Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes.

Genome Biology and Evolution
Julia Brueckner, William F. Martin

Abstract

Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described fo...Continue Reading

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Citations

Jul 28, 2020·Frontiers in Microbiology·Josip Skejo, Damjan Franjević
Nov 26, 2020·Viruses·Tsu-Wang SunChuan Ku
Apr 17, 2021·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Michael Brandeis
Jun 3, 2021·International Journal of Molecular Sciences·Ahmad IbrahimDidier Raoult
Apr 24, 2021·Genome Biology and Evolution·Michael KnoppSven B Gould
May 9, 2021·Genome Biology and Evolution·Josip SkejoWilliam F Martin
Oct 17, 2021·FEBS Open Bio·Bhanu Pratap Singh ChouhanPaola Laurino

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Methods Mentioned

BETA
scanning electron microscopy

Software Mentioned

EMBOSS
MCL
rBBH
BLAST
blastp

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