Ma Dongna, Ding Qiansu, Guo Zejun, Xu Chaoqun, Liang Pingping, Zhao Zhizhu, Song Shiwei, Zheng Hai-Lei
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China.
Planta. 2022 Jun 9;256(1):6. doi: 10.1007/s00425-022-03916-0.
Whole-genome duplication, gene family and lineage-specific genes analysis based on high-quality genome reveal the adaptation mechanisms of Avicennia marina to coastal intertidal habitats. Mangrove plants grow in a complex habitat of coastal intertidal zones with high salinity, hypoxia, etc. Therefore, it is an interesting question how mangroves adapt to the unique intertidal environment. Here, we present a chromosome-level genome of the Avicennia marina, a typical true mangrove with a size of 480.43 Mb, contig N50 of 11.33 Mb and 30,956 annotated protein-coding genes. We identified 621 Avicennia-specific genes that are mainly related to flavonoid and lignin biosynthesis, auxin homeostasis and response to abiotic stimulus. We found that A. marina underwent a novel specific whole-genome duplication, which is in line with a brief era of global warming that occurred during the paleocene-eocene maximum. Comparative genomic and transcriptomic analyses outline the distinct evolution and sophisticated regulations of A. marina adaptation to the intertidal environments, including expansion of photosynthesis and oxidative phosphorylation gene families, unique genes and pathways for antibacterial, detoxifying antioxidant and reactive oxygen species scavenging. In addition, we also analyzed salt gland secretion-related genes, and those involved in the red bark-related flavonoid biosynthesis, while significant expansions of key genes such as NHX, 4CL, CHS and CHI. High-quality genomes in future investigations will facilitate the understand of evolution of mangrove and improve breeding.
基于高质量基因组的全基因组复制、基因家族和谱系特异性基因分析揭示了白骨壤对沿海潮间带生境的适应机制。红树林植物生长在盐度高、缺氧等复杂的沿海潮间带生境中。因此，红树林如何适应独特的潮间带环境是一个有趣的问题。在此，我们展示了白骨壤的染色体水平基因组，这是一种典型的真红树林，大小为480.43 Mb，重叠群N50为11.33 Mb，有30,956个注释的蛋白质编码基因。我们鉴定出621个白骨壤特异性基因，它们主要与类黄酮和木质素生物合成、生长素稳态以及对非生物刺激的反应有关。我们发现白骨壤经历了一次新的特异性全基因组复制，这与古新世 - 始新世极热事件期间发生的短暂全球变暖时期一致。比较基因组和转录组分析概述了白骨壤适应潮间带环境的独特进化和复杂调控，包括光合作用和氧化磷酸化基因家族的扩展、抗菌、解毒抗氧化和活性氧清除的独特基因和途径。此外，我们还分析了盐腺分泌相关基因，以及参与红树皮相关类黄酮生物合成的基因，同时NHX、4CL、CHS和CHI等关键基因有显著扩增。未来研究中的高质量基因组将有助于理解红树林的进化并改善育种。
