State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong, China.
Plant Biotechnol J. 2024 Jun;22(6):1491-1503. doi: 10.1111/pbi.14281. Epub 2023 Dec 29.
Mangrove species are broadly classified as true mangroves and mangrove associates. The latter are amphibious plants that can survive in the intertidal zone and reproduce naturally in terrestrial environments. Their widespread distribution and extensive adaptability make them ideal research materials for exploring adaptive evolution. In this study, we de novo assembled two genomes of mangrove associates (the allotetraploid Barringtonia racemosa (2n = 4x = 52) and diploid Barringtonia asiatica (2n = 2x = 26)) to investigate the role of allopolyploidy in the evolutionary history of mangrove species. We developed a new allotetraploid-dividing tool Allo4D to distinguish between allotetraploid scaffold-scale subgenomes and verified its accuracy and reliability using real and simulated data. According to the two subgenomes of allotetraploid B. racemosa divided using Allo4D, the allopolyploidization event was estimated to have occurred approximately one million years ago (Mya). We found that B. racemosa, B. asiatica, and Diospyros lotus shared a whole genome duplication (WGD) event during the K-Pg (Cretaceous-Paleozoic) period. K-Pg WGD and recent allopolyploidization events contributed to the speciation of B. racemosa and its adaptation to coastal habitats. We found that genes in the glucosinolates (GSLs) pathway, an essential pathway in response to various biotic and abiotic stresses, expanded rapidly in B. racemosa during polyploidization. In summary, this study provides a typical example of the adaptation of allopolyploid plants to extreme environmental conditions. The newly developed tool, Allo4D, can effectively divide allotetraploid subgenomes and explore the evolutionary history of polyploid plants, especially for species whose ancestors are unknown or extinct.
红树物种广泛分为真红树和红树伴生种。后者是两栖植物，能在潮间带生存，并在陆地环境中自然繁殖。它们广泛的分布和广泛的适应性使它们成为探索适应性进化的理想研究材料。在这项研究中，我们从头组装了两种红树伴生种（同源四倍体海杧果（2n=4x=52）和二倍体海杧果（2n=2x=26））的基因组，以研究异源多倍体在红树物种进化历史中的作用。我们开发了一种新的异源四倍体划分工具 Allo4D，用于区分异源四倍体支架尺度亚基因组，并使用真实和模拟数据验证了其准确性和可靠性。根据 Allo4D 对同源四倍体 B. racemosa 的两个亚基因组的划分，异源多倍体化事件估计发生在大约 100 万年前（Mya）。我们发现，海杧果、海杧果和乌木共享一个全基因组复制（WGD）事件在 K-Pg（白垩纪-古生代）时期。K-Pg WGD 和最近的异源多倍体化事件促成了 B. racemosa 的物种形成及其对沿海生境的适应。我们发现，在多倍体化过程中，参与响应各种生物和非生物胁迫的硫代葡萄糖苷（GSLs）途径的基因在海杧果中迅速扩张。总之，本研究为异源多倍体植物对极端环境条件的适应提供了一个典型的例子。新开发的工具 Allo4D 可以有效地划分异源四倍体亚基因组，并探索多倍体植物的进化历史，特别是对于那些祖先未知或已灭绝的物种。
