Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

A - Papers appearing in refereed journals

Usai, G., Mascagni, F., Giordani, T., Vangelisti, A., Bose, E., Zuccolo, A., Ceccarelli, M., King, R., Hassani-Pak, K., Zambrano, L. S., Cavallini, A. and Natali, L. 2020. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. The Plant Journal.

AuthorsUsai, G., Mascagni, F., Giordani, T., Vangelisti, A., Bose, E., Zuccolo, A., Ceccarelli, M., King, R., Hassani-Pak, K., Zambrano, L. S., Cavallini, A. and Natali, L.
Abstract

Due to DNA heterozygosity and repeat content, assembly of non‐model plant genomes is challenging. Herein, we report a high‐quality genome reference of one of the oldest known domesticated species, fig (Ficus carica L.), using Pacific Biosciences single‐molecule, real‐time sequencing. The fig genome is ~ 333 Mbp in size, of which 80% has been anchored to 13 chromosomes. Genome‐wide analysis of N6‐methyladenine and N4‐methylcytosine revealed high methylation levels in both genes and transposable elements, and a prevalence of methylated over non‐methylated genes. Furthermore, the characterization of N6‐methyladenine sites led to the identification of ANHGA, a species‐specific motif, which is prevalent for both genes and transposable elements. Finally, exploiting the contiguity of the 13 pseudomolecules, we identified 13 putative centromeric regions. The high‐quality reference genome and the characterization of methylation profiles, provides an important resource for both fig breeding and for fundamental research into the relationship between epigenetic changes and phenotype, using fig as a model species.

KeywordsFicus carica L.; Single-molecule real-time sequencing; Genome assembly; N6-methyladenine; N4-methylcytosine
Year of Publication2020
JournalThe Plant Journal
Digital Object Identifier (DOI)doi:10.1111/tpj.14635
PubMed ID31808196
Web address (URL)https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14635
Open accessPublished as bronze (free) open access
FunderBiotechnology and Biological Sciences Research Council
Rothamsted Research
Funder project or codeDFW - Designing Future Wheat - Work package 4 (WP4) - Data access and analysis
Publisher's version
Supplemental file
Copyright license
CC BY
Output statusPublished
Publication dates
Online05 Dec 2019
Publication process dates
Accepted26 Nov 2019
PublisherWiley-Blackwell
ISSN0960-7412

Permalink - https://repository.rothamsted.ac.uk/item/96zyx/epigenetic-patterns-within-the-haplotype-phased-fig-ficus-carica-l-genome

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