This GitHub repository serves as a resource for the scripts and data utilized in the research article titled "ORFans in Mitochondrial Genomes of Marine Polychaete Polydora."
🪱 We have sequenced and analyzed the mitochondrial genome of Polydora cf. ciliata, a marine polychaete worm, as well as analysed the mitochondrial genomes of related taxa. During our investigation, we discovered regions that do not resemble standard metazoan mitochondrial DNA genes but lack stop codons in one of the reading frames in several related species, we refer to these regions as "ORFans.” Our study also includes the analysis of the phylogeny of the newly sequenced Polydora cf. ciliata, a detailed examination of ORFan regions, and various other aspects related to this research.
📁 Repository Contents:
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Scripts utilized for mitochondrial genome analysis, ORFan identification, data visualization and more:
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Script for Figure 1: CircularChromosome_gb_Polydora.R
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Scripts for Figure 2: Make_genome_aligments_and_trees.ipynb
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Scripts for Figure 3: ORFans_domains_and_conservation.ipynb, TMDs_and_hidrophobicity_plot.ipynb
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Script for Figure 4: DnDs_CAI_plot.R
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Scripts for Figures S2-S4: Make_genes_trees.ipynb
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Scripts for Figure S5 and ORFans detection: stopcodons_maps_scripts/
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Data: Utilized datasets, including mitochondrial genome sequences and annotations, ORFan sequences, phylogenetic analysis data