<b><i>De novo</i></b><b> whole-genome assembly of </b><b>the 10-gigabase</b><b> </b><b><i>Fokienia hodginsii </i></b><b>genome to reveal differential epigenetic events between callus and xylem</b>

<i>Fokienia hodginsii</i><b><i> </i></b>(<i>F</i>.<i> hodginsii</i>), belonging to the genus Fokienia of the Cupressaceae, grows in evergreen broadleaf forest and exhibits a diversity of community type in subtropical zone. <i>F</i>.<i> hodginsii </i>has significant application value due to its wood properties. Additionally, it holds great research value in evolutionary studies as a gymnosperm. However, the genome<i> </i>of <i>F</i>.<i> hodginsii</i> remained unknown due to the challenges posed by repetitive sequences and the large size of gymnosperms genome. This study aimed to generate a chromosome-level genome of <i>F. hodginsii</i> and elucidate the epigenetic regulation in gymnosperms. We employed Pacific Bioscience sequencing, Hi-C mapping, whole-genome Bisulfite Sequencing (BS-Seq), long-read isoform sequencing (Iso-Seq), direct RNA sequencing (DRS), quantitative proteomics, and metabonomics analysis to facilitate genome assembly, gene annotation, and investigation into epigenetic mechanisms. In this study, we assembled the 10G <i>F</i>.<i> hodginsii </i>genome into 11 chromosomes. Furthermore, we annotated 50,521 protein-coding genes based on from different tissues and determined that 65% of <i>F</i>.<i> hodginsii </i>genome comprises repetitive sequences. We discovered that transposable element (TE)-including introns was associated with higher expression. The DNA methylome of <i>F</i>.<i> hodginsii </i>revealed that stem-differentiating xylem (SDX) had a higher DNA methylation level compared to callus. Quantitative proteomics revealed that up-regulated proteins in callus were enriched in KEGG pathways related to RNA degradation. Moreover, DRS revealed the significant alterations in RNA full-length ratio, which potentially associated with poly(A) length (PAL) and alternative polyadenylation (APA). Finally, the investigation of 14 different cultivars revealed difference in growth based on morphology measurement and metabonomics analysis. In summary, we generate <i>de novo </i>assembly on <i>F. hodginsii</i> genomes and epigenetics datasets, that provide a molecular basis for callus formation in the gymnosperm family.You can send any questions to ​[e-mail] by email.<br>福建柏（Fokienia hodginsii，简称F. hodginsii）隶属于柏科（Cupressaceae）福建柏属，多生长于亚热带常绿阔叶林，具有多样的群落类型。该树种凭借其优良的木材特性拥有重要的应用价值，同时作为裸子植物，在进化生物学研究中具备极高的科研价值。此前，由于裸子植物基因组存在大量重复序列且基因组规模庞大，福建柏的基因组信息长期处于未知状态。本研究旨在构建福建柏的染色体级参考基因组，解析裸子植物的表观遗传调控机制。我们采用Pacific Bioscience测序、Hi-C作图、全基因组亚硫酸氢盐测序（whole-genome Bisulfite Sequencing, BS-Seq）、长读长异构体测序（long-read isoform sequencing, Iso-Seq）、直接RNA测序（direct RNA sequencing, DRS）、定量蛋白质组学及代谢组学分析技术，用于基因组组装、基因注释及表观遗传机制探究。本研究将总规模为10G的福建柏基因组组装为11条染色体。进一步基于多组织样本注释得到50521个蛋白质编码基因，同时发现福建柏基因组中65%的序列为重复序列。我们揭示了包含内含子在内的转座因子（transposable element, TE）与更高的基因表达水平存在关联。福建柏的DNA甲基化组分析显示，茎分化木质部（stem-differentiating xylem, SDX）的DNA甲基化水平显著高于愈伤组织。定量蛋白质组学分析表明，愈伤组织中上调表达的蛋白富集于RNA降解相关的KEGG通路。此外，直接RNA测序结果显示RNA全长比例发生显著改变，该变化可能与poly(A)长度（poly(A) length, PAL）及可变聚腺苷酸化（alternative polyadenylation, APA）相关。最后，针对14个不同栽培品种的分析显示，基于形态学测量与代谢组学分析，不同品种的生长性状存在显著差异。综上，本研究完成了福建柏基因组与表观基因组的从头组装，为裸子植物愈伤组织形成机制的研究提供了分子基础。您可通过邮箱[e-mail]咨询相关问题。