Macas, J., Novák, P., Pellicer, J., Čížková, J., Koblížková, A., Neumann, P., Fuková, I., Doležel, J., Kelly, L.J., Leitch, I.J.
PLoS ONE
10:
e0143424,
2015
Klíčová slova:
Abstrakt:
The differential accumulation and elimination of repetitive DNA are key drivers of genome
size variation in flowering plants, yet there have been few studies which have analysed how
different types of repeats in related species contribute to genome size evolution within a
phylogenetic context. This question is addressed here by conducting large-scale comparative
analysis of repeats in 23 species from four genera of the monophyletic legume tribe
Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and
genome size reconstruction revealed that this diversity arose from genome size expansions
and contractions in different lineages during the evolution of Fabeae. Employing a combination
of low-pass genome sequencing with novel bioinformatic approaches resulted in identification
and quantification of repeats making up 55–83% of the investigated genomes. In
turn, this enabled an analysis of how each major repeat type contributed to the genome size
variation encountered. Differential accumulation of repetitive DNA was found to account for
85% of the genome size differences between the species, and most (57%) of this variation
was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre
elements. Although the amounts of several other lineages of LTR-retrotransposons and the
total amount of satellite DNA were also positively correlated with genome size, their contributions
to genome size variation were much smaller (up to 6%). Repeat analysis within a
phylogenetic framework also revealed profound differences in the extent of sequence conservation
between different repeat types across Fabeae. In addition to these findings, the
study has provided a proof of concept for the approach combining recent developments in
sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a
large number of non-model species without the need to assemble their genomes.
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Jaroslav Doležel
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English