysis: selection of transcripts according to annotation, code for constructing heatmaps

Folders

data

• ANTP.fasta, all_prot.fasta, paired.fasta - files contain sequences for alignment in fasta format
• mafft.tree, NKL.tre - phylogenetic trees in Newick format for visualization
• Amar_maNOG.emapper.annotations, Pele_maNOG.emapper.annotations, Pdum_maNOG.emapper.annotations - eggNOG-mapper-annotated transcripts

imgs

• my_tree.png - visualization of the phylogenetic tree for all analyzed transcripts
• DiffExp1.png - hitmap of putative developmental genes found only in Pygospio elegans
• DiffExp2.png - hitmap of putative developmental genes found in annelids with posterior regeneration
• DiffExp3.png - hitmap of putative developmental genes found in all three annelids

Results

• Possible candidate genes to explain anterior regeneration could be BARX1, GSC
• Possible candidate gene to explain posterior regenerationn could be caudal

Authors

• Belikova Angelina - BI student
• Elena Novikova - supervisor
• Maxim Nesterenko - supervisor

If you have any questions or suggestions regarding this work, feel free to adress via email: Belikova Angelina - kiit8321@gmail.com