Atypical DNA methylation, sRNA size distribution and female gametogenesis correlate with genome compaction in Utricularia gibba

Cerantes-Perez, S. A.; Yong-Villalobos, L.; Florez-Zapata, N. M. V.; Oropeza-Aburto, A.; Rico-Resendiz, F.; Amasende-Morales, I.; Lan, T.; Martinez, O.; Vielle-Calzada, J. P.; Albert, V. A.; Herrera-Estrella, L.

doi:10.1101/2020.12.05.413054

bioRxiv · 10.1101/2020.12.05.413054

Atypical DNA methylation, sRNA size distribution and female gametogenesis correlate with genome compaction in Utricularia gibba

Cerantes-Perez, S. A.·Yong-Villalobos, L.·Florez-Zapata, N. M. V.·Oropeza-Aburto, A.·Rico-Resendiz, F.·Amasende-Morales, I.·Lan, T.·Martinez, O.·Vielle-Calzada, J. P.·Albert, V. A.·Herrera-Estrella, L.

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Abstract

O_LIThe most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), which is a conserved mechanism that involves noncoding-RNAs to control the expansion of intergenic regions. However, little is known about relationship between plant genome size reductions and DNA methylation. C_LIO_LIBecause the compact genome size of the carnivorous plant Utricularia gibba, we investigate in this plant the noncoding-RNA landscape and DNA methylation through a combination of cytological, evolutionary, and genome-wide transcriptomic and methylation approaches. C_LIO_LIWe report an unusual distribution of noncoding RNAs in U. gibba in comparison with other characterized angiosperms, which correlated with a lower level of global genome methylation, as determined by a novel strategy based on long-read DNA sequencing and corroborated by whole-genome bisulfite analysis. Moreover, found that genes involved in the RdDM pathway may not be functionally active in U. gibba, including a truncated DICER-LIKE 3 (DCL3), involved in the production of 24-nt small-RNAs. C_LIO_LIOur findings suggest that selective pressure to conserve a fully functional RdDM pathway might be reduced in compact genomes and a defective DCL3 correlate with a decreased proportion of 24-nt small-RNAs and developmental alterations in U. gibba, which could represent an initial step in the evolution of apomixis. C_LI

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Cerantes-Perez, S. A., Yong-Villalobos, L., Florez-Zapata, N. M. V., Oropeza-Aburto, A., Rico-Resendiz, F., Amasende-Morales, I., Lan, T., Martinez, O., Vielle-Calzada, J. P., Albert, V. A., Herrera-Estrella, L.. 2020-12-06. Atypical DNA methylation, sRNA size distribution and female gametogenesis correlate with genome compaction in Utricularia gibba. https://doi.org/10.1101/2020.12.05.413054

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