Supporting data for "Genomic insights into endangerment and conservation of the garlic-fruit tree (<i>Malania oleifera</i>), a plant species with extremely small populations"

Advanced whole genome sequencing techniques enable covering nearly all genome nucleotide variations, thus can provide deep insights into protecting endangered species. However, the use of genomic data to make conservation strategies is still rare, particularly for endangered plants. Here we performed comprehensive conservation genomic analysis for <i>Malania oleifera</i>, an endangered tree species with a high amount of nervonic acid. We used whole-genome resequencing data of 165 samples, covering 16 populations across the entire distribution range to investigate the formation reasons of its extremely small population sizes and to evaluate the possible genomic offsets and changes of ecology niche suitability under future climate change.<br>Although <i>M. oleifera</i> maintains relatively high genetic diversity among endangered woody plants ( = 3.87e3), high levels of inbreeding have been observed, which has reduced genetic diversity in three populations (JM, NP and BM2) and caused the accumulation of deleterious mutations. Repeated bottleneck events, recent inbreeding (~490 years ago) and anthropogenic disturbance to wild habitats have aggravated the fragmentation and endangered status of <i>M. oleifera</i>. Due to the significant effect of higher average annual temperature, populations distributed in low altitudes exhibit greater genomic offset. Furthermore, ecological niche modeling shows the suitable habitats for <i>M. oleifera</i> will decrease by 71.15% and 98.79% by 2100 under scenarios SSP126 and SSP585, respectively.<br>The basic realizations concerning the threats to <i>M. oleifera</i> provides a scientific foundation for defining management and adaptive units and prioritizing populations for genetic rescue. Meanwhile, we highlight the importance of integrating genomic offset and ecological niche modeling to make targeted conservation actions under future climate change. Overall, our study provides a paradigm for genomics-directed conservation.