State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China.
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Mol Ecol Resour. 2021 May;21(4):1186-1199. doi: 10.1111/1755-0998.13334. Epub 2021 Feb 8.
Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early-diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they survived during repeated climatic oscillations in the Quaternary. We sequenced the genome of Te. sinense and compared it with that of Tr. aralioides. We found that Te. sinense has a smaller genome size (986.3 Mb) than that of Tr. aralioides (1610 Mb). Repetitive elements made the major contribution to the contrasting genome sizes in the two species, with most bursts of repeats occurring within the past four million years when the climate oscillated greatly. These species share two rounds of whole-genome duplications. The mainland species Te. sinense had a larger effective population size than the island species Tr. aralioides after the largest glaciation during the Quaternary climatic oscillation. However, soon after this recovery stage, the effective population sizes of both species continued to decrease, although the current effective population size of Te. sinense is still larger than that of Tr. aralioides. We recovered three distinctly diverged clades through resequencing the genomes of 50 individuals across the distributional range of Te. sinense in China. Our results provide an important genomic resource with which to examine early trait evolution in the core eudicots and assist efforts to conserve this relict tree species.
水杉和珙桐是东亚大陆和岛屿上的两种三叠纪孑遗物种，属于昆栏树目，是四个早期分化的真双子叶植物谱系之一。这两个孑遗物种为研究它们在第四纪反复气候波动中幸存下来时发生的基因组变化提供了一个很好的系统。我们对水杉的基因组进行了测序，并将其与珙桐的基因组进行了比较。我们发现，水杉的基因组大小（986.3 Mb）比珙桐的基因组大小（1610 Mb）小。重复序列是导致这两个物种基因组大小差异的主要因素，大部分重复序列爆发发生在过去的四百万年内，当时气候波动很大。这两个物种共享两轮全基因组复制。在第四纪气候波动中最大的冰川期后，大陆物种水杉的有效种群大小大于岛屿物种珙桐。然而，在这个恢复阶段之后，两个物种的有效种群大小都继续减少，尽管目前水杉的有效种群大小仍然大于珙桐。通过对分布在中国境内的 50 个水杉个体的基因组进行重测序，我们发现了三个明显分化的分支。我们的研究结果提供了一个重要的基因组资源，可用于研究真双子叶植物核心类群的早期特征进化，并有助于保护这种孑遗树种。
