Abstract
Introduction: It has been proposed that the recently discovered
superphylum of Asgard archaea may represent a historical link/bridge
between the Archaea and Eukarya. The arrangement of genes in genomes is
a window to understand how organisms are related. In particular, the
translation machinery and the genes that encode the same have a long
evolutionary history. In order to gain further insight into the
evolutionary position of the Asgard archaea, the genome order of
ribosomal protein coding genes was analyzed. The Asgard archaea were
compared with non-Asgard archaeal and bacterial genomes. Results: A core
of co-occurring 15 genes belonging to the segment of the S10 and spc
cluster (which are characterized and established as operons in
Bacteria), was identified as conserved in gene order, arrangement and
genome location in Asgard archaea, non-Asgard archaea and Bacteria. This
core occurs as a complete set in the genomes of Lokiarchaeota MK-D1
(Candidatus Prometheoarchaeum syntrophicum), and Candidatus
Odinarchaeota archaeon LCB_4. The genome assemblies of the other Asgard
genomes are incomplete and occur in multiple contigs (>50)
and hence this cluster is found in sections across contigs, with a
section often either ending or beginning a contig. The cluster
organization is indicative of co-occurrence, if the genome was complete.
A second smaller cluster comprising the homologs of the most conserved
genes of the bacterial S10 operon/cluster namely, uS10-uL3-uL4-uL23-uL2
occurs independently on the Asgard genomes, separate from the rest, a
feature shared by many non-Asgard archaea as well. Other clusters. A new
cluster L7ae-infB was identified to co-occur with the minor S24e-S27ae
cluster in the two complete Asgard genomes. The L7ae-infB cluster
co-occurs with the S24e-S27ae cluster in some (non-Asgard) Crenarchaeota
(Desulfurococcacea) and Euryarchaeota (Methanobacteriaceae), while it
co-occurs with the (Alpha operon) L18e cluster in some (non-Asgard)
Euryarchaeota (Halobacteriaceae). Overall, the organization of the most
universal and highly conserved S10 and spc cluster in Asgard archaea
resembles that of the non-Asgard Thaumarchaeota and the DPANN group.
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