Aegiceras corniculatum is a major mangrove plant species adapted to waterlogging and saline conditions, grows in the coastal intertidal zone of tropical and subtropical regions. Here, we present a chromosome-level genome assembly of A. corniculatum by incorporating PacBio long-read sequencing and Hi-C technology. The results showed that the PacBio draft genome size is 906.63 Mb. Hi-C scaffolding anchored 885.06 Mb contigs (97.62% of draft assembly) onto 24 pseudochromosomes. The contig N50 and scaffold N50 were 7.1 Mb and 37.74 Mb, respectively. Out of 40,727 protein-coding genes predicted in the study, 89% have functional annotations in public databases. We also showed that of the 603.93 Mb repetitive sequences predicted in the assembled genome, long terminal repeat retrotransposons constitute 41.52%. The genome evolution analysis showed that the A. corniculatum genome experienced two whole-genome duplication events and shared the ancient γ whole-genome triplication event. A comparative genomic analysis revealed an incidence of expansion in 1,488 gene families associated with essential metabolism and biosynthetic pathways, including photosynthesis, oxidative phosphorylation, phenylalanine, glyoxylate, dicarboxylate metabolism, and DNA replication, which probably constitute adaptation traits that allow the A. corniculatum to survive in the intertidal zone. Also, the systematic characterization of genes associated with flavonoid biosynthesis pathway and the AcNHX gene family conducted in this study will provide insight into the adaptation mechanism of A. corniculatum to intertidal environments. The high-quality genome reported here can provide historical insights into genomic transformations that support the survival of A. corniculatum under harsh intertidal habitats.

中文翻译：

---

通过 Illumina、PacBio 和 Hi-C 测序技术生成的红树林植物 Aegiceras Corniculatum 基因组的染色体水平组装

Aegiceras Corniculatum是适应涝渍和盐碱地的主要红树林植物种类，生长在热带和亚热带地区的沿海潮间带。在这里，我们提出了一个染色体水平的基因组组装的桐花树通过结合 PacBio 长读长测序和 Hi-C 技术。结果表明，PacBio 基因组草图大小为 906.63 Mb。Hi-C 支架将 885.06 Mb 重叠群（组装草案的 97.62%）锚定到 24 个假染色体上。contig N50 和支架 N50 分别为 7.1 Mb 和 37.74 Mb。在该研究预测的 40,727 个蛋白质编码基因中，89% 在公共数据库中具有功能注释。我们还表明，在组装基因组中预测的 603.93 Mb 重复序列中，长末端重复反转录转座子占 41.52%。基因组进化分析表明，A.corniculatum基因组经历了两次全基因组复制事件，并共享了古老的γ全基因组三重复制事件。甲比较基因组分析揭示膨胀的入射与必需代谢和生物合成途径，包括光合作用，氧化磷酸化，苯丙氨酸，乙醛酸，二羧酸酯代谢，DNA复制，这可能构成适应性状，其允许相关的1488个基因家族桐花到在潮间带生存。此外，类黄酮生物合成途径及相关基因的系统性特征AcNHX在这项研究中进行基因家族将提供洞察的适应机制桐花到潮间带环境。这里报告的高质量基因组可以提供对支持A.corniculatum在恶劣潮间带栖息地生存的基因组转化的历史见解。