DOI: 10.5061/dryad.j69p2
title: Data from: Horizontal gene transfer and genome evolution in Methanosarcina

description: Background: Genomes of Methanosarcina spp. are among the largest archaeal
 genomes. One suggested reason for that is massive horizontal gene transfer
 (HGT) from bacteria. Genes of bacterial origin may be involved in the
 central metabolism and solute transport, in particular sugar synthesis,
 sulfur metabolism, phosphate metabolism, DNA repair, transport of small
 molecules etc. Horizontally transferred (HT) genes are considered to play
 the key role in the ability of Methanosarcina spp. to inhabit diverse
 environments. At the moment, genomes of three Methanosarcina spp. have
 been sequenced, and while these genomes vary in length and number of
 protein-coding genes, they all have been shown to accumulate HT genes.
 However, previous estimates had been made when fewer archaeal genomes were
 known. Moreover, several Methanosarcinaceae genomes from other genera have
 been sequenced recently. Here, we revise the census of genes of bacterial
 origin in Methanosarcinaceae. Results: About 5 % of Methanosarcina genes
 have been shown to be horizontally transferred from various bacterial
 groups to the last common ancestor either of Methanosarcinaceae, or
 Methanosarcina, or later in the evolution. Simulation of the composition
 of the NCBI protein non-redundant database for different years
 demonstrates that the estimates of the HGT rate have decreased drastically
 since 2002, the year of publication of the first Methanosarcina genome.
 The phylogenetic distribution of HT gene donors is non-uniform. Most HT
 genes were transferred from Firmicutes and Proteobacteria, while no HGT
 events from Actinobacteria to the common ancestor of Methanosarcinaceae
 were found. About 50 % of HT genes are involved in metabolism. Horizontal
 transfer of transcription factors is not common, while 46 % of
 horizontally transferred genes have demonstrated differential expression
 in a variety of conditions. HGT of complete operons is relatively
 infrequent and half of HT genes do not belong to operons. Conclusions:
 While genes of bacterial origin are still more frequent in
 Methanosarcinaceae than in other Archaea, most HGT events described
 earlier as Methanosarcina-specific seem to have occurred before the
 divergence of Methanosarcinaceae. Genes horizontally transferred from
 bacteria to archaea neither tend to be transferred with their regulators,
 nor in long operons.
description: Orthology groups for
 Methanosarcinaceae speciesThis archive contains
 initial groups of orthologues proteins (GOPs) utilized in the
 research.Here you can find GOPs for 3 Methanosarcina species
 (Methanosarcina acetivorans CA, Methanosarcina barkeri Fusaro, and
 Methanosarcina mazei Go1) and 6 Methanosarcinaceae species: 3
 Methanosarcina and Methanococcoides burtonii DSM 6242, Methanohalobium
 evestigatum Z-7303, and Methanohalophilus mahii DSM 5219. GOPs were
 calculated by bidirectional best hits (BBHs) approach. The detailed
 description of method is provided in the original
 manuscript.GOPs.tarHorizontally transferred genes in Methanosarcina spp.This archive contains detailed information about horizontally transferred genes in Methanosarcina, such as list of genes of bacterial origin in 3 Methanosarcina species, corresponding alignments (produced by MUSCLE), neighbor-joining (NJ) trees with 100 bootstrap replicas generated by ClustalW software with default parameters (BLOSUM distance matrix), and a maximum-likelihood (ML) cladograms produced with PhyML v3.0 with default parameters.HGT_methanosarcina.tar