Chromosomal‐level reference genome of the incense tree Aquilaria sinensis

Trees in the genus <i>Aquilaria</i> (Thymelaeaceae) are known as lign aloes, and are native to the forests of southeast Asia. Lign aloes produce agarwood as an antimicrobial defence. Agarwood has a long history of cultural and medicinal use, and is of considerable commercial value. However, due to habitat destruction and over collection, lign aloes are threatened in the wild. We present a chromosomal‐level assembly for <i>Aquilaria sinensis</i>, a lign aloe endemic to China known as the incense tree, based on Illumina short‐read, 10X Genomics linked‐read, and Hi‐C sequencing data. Our 783.8 Mbp <i>A. sinensis</i> genome assembly is of high physical contiguity, with a scaffold N50 of 87.6 Mbp, and high completeness, with a 95.8% BUSCO score for eudicotyledon genes. We include 17 transcriptomes from various plant tissues, providing a total of 35,965 gene models. We reveal the first complete set of genes involved in sesquiterpenoid production, plant defence, and agarwood production for the genus <i>Aquilaria</i>, including genes involved in the biosynthesis of sesquiterpenoids via the mevalonic acid (MVA), 1‐deoxy‐D‐xylulose‐5‐phosphate (DXP), and methylerythritol phosphate (MEP) pathways. We perform a detailed repeat content analysis, revealing that transposable elements account for ~61% of the genome, with major contributions from <i>gypsy</i>‐like and <i>copia</i>‐like LTR retroelements. We also provide a comparative analysis of repeat content across sequenced species in the order Malvales. Our study reveals the first chromosomal‐level genome assembly for a tree in the genus <i>Aquilaria</i> and provides an unprecedented opportunity to address a variety of applied, genomic and evolutionary questions in the Thymelaeaceae more widely.

沉香属（Aquilaria）隶属于瑞香科（Thymelaeaceae），其植株俗称沉香木（lign aloes），原产于东南亚森林。沉香木可合成沉香（agarwood）作为抗菌防御机制。沉香在文化与医药领域应用历史悠久，且具备极高的商业价值。然而，受栖息地破坏与过度采收影响，野生沉香属植物正面临生存威胁。
本研究基于Illumina短读长测序（Illumina short-read）、10X Genomics连锁读长测序（10X Genomics linked-read）以及Hi-C测序（Hi-C sequencing）数据，报道了中国特有的沉香木——白木香（Aquilaria sinensis，俗称莞香树（incense tree））的染色体级基因组组装。本研究组装的白木香基因组大小为783.8 Mbp，具有极高的物理连续性，其scaffold N50达到87.6 Mbp；同时基因组完整性优异，真双子叶植物（eudicotyledon）基因集的BUSCO评估得分为95.8%。本研究整合了来自不同植物组织的17套转录组（transcriptomes）数据，共预测得到35965个基因模型。
本研究首次解析了沉香属中与倍半萜（sesquiterpenoid）合成、植物防御及沉香形成相关的全套基因，包括通过甲羟戊酸（MVA）、1-脱氧-D-木酮糖-5-磷酸（DXP）以及甲基赤藓醇磷酸（MEP）通路合成倍半萜的相关基因。我们对基因组重复序列开展了详细分析，发现转座元件（transposable elements）约占基因组的61%，其中以gypsy型（gypsy-like）和copia型（copia-like）长末端重复序列（LTR）反转录转座子贡献最为显著。此外，本研究还对锦葵目（Malvales）已测序物种的重复序列内容进行了比较分析。
本研究首次报道了沉香属树木的染色体级基因组组装，为全面解析瑞香科（Thymelaeaceae）各类应用基因组学与进化生物学问题提供了前所未有的研究契机。