The genome assembly and annotation of Dipteris shenzhenensis

<i>Dipteris</i> is a relic plant genus and the important indicator of global climate warming and plant geography during the Mesozoic era. However, the lack of genomic resources has hindered the study of paleoclimate, systematic evolution, and medicinal value of this genus. Here, we sequenced and assembled the first chromosome-level genome of <i>Dipteris shenzhenensis</i>. The assembled genome was 1.9 Gb with a contig N50 length of 4.75 Mb, GC content of 42.28% and BUSCO value of 98.3%, and 98.37% of the assembled sequences were anchored onto 33 pseudochromosomes. 71.97% of the genome were predicted to be repetitive sequences, and a total of 26,471 protein coding genes were predicted, in which, 24,485 (92.5%) genes could be functionally annotated. Phylogenomic and comparative analyses suggested that <i>D. shenzhenensis</i> had experienced a whole genome duplication event after it diverged with other ferns at about 283.5 million years ago. The first high-quality genome of <i>Dipteris</i> will provide important genome resources for understanding the systematic evolution, paleoclimate and medicinal value of ferns.

双扇蕨属（Dipteris）是一类孑遗植物类群，同时是中生代时期全球气候变暖与植物地理学研究的重要指示类群。然而当前基因组资源的匮乏，阻碍了该属古气候、系统演化与药用价值相关研究的推进。本研究完成了深圳双扇蕨（Dipteris shenzhenensis）的首个染色体级基因组测序与组装工作：组装后的基因组大小为1.9 Gb，重叠群（contig）N50长度达4.75 Mb，GC含量为42.28%，BUSCO评估值为98.3%；且98.37%的组装序列被锚定至33条假染色体（pseudochromosomes）上。该基因组中71.97%的序列为重复序列，共预测得到26471个蛋白质编码基因，其中24485个（占比92.5%）基因可获得功能注释。系统基因组学与比较基因组学分析显示，深圳双扇蕨在约2.835亿年前与其他蕨类植物分化后，经历了一次全基因组复制事件。首个高质量的双扇蕨属基因组将为解析蕨类植物的系统演化、古气候及药用价值提供重要的基因组资源。