Data for: "Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales" (Hallgren et al., 2025)
type: Dataset
description: Additional data for the article "Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales" (Hallgren et al., 2025). The data includes the following: - Sequence alignment files and tree files for all species phylogenies and gene phylogenies of the article. - Genome annotation data files for all genomes of the "core" and "extended" datasets of the article. Genome annotations have been generated as outlined in the article using the following tools and methods: DIAMOND blastp, eggNOG-mapper (emapper), GhostKOALA, InterProScan, and the reciprocal best blast hit algorithm (RBH). Datasets have been compressed into a .zip archive that contains the following folders: CORE-dataset_Gene_Annotations/ CORE-dataset_Gene_Phylogenies/ CORE-dataset_Species_Phylogenies/ EXTENDED-dataset_Gene_Annotations/ EXTENDED-dataset_Species_Phylogenies/ Some of these folders include files that in turn have been packaged into .tar.gz archives, which can be unpacked using the "tar" command in the Linux, macOS, or Windows (Windows 10 or later) command line. Description of datasets: 1. CORE-dataset_Gene_Annotations/ contains the following data files: all_genomes.annotations.tar.gz all_genomes.diamond-blastp.tar.gz all_genomes.emapper.annotations.tar.gz all_genomes.ghostKOALA-KOs.tar.gz all_genomes.interproscan.tar.gz all_genomes.RBH.tar.gz These .tar.gz packages contain the genome annotation data files for the genomes of the "core" dataset of the article. Genome annotations have been generated as outlined in the article using the following tools and methods: DIAMOND blastp, eggNOG-mapper (emapper), GhostKOALA, InterProScan, and the reciprocal best blast hit algorithm (RBH). Moreover, all annotations, with the exception of RBH annotations, have been compiled into an overview table (all_genomes.annotations.tar.gz). 2. CORE-dataset_Gene_Phylogenies/ contains the following folders: bchY/ creS_ALL/ creS_SUBSET/ pufM/ These folders corres…
citation: CreativeWork
  name: Joel Hallgren, Jennah E. Dharamshi, Alejandro Rodríguez-Gijón, Julia Nuy, Sarahi L. Garcia, Kristina Jonas. Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales. 2025. Nature Communications. 16: 11003.
citation: CreativeWork
  name: Joel Hallgren, Jennah E. Dharamshi, Alejandro Rodríguez-Gijón, Julia Nuy, Sarahi L. Garcia, Kristina Jonas. Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales. bioRxiv 2025.05.26.656076 [preprint]
conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
conditions of access: info:eu-repo/semantics/openAccess
contributor: Jennah Dharamshi
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Joel Hallgren
creator: Kristina Jonas
date modified: 2025-12-12
date published: 2025-06-19
language: English
is based on: https://github.com/jennahd/anno-utils/
is based on: https://github.com/jennahd/tree-utils/
is based on: https://github.com/j-hallgren/make-RBH/
is part of: https://doi.org/10.58141/5jzz-rp03
keywords: Natural Sciences
  type: DefinedTerm
  term code: 1
keywords: Biological Sciences
  type: DefinedTerm
  term code: 106
keywords: Cell Biology
  type: DefinedTerm
  term code: 10604
keywords: Microbiology
  type: DefinedTerm
  term code: 10606
keywords: Genetics and Genomics
  type: DefinedTerm
  term code: 10609
keywords: Bioinformatics and Computational Biology
  type: DefinedTerm
  description: Including: Modelling, Machine Learning
  term code: 10610
keywords: Ecology
  type: DefinedTerm
  description: Including: Biodiversity Conservation
  term code: 10611
keywords: Biological Systematics
  type: DefinedTerm
  term code: 10612
keywords: Evolutionary Biology
  type: DefinedTerm
  term code: 10615
keywords: phylogenetic tree
keywords: microbiology
keywords: phylogenetic relationship
keywords: phylogenetic diversity
keywords: bacteria
keywords: DNA sequence analysis
keywords: microbial ecology
keywords: phylogenetic analysis
keywords: bacterial diversity
keywords: bioinformatics
keywords: cell biology
keywords: genome
  type: DefinedTerm
  description: An organism`s genetic complement as represented in its DNA or, in some cases, its RNA.
  term code: 64570
keywords: microbiology
  type: DefinedTerm
  term code: 47420
keywords: parvularculaceae garrity et al., 2003
keywords: caulobacterales henrici & johnson, 1935
keywords: alphaproteobacteria garrity et al., 2006
keywords: hyphomonadaceae lee et al., 2005
keywords: caulobacteraceae henrici & johnson, 1935
keywords: caulobacter vibrioides henrici & johnson, 1935
keywords: Caulobacter crescentus (syn. Caulobacter vibrioides)
license: https://creativecommons.org/licenses/by/4.0/
publisher: Stockholm University
distribution: data/REPOSITORY_FILES.zip
  type: DataDownload
  additional type: data
  conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
  conditions of access: info:eu-repo/semantics/openAccess
  content size: 928329322
  encoding format: application/zip
distribution: documentation/README.txt
  type: DataDownload
  additional type: documentation
  conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
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version: 1

