The fig tree (Ficus carica L.), one of the oldest known domesticated species, still has a great potential for expansion thanks to valuable nutritional and nutraceutical characteristics, combined with the ability to adapt well to marginal soils and difficult environmental conditions. Despite its long history, this species is hampered by the lack of a high-quality reference genome and missing epigenetic information which can give it new breeding perspectives. Actually, assembly of nonmodel plant species is challenging due to high DNA heterozygosity and repeat content. Here, we report our work to build a high-quality genome reference for fig, using single-molecule, real-time sequencing technology of Pacific Biosciences (PacBio). The assembled fig genome is ~333 Mb of which 80% have been anchored to 13 haplotype phased, fully annotated pseudomolecules, which represent the 13 chromosomes of fig. The genome has an estimated repeat content of 37% and contains 37,840 protein‐coding genes. Latest in silico technologies allow the identification of new epigenetic markers as N4-methylcytosine and N6- methyladenine which have revealed new methylation motifs and high methylation levels in both genes and transposable elements and a prevalence of methylated over un-methylated genes. The production of a high-quality reference genome sequence for F. carica L. presents interesting insights into the genomic structure of a highly heterozygous plant diploid species. Furthermore, the characterization of the methylation profile of two unconventional DNA modifications provides an important basis for future studies, opening up new possibilities to investigate how specific epigenetic changes affect the phenotype of plants.
De novo assembly of the highly heterozygous fig (Ficus carica L.) genome reveals epigenetic patterns.
USAI G.;MASCAGNI F.;GIORDANI T.;VANGELISTI A.;BOSI E.;ZUCCOLO A.;CAVALLINI A.;NATALI L.
2019-01-01
Abstract
The fig tree (Ficus carica L.), one of the oldest known domesticated species, still has a great potential for expansion thanks to valuable nutritional and nutraceutical characteristics, combined with the ability to adapt well to marginal soils and difficult environmental conditions. Despite its long history, this species is hampered by the lack of a high-quality reference genome and missing epigenetic information which can give it new breeding perspectives. Actually, assembly of nonmodel plant species is challenging due to high DNA heterozygosity and repeat content. Here, we report our work to build a high-quality genome reference for fig, using single-molecule, real-time sequencing technology of Pacific Biosciences (PacBio). The assembled fig genome is ~333 Mb of which 80% have been anchored to 13 haplotype phased, fully annotated pseudomolecules, which represent the 13 chromosomes of fig. The genome has an estimated repeat content of 37% and contains 37,840 protein‐coding genes. Latest in silico technologies allow the identification of new epigenetic markers as N4-methylcytosine and N6- methyladenine which have revealed new methylation motifs and high methylation levels in both genes and transposable elements and a prevalence of methylated over un-methylated genes. The production of a high-quality reference genome sequence for F. carica L. presents interesting insights into the genomic structure of a highly heterozygous plant diploid species. Furthermore, the characterization of the methylation profile of two unconventional DNA modifications provides an important basis for future studies, opening up new possibilities to investigate how specific epigenetic changes affect the phenotype of plants.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
