Estimating total plant diversity in extreme or hyperarid environments can be challenging, as adaptations to pronounced climate variability include evading prolonged stress periods through seeds or specialized underground organs. Short‐term surveys of these ecosystems are thus likely poor estimators of actual diversity. Here we develop a multimethod strategy to obtain a more complete understanding of plant diversity from a community in the Atacama Desert. We explicitly test environmental DNA‐based techniques (eDNA) to see if they can reveal the observed and ‘hidden' (dormant or locally rare) species. To estimate total plant diversity, we performed long‐term traditional surveys during eight consecutive years, including El Niño and La Niña events, we then analyzed eDNA from soil samples using high‐throughput sequencing. We further used soil pollen analysis and soil seed bank germination assays to identify ‘hidden' species. Each approach offers different subsets of current biodiversity at different taxonomic, spatial and temporal resolution, with a total of 92 taxa identified along the transect. Traditional field surveys identified 77 plant species over eight consecutive years. Observed community composition greatly varies interannually, with only 22 species seen every year. eDNA analysis revealed 37 taxa, eight of which were ‘hidden' in our field surveys. Soil samples contain a viable seed bank of 21 taxa. Soil pollen (27 taxa) and eDNA analysis show affinities with vegetation at the landscape scale but a weak relationship to local plot diversity. Multimethod approaches (including eDNA) in deserts are valuable tools that add to a comprehensive assessment of biodiversity in such extreme environments, where using a single method or observations over a few years is insufficient. Our results can also explain the resilience of Atacama plant communities as ‘hidden' taxa may have been active in the recent past or could even emerge in the future as accelerated global environmental change continues unabated.

A critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including Brassica napus. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source–sink (S–S) ratios in order to examine the relationship between SW and SN under different field conditions. A multifactorial analysis of the RNA-seq data was used to identify a group of 1014 genes exclusively regulated by the S–S ratio. We found that a reduction in the S–S ratio during seed filling induces the expression of genes involved in sucrose transport, seed weight, and stress responses. Moreover, we identified five co-expression modules that are positively correlated with SW and negatively correlated with SN. Interestingly, one of these modules was significantly enriched in transcription factors (TFs). Furthermore, our network analysis predicted several NAC TFs as major hubs underlying SW and SN compensation. Taken together, our study provides novel insights into the molecular factors associated with the SW–SN relationship in rapeseed and identifies TFs as potential targets when improving crop yield.