Published August 14, 2022 | Version 1.0
Dataset Open

Data from the article "Plastome sequencing of South American Podocarpus species reveals low rearrangement rates despite ancient Gondwanan disjunctions"

Authors/Creators

  • 1. INIBIOMA, Universidad Nacional del Comahue, CONICET, Quintral 1250, Bariloche (8400), Argentina
  • 2. Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, R. Prof. Moraes Rego, s/n, CDU, 50670-420, Recife, PE, Brazil

Description

Input data, intermediate and final analysis output files associated to the manuscript "Plastome sequencing of South American Podocarpus species reveals low rearrangement rates despite ancient Gondwanan disjunctions"

We sequenced the plastomes of four South American species of Podocarpus from Patagonia, southern Yungas, and Brazilian subtropical forests: P. nubigenus, P. parlatorei, P. salignus and P. selowii. We compared their plastomes to those published from Brazil, Africa, New Zealand, and Southeast Asia, along with representatives from other genera within Podocarpaceae as outgroups. The four newly sequenced plastomes ranged in size between 133,791 bp and 133,991 bp. Gene content and order among chloroplasts from South American, African and Asian Podocarpus were conserved and different from the plastome of P. totara, from New Zealand. Most genes showed substitution patterns consistent with a conservative selective regime. Phylogenies inferred from either complete sequences or protein coding regions were mostly congruent with previous studies, but showed earlier branching of P. salignus, P. totara and P. sellowii.

Notes

"ARC_output_files.tar.gz" includes, for each of the four species: - ARC_config.txt: the ARC configuration file -contigs.fasta: the contigs assembled by ARC -log.txt: the log file of the ARC run -mapping_stats.tsv: the number of reads used by ARC for plastome assembly -target_summary_table.tsv: the summary of reference assembly, reads used, number of contigs and contig length "CODEML_analysis.tar.gz" includes - A "cds" folder including aligments for each of 83 coding genes in PHYLIP format, plus a file "all.cds" including all coding sequences for all species and a file "podocarpus.all.cds" including all coding sequences for Podocarpus species only. - A "family_level_analysis" containing all files generated by CODEML for the analysis including all 17 species from Podocarpaceae - A "genus_level_analysis" containing all files generated by CODEML for the analysis including the 9 species from Podocarpus "Geneious_assembly_files.tar.gz", for each of the four species: - A .fasta file with the final plastome assembly for the species in FASTA format. - A .gb file with the final plastome assembly for the species in GenBank format. - A .geneious file with the final plastome assembly including annotations for the species in Geneious 8.0 format. - A .tbl file with the annotations for the final plastome assembly for the species in GenBank Feature Table File format. "Mauve_Alignment.tar.gz" includes the output files for the progressiveMauve whole genome alignment, as implemented in Geneious 8.0

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Additional details

Related works

Is published in
Journal article: 10.1007/s11033-022-07969-y (DOI)

References