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.
Highlights
The emergence of third-generation sequencing (TGS) technologies (Ansorge et al, 2016) including singlemolecule, real-time (SMRT) sequencing developed by Pacific Biosciences (PacBio), has led to the production of high-quality genome assemblies (Daccord et al, 2017; Vogel et al, 2018; Ye et al, 2018)
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
Fig DNA sequencing The genomic DNA of a wild-type diploid F. carica cultivar Dottato female plant was extracted from young leaf tissue and sequenced using the SMRT technology of PacBio
Summary
The emergence of third-generation sequencing (TGS) technologies (Ansorge et al, 2016) including singlemolecule, real-time (SMRT) sequencing developed by Pacific Biosciences (PacBio), has led to the production of high-quality genome assemblies (Daccord et al, 2017; Vogel et al, 2018; Ye et al, 2018). Our de novo assembly of PacBio data using FALCON-Unzip (Chin et al, 2016) and published genetic marker information from Japanese cultivar Horaishi (Mori et al, 2017) resulted in 13 pseudomolecules which represent the 13 chromosomes of fig This chromosome-scale assembly was complemented by a detailed de novo annotation of the genes and of the non-coding component of the genome. We produced a genome-wide DNA methylation map at single-base resolution, reporting global profiling of 6mA and 4mC sites This analysis led to the identification of several DNA methylation motifs and patterns present in the fig genome, genes and mobile elements. This work represents an attempt of sequencing the genome of a heterozygous plant by long-read assembly, providing a high-quality genomic resource for future genetic and epigenomic studies in fig, potentially useful for the breeding of this promising commercial crop
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