Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, Scaevola taccada and S. hainanensis-Insight into Adaptation Outside of the Common Range.
Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, Scaevola taccada and S. hainanensis-Insight into Adaptation Outside of the Common Range.
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DOI：
10.3390/ijms24087355
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发表时间：
2023-04-16
影响因子：
5.6
通讯作者：
Shi, Suhua
中科院分区：
文献类型：
--
作者：
Li, Sen;Mao, Xiaomeng;He, Ziwen;Xu, Shaohua;Guo, Zixiao;Shi, Suhua
古登氏菌科除草菇属外，大部分种类为澳大拉西亚特有种; taccada和S.海南种已将其分布范围扩大到大西洋和印度洋的热带海岸线。S. taccada似乎非常适应沿海桑迪和悬崖，在某些地方已经成为入侵性物种。S.海南种主要分布于红树林附近的盐沼地区，现已濒临灭绝。这两个物种提供了一个很好的系统，调查适应性进化的共同分布范围以外的这一分类组。在这里，我们报告了他们的染色体规模的基因组组装，目的是探索他们的基因组机制，离开澳大拉西亚后的分歧适应。将支架组装成8个染色体规模的假分子，分别占S. taccada和S. hainanensis，分别为。有趣的是，与许多红树林不同，这两个物种都没有经历过全基因组复制。我们发现，私人基因，特别是拷贝数扩增基因是必不可少的压力反应，光合作用，和碳固定。在S. hainanensis和S. taccada可能促进了S.海南种。此外，S.海南花对胁迫的反应以及对洪水和缺氧环境的耐受性做出了贡献。与S. hainanensis中FAR 1基因的拷贝数扩增比S. taccada可能促进了它对桑迪沿海土地上较强的光辐射的适应。总之，我们对S。taccada和S. hainanensis提供了新的见解，他们的基因组进化后离开澳大拉西亚。
While most of the species in Goodeniaceae family, excluding the Scaevola genus, are endemic to Australasia, S. taccada and S. hainanensis have expanded their distribution range to the tropical coastlines of the Atlantic and Indian Oceans. S. taccada appears to be highly adapted to coastal sandy lands and cliffs, and it has become invasive in places. S. hainanensis is found mainly in salt marshes near mangrove forests, and is at risk of extinction. These two species provide a good system to investigate adaptive evolution outside the common distribution range of this taxonomic group. Here, we report their chromosomal-scale genome assemblies with the objective of probing their genomic mechanisms related to divergent adaptation after leaving Australasia. The scaffolds were assembled into eight chromosome-scale pseudomolecules, which covered 90.12% and 89.46% of the whole genome assembly for S. taccada and S. hainanensis, respectively. Interestingly, unlike many mangroves, neither species has undergone whole-genome duplication. We show that private genes, specifically copy-number expanded genes are essential for stress response, photosynthesis, and carbon fixation. The gene families that are expanded in S. hainanensis and contracted in S. taccada might have facilitated adaptation to high salinity in S. hainanensis. Moreover, the genes under positive selection in S. hainanensis have contributed to its response to stress and its tolerance of flooding and anoxic environments. In contrast, compared with S. hainanensis, the more drastic copy number expansion of FAR1 genes in S. taccada might have facilitated its adaptation to the stronger light radiation present in sandy coastal lands. In conclusion, our study of the chromosomal-scale genomes of S. taccada and S. hainanensis provides novel insights into their genomic evolution after leaving Australasia.
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