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Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.

ABSTRACT: Genome size varies greatly across angiosperms. It is well documented that, in addition to polyploidization, retrotransposon amplification has been a major cause of genome expansion. The lack of evidence for counterbalancing mechanisms that curtail unlimited genome growth has made many of us wonder whether angiosperms have a "one-way ticket to genomic obesity." We have therefore investigated an angiosperm with a well-characterized and notably small genome, Arabidopsis thaliana, for evidence of genomic DNA loss. Our results indicate that illegitimate recombination is the driving force behind genome size decrease in Arabidopsis, removing at least fivefold more DNA than unequal homologous recombination. The presence of highly degraded retroelements also suggests that retrotransposon amplification has not been confined to the last 4 million years, as is indicated by the dating of intact retroelements.

SUBMITTER: Devos KM

PROVIDER: S-EPMC186626 | biostudies-literature | 2002 Jul

REPOSITORIES: biostudies-literature

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Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.

Devos Katrien M KM Brown James K M JK Bennetzen Jeffrey L JL

Genome research 20020701 7

Genome size varies greatly across angiosperms. It is well documented that, in addition to polyploidization, retrotransposon amplification has been a major cause of genome expansion. The lack of evidence for counterbalancing mechanisms that curtail unlimited genome growth has made many of us wonder whether angiosperms have a "one-way ticket to genomic obesity." We have therefore investigated an angiosperm with a well-characterized and notably small genome, Arabidopsis thaliana, for evidence of ge ...[more]

PMID: 12097344

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Project description:BACKGROUND AND AIMS: Plant evolution is well known to be frequently associated with remarkable changes in genome size and composition; however, the knowledge of long-term evolutionary dynamics of these processes still remains very limited. Here a study is made of the fine dynamics of quantitative genome evolution in Festuca (fescue), the largest genus in Poaceae (grasses). METHODS: Using flow cytometry (PI, DAPI), measurements were made of DNA content (2C-value), monoploid genome size (Cx-value), average chromosome size (C/n-value) and cytosine + guanine (GC) content of 101 Festuca taxa and 14 of their close relatives. The results were compared with the existing phylogeny based on ITS and trnL-F sequences. KEY RESULTS: The divergence of the fescue lineage from related Poeae was predated by about a 2-fold monoploid genome and chromosome size enlargement, and apparent GC content enrichment. The backward reduction of these parameters, running parallel in both main evolutionary lineages of fine-leaved and broad-leaved fescues, appears to diverge among the existing species groups. The most dramatic reductions are associated with the most recently and rapidly evolving groups which, in combination with recent intraspecific genome size variability, indicate that the reduction process is probably ongoing and evolutionarily young. This dynamics may be a consequence of GC-rich retrotransposon proliferation and removal. Polyploids derived from parents with a large genome size and high GC content (mostly allopolyploids) had smaller Cx- and C/n-values and only slightly deviated from parental GC content, whereas polyploids derived from parents with small genome and low GC content (mostly autopolyploids) generally had a markedly increased GC content and slightly higher Cx- and C/n-values. CONCLUSIONS: The present study indicates the high potential of general quantitative characters of the genome for understanding the long-term processes of genome evolution, testing evolutionary hypotheses and their usefulness for large-scale genomic projects. Taken together, the results suggest that there is an evolutionary advantage for small genomes in Festuca.

Project description:Template-dependent RNA replication mechanisms render picornaviruses susceptible to error catastrophe, an overwhelming accumulation of mutations incompatible with viability. Viral RNA recombination, in theory, provides a mechanism for viruses to counteract error catastrophe. We tested this theory by exploiting well-defined mutations in the poliovirus RNA-dependent RNA polymerase (RDRP), namely, a G64S mutation and an L420A mutation. Our data reveal two distinct mechanisms by which picornaviral RDRPs influence error catastrophe: fidelity of RNA synthesis and RNA recombination. A G64S mutation increased the fidelity of the viral polymerase and rendered the virus resistant to ribavirin-induced error catastrophe, but only when RNA recombination was at wild-type levels. An L420A mutation in the viral polymerase inhibited RNA recombination and exacerbated ribavirin-induced error catastrophe. Furthermore, when RNA recombination was substantially reduced by an L420A mutation, a high-fidelity G64S polymerase failed to make the virus resistant to ribavirin. These data indicate that viral RNA recombination is required for poliovirus to evade ribavirin-induced error catastrophe. The conserved nature of L420 within RDRPs suggests that RNA recombination is a common mechanism for picornaviruses to counteract and avoid error catastrophe.IMPORTANCE Positive-strand RNA viruses produce vast amounts of progeny in very short periods of time via template-dependent RNA replication mechanisms. Template-dependent RNA replication, while efficient, can be disadvantageous due to error-prone viral polymerases. The accumulation of mutations in viral RNA genomes leads to error catastrophe. In this study, we substantiate long-held theories regarding the advantages and disadvantages of asexual and sexual replication strategies among RNA viruses. In particular, we show that picornavirus RNA recombination counteracts the negative consequences of asexual template-dependent RNA replication mechanisms, namely, error catastrophe.

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Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.

Publications

Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.

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