Cladophorales Plastids Sequence Data and Supplementary

Data for article "Stepwise evolutionary transitions in Cladophorales plastid genomes reveals origins of hairpin chromosomes"<br>Files and Folders:<br>Okellya_plastids.fastaFast file of plastid sequences of Okellya marina and Okellya sp. SL. <br>Plastid_chromosomes.csv:CSV file of nr90 chromosomes assembled from Aegagropila linnaei and Chaetomorpha tokyoensis. Each row contains the raw assembled sequence of each chromosome (in which ends may be overlapping), non-overlapping unit sequence, GC content and genes detected. Details of start/stop coordinates or if genes detected are functional or pseudogenes are not included. Gene_annotations.csv:CSV file of best gene copies found in Aegagropila linnaei and Chaetmorpha tokyoensis chromosomes, determined by BLASTX e-values to other green algae, and genes present in Okellya marina and Okellya sp. SL plastid genomes. Each row contains the nucleotide sequence, translated sequence, full matching transcript sequence if present (for A. linnaei and C. tokyoensis), chromosome gene copy is found in (for A. linnaei and C. tokyoensis) and relevant notes. Note that exact start codons are uncertain in all species. <br>Phylogeny:Data for ML phylogeny. AA files were aligned with mafft (--linsi) and trimmed with trimAl (-gt 0.8). <br>Codon_alignments: Data for dN/dS analysis. Some Cladophorales species with partial sequences have been removed. Codon-aware alignments have internal TAG codons changed to NNN. AA files were aligned with mafft (--linsi) and codon-aware alignments made with PAL2NAL (https://www.bork.embl.de/pal2nal/).