Conifers are essential components of forest ecosystems; however, their reproductive development remains largely understudied due to their genomes' complexity. Here, we present a time-resolved spatial transcriptomics (ST) atlas of 88 tissue sections across three time points from developing reproductive and vegetative shoots in wild-type Norway spruce (Picea abies), as well as transition shoots from the acrocona mutant. By studying their different spatiotemporal gene expression dynamics, we identified molecular processes active during the vegetative-to-reproductive shift and their specific spatial domains in the shoots. We also identified and experimentally characterized the MADS-box gene DAL55, which is active during lateral organ development. Moreover, we shed light on the evolutionary relationships between gymnosperm and angiosperm YABBY genes, responsible for inner or outer cell layers in complex structures. Overall, our spatiotemporal atlas identifies genes, pathways, and evolutionary relationships associated with plant reproductive organs, providing a valuable resource for studying conifer reproductive development.
Sami Saarenpää, N. Zivi, Yuvarani Masarapu et al.· Cell· 0 citations
• Climate change is reducing the boreal snowpack that insulates soils, exposing tree roots to more frequent freezing. The molecular cold response of roots is poorly characterised, and its conservation across the angiosperm–gymnosperm divide is unknown. We asked how much of the root cold response is shared among divergent boreal trees. • We profiled fine-root transcriptomes of four boreal trees (Picea abies, Pinus sylvestris, Betula pendula and Populus tremula) and two Arabidopsis thaliana ecotypes during a ten-day 5 °C treatment by RNA sequencing, and used comparative co-expression to detect conserved regulation independently of response timing. • Expressed genes were largely shared, but the genes differentially expressed, and the timing of their response, diverged between species. Despite this, a core of orthologues retained conserved co-expression neighbourhoods across more than 300 million years, enriched for growth regulation, metabolism and stress signalling, including a gibberellin-related metabolic component of the growth response. • The root cold response is therefore species specific in identity and timing, yet underlain by a conserved co-expression core.
Tuuli Aro, Elena M. van Zalen, Alexander Vergara et al.· bioRxiv· 0 citations
Comparing Norway spruce and Scots pine, two species separated by a deep evolutionary divergence, it is shown that the genes whose co-expression is most broadly conserved between the species are also those under the strongest purifying selection on their protein-coding sequences.
Elena M. van Zalen, Camilla Canovi, Vikash Kumar et al.· bioRxiv· 0 citations
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