Inference-of-the-genes-in-the-ancestor-of-amniotes-and-the-genomic-basis-for-the-origin-of-the-egg

Inference of the genes in the ancestor of amniotes and the genomic basis for the origin of the egg

Amniotes are the first fully terrestrial vertebrate animals with several evolutionary innovations in their common ancestor that allowed them to become fully independent of the aquatic environment, including a more complex egg with shell and additional structures. During evolution, organisms’ form and functions evolve, and so do their genomes, which are the ultimately responsible for the observed changes. In fact, genomes are evolutionarily labile and experience changes in gene content and structure. This project aims to investigate the genomic basis for the origin of amniotes and their evolutionary innovations. From a bioinformatic point of view, this work involves: (i). choosing the highest quality vertebrate genomes to use in our analysis; (ii). estimating the genes that originated in the common ancestor of reptiles, birds and mammals by searching for sequence similarity and clustering of homologous genes; (iii). functionally characterizing the novel genes that originated in the common ancestor of amniotes and identifying any relationship with the origin of the amniote egg.

Structure followed of the data published:

-Selection_Of_Species

     *Genomes.tar.gz

     *all_proteomes_db.tar.gz

-Phylogenetic_Aware_Parsing_Script

     *Searching_Protein_Sequence_Similarities_With_DIAMOND

           +all_blastp_output.tar.gz

     *Gene_Clustering_In_HGs_With_MCL

           +mcxdeblast_all_blastp_output.tar.gz

           +mcl_all_blastp_output.tar.gz

     *Preparation_Of_PAPS_and_Inferring_Ancestral_And_Novel_Genes

           +Ancestral_Novel_HGs.tar.gz

-Removal_Of_False_Positives

     *Amniota_novel_seq.fa.tar.gz

-Annotation_With_GO_terms.tar.gz