DataSheet_1_The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangered Artocarpus nanchuanensis.doc

IntroductionWhole-genome resequencing technology covers almost all nucleotide variations in the genome, which makes it possible to carry out conservation genomics research on endangered species at the whole-genome level.
MethodsIn this study, based on the whole-genome resequencing data of 101 critically endangered Artocarpus nanchuanensis individuals, we evaluated the genetic diversity and population structure, inferred the demographic history and genetic load, predicted the potential distributions in the past, present and future, and classified conservation units to propose targeted suggestions for the conservation of this critically endangered species.
ResultsWhole-genome resequencing for A. nanchuanensis generated approximately 2 Tb of data. Based on abundant mutation sites (25,312,571 single nucleotide polymorphisms sites), we revealed that the average genetic diversity (nucleotide diversity, π) of different populations of A. nanchuanensis was relatively low compared with other trees that have been studied. And we also revealed that the NHZ and QJT populations harboured unique genetic backgrounds and were significantly separated from the other five populations. In addition, positive genetic selective signals, significantly enriched in biological processes related to terpene synthesis, were identified in the NHZ population. The analysis of demographic history of A. nanchuanensis revealed the existence of three genetic bottleneck events. Moreover, abundant genetic loads (48.56% protein-coding genes) were identified in Artocarpus nanchuanensis, especially in genes related to early development and immune function of plants. The predication analysis of suitable habitat areas indicated that the past suitable habitat areas shifted from the north to the south due to global temperature decline. However, in the future, the actual distribution area of A. nanchuanensis will still maintain high suitability.
DiscussionBased on total analyses, we divided the populations of A. nanchuanensis into four conservation units and proposed a number of practical management suggestions for each conservation unit. Overall, our study provides meaningful guidance for the protection of A. nanchuanensis and important insight into conservation genomics research.

**引言**：全基因组重测序（whole-genome resequencing）技术可覆盖基因组内几乎所有核苷酸变异，这使得在全基因组层面开展濒危物种的保护基因组学研究成为可能。
**研究方法**：本研究以101株极危南川木波罗（Artocarpus nanchuanensis）个体的全基因组重测序数据为基础，对其遗传多样性与种群结构进行评估，推断种群历史动态与遗传负荷，预测其过去、当前及未来的潜在适生分布区，并划分保护单元，以期为该极危物种的保护提出针对性建议。
**研究结果**：针对南川木波罗的全基因组重测序共产生约2 Tb数据。基于海量突变位点（25,312,571个单核苷酸多态性位点），本研究发现，相较于已报道的其他树种，南川木波罗不同种群的平均遗传多样性（核苷酸多样性π）相对偏低。同时，本研究揭示NHZ与QJT种群拥有独特的遗传背景，与其余5个种群存在显著遗传分化。此外，NHZ种群中检测到正向遗传选择信号，且这些信号显著富集于萜类合成相关的生物学过程。南川木波罗的种群历史动态分析显示其曾经历三次遗传瓶颈事件。另外，本研究在南川木波罗中鉴定到大量遗传负荷（占蛋白编码基因的48.56%），尤其富集于植物早期发育与免疫功能相关基因。适生栖息地预测分析表明，受全球气温下降影响，其过去的适生分布区曾由北向南迁移。但在未来，南川木波罗的实际分布区仍将保持较高的适生性。
**讨论**：基于综合分析结果，本研究将南川木波罗种群划分为4个保护单元，并针对每个保护单元提出了若干切实可行的管理建议。总体而言，本研究为南川木波罗的保护工作提供了具有参考价值的指导，同时也为保护基因组学研究提供了重要的学术见解。