Cladophorales plastome data
Description
Okellya_plastids.fasta - fasta file of plastid sequences of Okellya marina and Okellya sp. SL. 18S.fasta - Nuclear 18S sequences for Okellya marina, Okellya sp. SL, Aegagropila linnaei and Chaetomorpha tokyoensis. Table_S2_Plastid_chromosomes.xlsx - nr90 chromosomes assembled from Aegagropila linnaei and Chaetomorpha tokyoensis. Each row contains the raw assembled sequence of each contig (in which ends may be overlapping), the extracted non-overlapping chromosome sequence, GC content, length and genes detected on original assembled sequence. Genes were detected by jackhmmer search of 6-frame translations to the UniProtKB/Swiss-Prot database. Details of start/stop coordinates or if genes detected are possibly functional or pseudogenes are not included. Note that as contigs are assembled from a large variant population, the exact chromosome sequence and length can differ slightly depending on the coordinates it is extracted from in the original assembly. Topology was noted as “Circular” if the chromosome originates from an over-assembly. If noted as “Unconfirmed, likely circular”, the assembly was linear but some reads aligned spanning each end in a manner that suggests similar circular chromosomes exist (i.e., the assembly was likely unable to close circularly due to a large variant population with sparse coverage). If noted as “Unconfirmed”, no evidence of circularity was found. Table_S1_Gene_annotations.xlsx- 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), the chromosome (or individual read) each gene copy is found in (for A. linnaei and C. tokyoensis) and relevant notes. Unknown ORFs found in minicircular genomes are not included. Note that start codons are uncertain in all species, and at times N-terminal homology is low, therefore exact N-terminal sequences should be taken with caution. 17_gene_phylogeny - Data for ML phylogeny. AA files were aligned with mafft (--linsi) and trimmed with trimAl (-gt 0.8). 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/).
Files
Institutions
- The University of MelbourneVictoria, Melbourne