Horizontal gene transfer and gene loss drive the divergent evolution of metabolic versatility of Micrarchaeota
Creators: name: RAO, YANGZHI
Publisher: name: Zenodo
Year: 2024

description: General Description

Repository with all analyses described in our paper: Horizontal gene transfer and gene loss drive the divergent evolution of metabolic versatility of Micrarchaeota. 

Please cite this work if it can be apply to your study.

Abstract

The DPANN superphylum represents a deep-branching radiation of Archaea with small cell and genome sizes. Most DPANN lineages were predicted or validated to be host-dependent. However, a departure from the common view, certain lineages have substantial biosynthetic capacities and are potentially less dependent on hosts or even free-living. Here, we reconstructed 163 Ca. Micrarchaeota genomes, comprising 48 assigned to previously undescribed orders and 115 affiliated with known orders. Investigation of the genetic repertoire reveals substantial metabolic versatility in Norongarragalinales, Wunengarchaeales-associated lineages, and Anstonellales, as evidenced by encoding complete or near complete glycolysis and de novo biosynthetic pathways of nucleotide, amino acid, co-factor, and cell envelope. We classified these genes as metabolic versatility proteins (MVPs) and proposed that their extensive presence in Norongarragalinales suggests a potential host-independent lifestyle. Reconstruction of evolutionary history revealed that free-living was not an ancestral feature in the last common ancestors of any DPANN lineages at the order level. They evolved from symbionts into less host-dependant organisms through the gradual acquisition of MVPs, driven mainly by horizontal gene transfer. Several Micrarchaeota lineages with streamlined genomes experienced reductive evolution due to thermal adaptation. Together, we depict the comprehensive panorama of the evolutionary history of this phylum.

Repository Contents

1_Figures_and_Tables folder contains all figures and tables of this study including:



Figs. 1-4

Supplementary Figs. 1-30

Supplementary Tables 1-12


2_Genome_files folder includes all Micrarchaeota MAGs and protein files generated in this study:



1_Micra_163_genome_files: original contigs of each MAG

2_Micra_163_protein_files: protein files generated by Prodigal (pro.fa)


3_Genome_annotation folder contains annotation files of 163 MAGs



1_Micra_163_genomes_arCOG_annotation folder: output of arCOG annotation of each MAG

2_Micra_163_genomes_kofam_annotation folder: output of kofam annotation of each MAG

3_Micra_163_genomes_Pfam_annotation folder: domain output of Pfam annotation of each MAG

4_Micra_163_genomes_hydDB_annotation folder: output of hydDB annotation of each MAG

5_Micra_163_genomes_annotation_concatenated.txt: a concatenated file of arCOG, kofam, and hydDB annotation corresponding to the CDSs of each MAG


4_Phylogeny_and_ALE_files folder includes the ALE input and output files folder and the MSA file for phylogenetic construction in Fig. 2:



ALE folder: 



1_species.3.tre file: species tree that generated from species tree from Fig.2 by removing genomes with <90% completeness or >5% contamination

2_ale_gene_tree: a folder containing all gene tree files used for reconciliation

3_uml_rec: a folder containing all uml_rec files generated by ALE

4_uTs: a folder containing all uTs files generated by ALE



GTDB.ar53.markers.MSA.fa: MSA file for tree construction in Fig. 2


5_Commands_and_scripts folder contains the main commands and scripts used to generate analyses and figures for this study



0.micra_code.R: R codes to process tables and generate figures in this study

1.all.micra.aa.propotion.txt: Amino acid usages of all Micrarchaeota genomes used in Fig. S30

2.metabolic.profiles.all.archaea.txt: a table of the proportion of genes processed by different lineages to generate metabolic profile heat map in Fig. 3

3.ordination.all.micra.arcog.csv: table for t-SNE ordination based on occurrences of arCOGs for Fig. S3

4.ordination.all.micra.ko.txt: table for t-SNE ordination based on occurrences of KOs for Fig. S3

5.all.micra.genome.stats.txt: table of genome statistics for all genomes used for Fig. S2

6.micra.crisprcas.summary.txt: table of screened CRISPR-Cas used for generating gene clusters of Fig. S6

7.all.gtdb.ar53.reroot.nwk.txt: tree reroot in DPANN used for evolutionary history inference

8.dtips.txt: a list of tree tips with genomes of <90% completeness or >5% contamination to remove from analyses

9.all.gtdb.ar53.reroot.evol.494.tre.nwk: tree with only branches of high-quality genomes

10.all.gtdb.ar53.reroot.reordered.evol.494.tre.txt: reorder tree on iTOL to generate favorable tree order in accordance with Fig. 2

11.all.gtdb.ar53.evol.reroot.reordered.494.distroot.tre: rate smoothed tree to align tree tips for Fig. 4

node.events.count.txt: ratio of inferred evolutionary events parsed from ALE results

node.presence.col.txt: the presence of each protein family ancestral nodes parsed from ALE results

node.dup.col.txt: duplication events of each protein family occurred on ancestral nodes parsed from ALE results

node.hgt.col.txt: HGT events of each protein family occurred on ancestral nodes parsed from ALE results

node.loss.col.txt: gene loss events of each protein family occurred on ancestral nodes parsed from ALE results

node.spec.col.txt: origination events of each protein families occurred on ancestral nodes parsed from ALE results

pathway_evol_rate.txt: ratio of pathway completeness in each ancestral node