In:
PLOS Biology, Public Library of Science (PLoS), Vol. 19, No. 7 ( 2021-7-29), p. e3001309-
Abstract:
Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome of Paramecium tetraurelia , genes are interrupted by tens of thousands of unique intervening sequences called internal eliminated sequences (IESs), which have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of 9 Paramecium species (from approximately 100 Mb in Paramecium aurelia species to 〉 1.5 Gb in Paramecium caudatum ). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single copy in present-day genomes, we identified several families of mobile IESs, including nonautonomous elements acquired via horizontal transfer, which generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs in Paramecium . The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across the aurelia clade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution of Paramecium IESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression.
Type of Medium:
Online Resource
ISSN:
1545-7885
DOI:
10.1371/journal.pbio.3001309
DOI:
10.1371/journal.pbio.3001309.g001
DOI:
10.1371/journal.pbio.3001309.g002
DOI:
10.1371/journal.pbio.3001309.g003
DOI:
10.1371/journal.pbio.3001309.g004
DOI:
10.1371/journal.pbio.3001309.g005
DOI:
10.1371/journal.pbio.3001309.t001
DOI:
10.1371/journal.pbio.3001309.t002
DOI:
10.1371/journal.pbio.3001309.s001
DOI:
10.1371/journal.pbio.3001309.s002
DOI:
10.1371/journal.pbio.3001309.s003
DOI:
10.1371/journal.pbio.3001309.s004
DOI:
10.1371/journal.pbio.3001309.s005
DOI:
10.1371/journal.pbio.3001309.s006
DOI:
10.1371/journal.pbio.3001309.s007
DOI:
10.1371/journal.pbio.3001309.s008
DOI:
10.1371/journal.pbio.3001309.s009
DOI:
10.1371/journal.pbio.3001309.s010
DOI:
10.1371/journal.pbio.3001309.s011
DOI:
10.1371/journal.pbio.3001309.s012
DOI:
10.1371/journal.pbio.3001309.s013
DOI:
10.1371/journal.pbio.3001309.s014
DOI:
10.1371/journal.pbio.3001309.s015
DOI:
10.1371/journal.pbio.3001309.s016
DOI:
10.1371/journal.pbio.3001309.s017
DOI:
10.1371/journal.pbio.3001309.s018
DOI:
10.1371/journal.pbio.3001309.s019
DOI:
10.1371/journal.pbio.3001309.s020
DOI:
10.1371/journal.pbio.3001309.s021
DOI:
10.1371/journal.pbio.3001309.s022
DOI:
10.1371/journal.pbio.3001309.s023
DOI:
10.1371/journal.pbio.3001309.s024
DOI:
10.1371/journal.pbio.3001309.r001
DOI:
10.1371/journal.pbio.3001309.r002
DOI:
10.1371/journal.pbio.3001309.r003
DOI:
10.1371/journal.pbio.3001309.r004
DOI:
10.1371/journal.pbio.3001309.r005
DOI:
10.1371/journal.pbio.3001309.r006
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2021
detail.hit.zdb_id:
2126773-X