PropertyValue
property ID: DOI
value: 10.58141/0bz5-dc62

PropertyValue
property ID: DOI
value: 10.1038/s41467-025-65642-x

PropertyValue
property ID: DOI
value: 10.1101/2025.05.26.656076

Jennah Dharamshi
type: Person
affiliation: Uppsala University
family name: Dharamshi
given name: Jennah

Uppsala University
type: Organization

Joel Hallgren
type: Person
affiliation: Stockholm University
family name: Hallgren
given name: Joel

Stockholm University
type: Organization
department: Department of Molecular Biosciences, The Wenner-Gren Institute

Kristina Jonas
type: Person
affiliation: Stockholm University
family name: Jonas
given name: Kristina

English
type: Language
alternate name: eng

phylogenetic tree
type: DefinedTerm
description: [Henderson's] diagram like a family tree that represents evolutionary relation­ships between different taxa or between different proteins.
term code: 21655

microbiology
type: DefinedTerm
description: [GEMET] The science and study of microorganisms, including protozoans, algae, fungi, bacteria, viruses, and rickettsiae.
term code: 21641

phylogenetic relationship
type: DefinedTerm
term code: 21645

phylogenetic diversity
type: DefinedTerm
description: [Beáta Faller] Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species.
term code: 21677

bacteria
type: DefinedTerm
description: [Henderson's] n. superkingdom or domain of prokaryotic microorganisms containing all prokaryotes that are not members of the Archaea. Distinguished from the Archaea on the basis of molecular phylogenetics and biochemistry. The Bacteria is an ex­tremely metabolically and ecologically diverse group of unicellular microorgan­isms, free-living in soil and water or as parasites and saprophytes of plants and animals, the parasitic forms causing many familiar infectious diseases. Bacteria typically possess cell walls, and reproduce by binary ﬁssion or asexual endospores and also transfer genetic material by sexual processes (conjugation) and by virus (bacteriophage)-mediated transfer (transduction). see Appendix 5 for the main groups distinguished within the Bacteria, which all have individual entries in the dictionary.
term code: 20662

DNA sequence analysis
type: DefinedTerm
term code: 20201

microbial ecology
type: DefinedTerm
description: the ecology of microorganisms: their relationship with one another and with their environment.
term code: 77

phylogenetic analysis
type: DefinedTerm
description: [Thomas M. Keane] Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families.
term code: 21638

bacterial diversity
type: DefinedTerm
term code: 22062

bioinformatics
type: DefinedTerm
description: Avser insamling, behandling och analys av biologisk och medicinsk information.
term code: p15748

cell biology
type: DefinedTerm
term code: p18492

parvularculaceae garrity et al., 2003
type: DefinedTerm
term code: 626BV

caulobacterales henrici & johnson, 1935
type: DefinedTerm
term code: W5

alphaproteobacteria garrity et al., 2006
type: DefinedTerm
term code: 7H

hyphomonadaceae lee et al., 2005
type: DefinedTerm
term code: 62583

caulobacteraceae henrici & johnson, 1935
type: DefinedTerm
term code: 7TK

caulobacter vibrioides henrici & johnson, 1935
type: DefinedTerm
term code: RX97