EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

Abstract

Background Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches. Results EasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson–Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines. Conclusions EasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github (https://github.com/zdf1987/EasyCGTree4).

Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae

“…In order to assess the phylotaxonomy of the family ‘ Rhodobacteraceae ’ and assign the 12 isolates into reasonable taxonomic positions, the program hmmsearch from the hmmer software package (http://hmmer.org/) was used for homologous gene calling of the four gene sets mentioned above, Clustal Omega [38] for multiple sequence alignments, trimAl [39] for trimming and conserved region selection, FastTree [40] and iq-tree [41] for phylogeny inference, and consense from the Phylip software package [42] was used to summarize a CS tree from gene trees. This workflow was implemented automatically using the pipeline EasyCGTree (https://github.com/zdf1987/EasyCGTree4) [37]. In this study, 16 different combinations of the four gene sets (rp1, rp2, bac120 and rhodo268), two tree-making approaches (SM and CS) and two phylogeny inference tools (FastTree and iq-tree ) were used to perform phylogenomic analysis.…”

“…Subsequently, amino acid sequences of each core gene cluster were gathered up into a single file from the proteomes of related genomes. Finally, the Perl (http://hmmer.org/) script ‘BuildHMM.pl’ in the EasyCGTree package (https://github.com/zdf1987/EasyCGTree4) [37] was used to generate profile HMM files for the rhodo268 gene set.…”

Ruegeria marisflavi sp. nov. and Ruegeria aquimaris sp. nov., isolated from seawater of the Yellow Sea

“…Genome-based phylogeny of the supermatrix approach from protein sequences of the bac120 gene set (120 single-copy genes prevalent in Bacteria ) was reconstructed by using EasyCGTree version 4.1 (https://github.com/zdf1987/EasyCGTree4) [3, 33]. The bac120 tree indicated that strains WL0004 T and XHP0148 T clustered together with R. marina CGMCC 1.9108 T and were close to the cluster formed by R. alba 1NDH52C T and R. pomeroyi DSS-3 T ().…”

Actomonas aquatica gen. nov., sp. nov., a marine lineage in the phylum Verrucomicrobiota with genetic potential for carbon and nitrogen fixation

“…As for the phylogenetic analysis based on the bac120 gene set (Fig. 3), 64 genomes (45 from type strains, one outgroup, and 18 from type strains) were used as an input of the pipeline EasyCGTree [39], and two isolates that shared 16S rRNA gene identities of >95 % against strain WL0086 T were excluded because of a low level of completeness. The genome of Opitutaceae bacterium AH-707-J18 (GCA_028257465.1) was derived from single-cell amplified genome sequencing with a completeness of 37.64 %, while that of uncultured bacterium FRAM_WSC20_S10_SRF_bin_82 was derived from metagenome sequencing (GCA_949373025.1) with a completeness of 64.19 %.…”