Data from: The role of transcriptomes linked with responses to light environment on seedling mortality in a subtropical forest, China

Differences in seedling survival in trees have a lasting imprint on seedling, juvenile and adult community structure. Identifying the drivers of these differences, therefore, is a critical research objective that ultimately requires knowledge regarding how organismal function interacts with the local environment to influence survival rates.
In tree communities, differences in light use strategies are frequently invoked to explain differences in seedling demographic performance through growth and survival trade-offs. For example, shade-tolerant species grow slowly and have higher survival rates, whereas shade-intolerant species grow quickly but have lower survival rates. Thus, functional traits related to photosynthesis should be strong predictors of demographic rates, but results in the literature are mixed indicating that additional or alternative information regarding organismal function should be considered.
Here, we provide a community-wide inventory of transcriptomes in a subtropical tree community. This information is utilized to determine the degree to which species share homologous genes related to gene ontologies for light use and harvesting. These species similarities are used in neighbourhood generalized linear mixed-effects models of seedling survival that evaluated seedling survival as a function of the transcriptomic, functional trait and phylogenetic composition of the local neighbourhood. The results show neighbourhood similarity in three of the 15 gene ontologies evaluated are significantly related to survival rates based on neighbourhood composition. For two of these ontologies, survival rates increase when neighbours are similar in their gene tree composition indicating the importance of abiotic filtering and performance hierarchies.
Synthesis. The present work takes a novel approach by sequencing the transcriptomes of naturally co-occurring tree species in a subtropical forest in China. The results show that the transcriptomic similarity of species is a significant predictor of differential survival. The study demonstrates that exploring the functional genomic similarity of non-model species in nature has the potential to increase the breadth and depth of our understanding of how gene function influences species co-occurrence and population dynamics in communities.

树木幼苗存活的差异会对幼苗、幼树乃至成年个体的群落结构产生持久印记。因此，明确这类差异的驱动因子是一项关键的研究目标，而这最终需要我们了解生物个体功能如何与局域环境相互作用，进而影响存活概率。
在树木群落中，光利用策略的差异常被用以解释幼苗种群动态表现的差异，该解释基于生长与存活之间的权衡关系。例如，耐阴树种生长缓慢但存活率更高，而不耐阴树种生长迅速但存活率更低。因此，与光合作用相关的功能性状本应能很好地预测种群动态速率，但现有文献中的研究结果并不一致，这表明我们需要考虑有关生物个体功能的额外或替代信息。
本研究针对一个亚热带树木群落，提供了全群落范围的转录组（transcriptome）编目数据。我们利用这些数据评估不同物种在光利用与光捕获相关的基因本体论（gene ontology）关联同源基因方面的共享程度。随后，将物种间的这类相似性纳入幼苗存活的邻域广义线性混合效应模型（neighbourhood generalized linear mixed-effects models）中，该模型以局域邻域的转录组、功能性状及系统发育组成作为自变量，评估幼苗存活情况。研究结果显示，在15个被评估的基因本体论中，有3个的邻域相似性与基于邻域组成的存活率显著相关。其中2个基因本体论对应的存活率会在邻域物种的基因树组成相似时升高，这体现了非生物过滤与性能层级的重要性。
综合分析：本研究通过对中国亚热带森林中自然共存的树木物种进行转录组测序，采用了一种全新的研究方法。结果表明，物种间的转录组相似性可显著预测幼苗存活的差异。本研究证实，探究自然界中非模式物种的功能基因组相似性，有望拓宽并加深我们对基因功能如何影响群落内物种共存与种群动态的理解。