Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy.
Plant J. 2020 May;102(3):600-614. doi: 10.1111/tpj.14635. Epub 2020 Jan 11.
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 N -methyladenine and N -methylcytosine revealed high methylation levels in both genes and transposable elements, and a prevalence of methylated over non-methylated genes. Furthermore, the characterization of N -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.
由于 DNA 杂合性和重复序列含量，非模式植物基因组的组装具有挑战性。在此，我们利用太平洋生物科学公司的单分子实时测序技术，报道了已知最古老的驯化物种之一——无花果（Ficus carica L.）的高质量基因组参考序列。该无花果基因组大小约为 3.33 亿 bp，其中 80%已锚定到 13 条染色体上。对 N-甲基腺嘌呤和 N-甲基胞嘧啶的全基因组分析表明，基因和转座元件的甲基化水平都很高，且甲基化基因比非甲基化基因更为普遍。此外，N-甲基腺嘌呤位点的特征分析导致了一种物种特异性基序——ANHGA 的鉴定，该基序在基因和转座元件中都很普遍。最后，利用 13 个假染色体的连续性，我们鉴定出了 13 个可能的着丝粒区域。该高质量的参考基因组和甲基化谱的特征分析，为无花果的培育以及利用无花果作为模式物种研究表观遗传变化与表型之间的关系提供了重要资源。
