Phylogenomics and female reproductive morphology reframe the classification of the Halymeniales (Rhodophyta)
Phylogenetic datasets associated with the study "Phylogenomics and female reproductive morphology reframe the classification of the Halymeniales (Rhodophyta)", Leliaert et al. ------- Content ------- Taxon sampling -------------- 01_taxon_sampling.tsv: taxon sampling, collection
Phylogenetic datasets associated with the study
"Phylogenomics and female reproductive morphology reframe the classification of the Halymeniales (Rhodophyta)",
Leliaert et al.
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Taxon sampling -------------- 01_taxon_sampling.tsv: taxon sampling, collection information, and GenBank accession numbers Annotated organellar genomes and nuclear rDNA cistrons ------------------------------------------------------ 02_ cpDNA_annotated_genomes.txt: annotated chloroplast genomes, GenBank format 03_cpDNA_published_genomes_reannotated.gb.txt: reannotated (corrections where needed) published chloroplast genomes, GenBank format 04_cpDNA_gene_content.csv: gene content of Halymeniales chloroplast genomes 05_ mtDNA_annotated_genomes.txt: annotated mitochondrial genomes, GenBank format 06_ nrDNA_annotated.txt: annotated nrDNA sequences, GenBank format Sequence alignments ------------------- 07_cpDNA_65taxa_170genes.fasta: concatenated alignemnt of 170 plastid genes, 65 taxa 08_cpDNA_65taxa_170genes_partitionbygene.nex: nexus file including gene partitions 09_mtDNA_66taxa_23genes.fasta: concatenated alignemnt of 23 mitochondrial genes, 66 taxa 10_mtDNA_66taxa_23genes_partitioned.nex: nexus file including gene partitions 11_rDNA_63taxa.fasta: concatenated alignment of SSU and LSU rDNA sequences, 63 taxa 12_rDNA_63taxa_trimAl.fasta: trimmed alignment using trimAl 13_rbcL_339taxa.fasta: rbcL alignment: rbcL alignment, 339 taxa, used for unconstrained analysis 14_rbcL_cpDNA_330taxa.fasta: rbcL + cpDNA alignment used for phylogenetic placement analysis
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Additional data
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Raw sequence data (Illumina fastq files), annotated organellar genomes and nrDNA sequences have been deposited in GenBank under BioProject PRJNA1489531 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1489531), and accession numbers PZ694660 – PZ694714 (chloroplast genomes), PZ694715 – PZ694768 (mitochondrial genomes), and PZ694769 – PZ694824 (nuclear rDNA cistrons).
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