The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188 bp long genome. The largest 32 scaffolds (22.4 Mb to 10.5 Mb) accounted for 98 % of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4 Kb to 1 Kb). We annotated 23,331 protein-coding genes using tissue-specific RNA-seq data, from which 13,312 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 92.3% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation, and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.

中文翻译：

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灰色红树林Avicennia码头的高质量基因组装配和注释

灰红树林[Avicennia marina（Forsk。）Vierh。]是分布最广的红树林物种，分布在整个印度西太平洋。它在表型特征和栖息地上都​​表现出显着的地理变异水平，通常在其分布的边缘处占据着极端的环境。然而，亚种进化关系和适应机制仍处于研究不足，特别是在西印度洋种群之间。解释这种可变性的高质量基因组资源也很少。在这里，我们报告A.玛丽娜基因组的第一个染色体水平的大会。我们使用先前发布的装配和草拟连接库芝加哥和Dovetail HiC草稿进行支架构建，产生了456,526,188 bp长的基因组。最大的32个支架（22.4 Mb至10。5 Mb）占基因组装配的98％，其余2％分布在短得多的3759个支架（62.4 Kb至1 Kb）之间。我们使用组织特异性RNA-seq数据注释了23,331个蛋白质编码基因，其中有13,312个与GO术语相关。与双子叶植物BUSCO数据集相比，基因组装配和基因注释集分别产生96.7％和92.3％的完整性评分。此外，基于重新排序数据的FST调查成功地识别出一组可能参与局部适应的候选基因，并揭示了与阿拉伯红树林种群中温度梯度相关的适应性变异模式。我们的A. marina基因组装配为基因组进化分析提供了非常有价值的资源，