| REAGENT or RESOURCE |
SOURCE |
IDENTIFIER |
| Chemicals, Peptides, and Recombinant Proteins |
| Phenol:Chloroform:Isoamyl Alcohol |
Sigma |
Cat#P2069 |
| Critical Commercial Assays |
| NEBNext Ultra DNA Library Prep |
NEB |
Cat#E7370L |
| TruSeq DNA PCR-free Library Preparation Kit |
Illumina |
Cat#20015963 |
| Nextera Mate Pair Sample Preparation Kit |
Illumina |
Cat#FC-132–1001 |
| Quant-iT PicoGreen ds DNA Assay Kit |
Quant-iT |
Cat#P11496
|
| Deposited Data |
| De novo assemblies |
DDBJ/ENA/GenBank |
See Table S1
|
| Genome annotations |
This study |
Figshare data repository: 10.6084/m9.figshare.5854692 |
| Data matrices |
This study |
Figshare data repository: 10.6084/m9.figshare.5854692 |
| Phylogenetic trees |
This study |
Figshare data repository: 10.6084/m9.figshare.5854692 |
| Alignments and ML trees for horizontally acquired genes |
This study |
Figshare data repository: 10.6084/m9.figshare.5854692 |
| Metabolic trait data |
This study |
Figshare data repository: 10.6084/m9.figshare.5854692 |
| Trait ancestral character state reconstructions |
This study |
Figshare data repository: 10.6084/m9.figshare.5854692 |
| Experimental Models: Organisms/Strains |
| 343 sampled species |
This study |
See Table S1
|
| Software and Algorithms |
| iWGS v1.1 |
Zhou et al., 2016 |
https://github.com/zhouxiaofan1983/iWGS/ |
| Trimmomatic v0.33 |
Bolger et al., 2014 |
http://www.usadellab.org/cmsUpage=trimmomatic |
| Lighter v1.1.1 |
Song et al., 2014 |
https://github.com/mourisl/Lighter/ |
| KmerGenie v1.6982 |
Chikhi and Medvedev, 2014 |
http://kmergenie.bx.psu.edu/ |
| ABYSS v1.5.2 |
Simpson et al., 2009 |
https://github.com/bcgsc/abyss |
| DISCOVAR r51885 |
Weisenfeld et al., 2014 |
https://software.broadinstitute.org/software/discovar/blog/ |
| MASURCA v2.3.2 |
Zimin et al., 2013 |
https://github.com/alekseyzimin/masurca |
| SGA v0.10.13 |
Simpson and Durbin, 2012 |
https://github.com/jts/sga |
| SOAPdenovo2 v2.04 |
Luo et al., 2012 |
https://github.com/aquaskyline/SOAPdenovo2 |
| SPADES v3.7.0 |
Bankevich et al., 2012 |
http://cab.spbu.ru/software/spades/ |
| QUAST v4.4 |
Gurevich et al., 2013 |
https://github.com/ablab/quast |
| NextClip v0.8 |
Leggett et al., 2014 |
https://github.com/richardmleggett/nextclip/ |
| ALLPATHS-LG v51828 |
Gnerre et al., 2011 |
ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/ |
| BUSCO v2.0.1 |
Waterhouse et al., 2018 |
https://busco.ezlab.org/ |
| OrthoDB Version 9 |
Zdobnov et al., 2017 |
https://busco.ezlab.org/ |
| AUGUSTUS v 3.2.2 |
Stanke and Waack, 2003. |
http://bioinf.uni-greifswald.de/augustus/downloads/ |
| MAKER v2.31.8 |
Holt and Yandell, 2011 |
http://www.yandell-lab.org/software/maker.html |
| GeneMark-ES v4.32 |
Ter-Hovhannisyan et al., 2008 |
http://exon.gatech.edu/GeneMark/gmes_instructions.html |
| SNAP v2013–11-29 |
Korf, 2004 |
http://korflab.ucdavis.edu/software.html |
| RepeatMasker v4.0.6 |
Institute for Systems Biology |
http://www.repeatmasker.org |
| Cuffcompare v2.2.1 |
Trapnell et al., 2012 |
https://github.com/gpertea/CuffCompare |
| MAFFT v7.299 |
Katoh and Standley, 2013 |
https://mafft.cbrc.jp/alignment/software/ |
| Pal2Nal v14 |
Suyama et al., 2006 |
http://www.bork.embl.de/pal2nal/#Download |
| PAML V4.8 |
Yang, 2007 |
http://abacus.gene.ucl.ac.uk/software/paml.html |
| MCMCtree v. 4.9 |
Yang, 2007 |
http://abacus.gene.ucl.ac.uk/software/paml.html |
| OrthoMCL v2.0 |
Li et al., 2003 |
http://orthomcl.org/common/downloads/software/v2.0/ |
| Phyutility v2.2.6 |
Smith and Dunn, 2008 |
https://github.com/blackrim/phyutility |
| FastTree v2.1.9 |
Price et al., 2010 |
http://www.microbesonline.org/fasttree/ |
| PhyloTreePruner v1.0 |
Kocot et al., 2013 |
http://sourceforge.net/projects/phylotreepruner |
| trimAl v1.4 |
Capella-Gutierrez et al., 2009 |
http://trimal.cgenomics.org/ |
| IQ-TREE v1.5.1 |
Nguyen et al., 2015 |
http://www.iqtree.org/ |
| phylomeDB v4 |
Huerta-Cepas et al., 2014 |
ftp://phylomedb.org/phylomedb/phylomes/phylome_0005/ |
| MARE v0.1.2 |
Zoological Research Museum Alexander Koenig |
http://mare.zfmk.de |
| RAxML v8.2.3 |
Stamatakis, 2014 |
https://sco.h-its.org/exelixis/web/software/raxml/index.html |
| ExaML v3.0.17 |
Kozlov et al., 2015 |
https://sco.h-its.org/exelixis/web/software/examl/index.html |
| ASTRAL-II v4.10.2 |
Mirarab and Warnow, 2015 |
https://github.com/smirarab/ASTRAL |
| MEGA7 |
Kumar et al., 2016 |
https://www.megasoftware.net/ |
| iTOL v3 |
Letunic and Bork, 2016 |
https://itol.embl.de/help.cgi#batch |
| BayesTraits v3 |
Pagel et al., 2004 |
http://www.evolution.rdg.ac.uk/BayesTraitsV3.0.1/BayesTraitsV3.0.1.html |
| R package igraph |
Csardi and Nepusz, 2006 |
https://cran.r-project.org/web/packages/igraph/index.html |
| R package infotheo |
Meyer, 2008 |
https://cran.r-project.org/web/packages/infotheo/index.html |
| R package minet |
Meyer et al., 2008 |
https://www.bioconductor.org/packages/release/bioc/html/minet.html |
| R package wgcna |
Langfelder and Horvath, 2008 |
https://cran.r-project.org/web/packages/WGCNA/index.html |
| R package topgo |
Alexa and Rahnenfuhrer, 2016 |
https://bioconductor.org/packages/release/bioc/html/topGO.html |
| GhostKOALA |
Kanehisa et al., 2016a |
https://www.kegg.jp/ghostkoala/ |
| ARACNE |
Margolin et al., 2006 |
https://bioconductor.org/packages/release/data/experiment/html/aracne.networks.html |
