Local adaptation insights from genomics and ecophysiology of a neotropical mangrove

Integrating genomic and ecological data is instrumental for understanding the mechanisms of adaptive processes in natural ecosystems. In non-model species, such studies can be particularly challenging but often yield results with implications for conservation. Here, we integrate molecular and ecophysiological approaches to assess the role of selection in the north-south organisation of genetic variation in the mangrove species Avicennia schaueriana, a new-world tree found in tropical to temperate coastal forests along the Atlantic coast of the Americas. We found substantial divergences between populations occurring north and south of the north-eastern extremity of South America, possibly reflecting the roles of contrasting environmental forces in shaping the genetic structure of the species. In a common garden experiment, individuals from equatorial and subtropical forests were found to be divergent in traits involved in water balance and carbon acquisition, suggesting a genetic basis of the observed differences. RNA-sequencing highlighted the molecular effects of different light, temperature and air humidity regimes on individuals under field conditions at contrasting latitudes. Additionally, genome-wide polymorphisms in trees sampled along most of the species range showed signatures of selection in sequences associated with the biogenesis of the photosynthetic apparatus, anthocyanin biosynthesis and osmotic and hypoxia stress responses. The observed functional divergence might differentially affect sensitivities of populations to our changing climate. We emphasize the necessity of independent conservation management for the long-term persistence of the species diversity. Moreover, we demonstrate the power of using a multidisciplinary approach in adaptation studies of non-model species.

Stems from Subtropical samples showed wider vessel diameter than did those from conductivity, at a detriment of hydraulic safety, than did those of Equatorial plants (Fig. 2).

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The total conductivity of the stems was not significantly different between sample groups.

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Plants from the contrasting origins exhibited different stem epidermis pigmentation, with 2 8 7 Equatorial seedlings reflecting more red light of long wavelengths (635-700 nm) and less 2 8 8 green light of medium wavelengths (520-560 nm) than did Subtropical seedlings (Fig. 3). In the absence of a reference genome, we used RNA-Seq (Z. Wang, Gerstein, & 2 9 2 Snyder, 2009) to obtain a de novo assembled transcriptome for A. schaueriana from leaves, which 30,227 (61%) were putative protein-coding sequences. Over 91.9% of these reads were 2 9 7 mapped to a single transcript, indicating minimum redundancy and a wide representation of 2 9 8 sequenced data (Supplemental Table 4). Moreover, searching for universal plant orthologous 2 9 9 . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/378612 doi: bioRxiv preprint RefSeq and TAIR databases (Supplemental Fig. 6c). More than 80% of these protein-coding  . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/378612 doi: bioRxiv preprint between Equatorial and Subtropical samples (Supplemental Fig. 7d and 7e). Among the total 3 2 4 2,741 DETs, 1,150 (41.91%) were putative protein-coding transcripts.

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The assignment of transcripts to GO terms was possible for 25,184 (83.31%) of 3 2 6 30,227 putative protein-coding sequences, allowing GO enrichment analyses of the DETs. Subtropical sites ( Equatorial than in Subtropical samples (which we refer to these as DET-Eq) and the other responses to UV, temperature stimulus and water stress; cell wall biosynthesis and cellular   Table 11). biosynthesis genes, were among the DET-Eq (Supplemental Table 11).

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Response to temperature: In the DET-St set, we observed putative genes presenting among the DET-Eq set, potentially enhancing tolerance to heat in equatorial plants.  Table 11).

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Response to water stress: Transcripts associated with the response and tolerance to 3 6 7 water deficits and with cellular ion homeostasis and osmotic adjustment were enriched among The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/378612 doi: bioRxiv preprint Supplemental Table 2). After quality filtering of the sequenced data, we selected 77  The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/378612 doi: bioRxiv preprint The increased levels of transcripts similar to heat-shock proteins, to drought-induced  we argue that the higher expression of several transcripts associated with cell wall diameter, leaf size, leaf angle and transpiration and stomatal conductance rates (Fig. 2, Fig. 3-4).  genes. The adaptive relevance of these findings is supported by the sign of natural selection insights into A. schaueriana light-related adaptations.  In response to abiotic stress conditions such as drought, heat and high light, plants The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/378612 doi: bioRxiv preprint genes (Bray, 2004;Han et al., 2009;Kimura et al., 2003;Moumeni et al., 2011;D. Wang et 5 3 7 al., 2011;C. Zhang et al., 2015). We argue that the lower expression of photosynthesis genes 5 3 8

Low water and low light availability presumably affect photosynthesis and cellular
in Equatorial than in Subtropical samples likely is further indicative of the role of water stress 5 3 9 in shaping divergent phenotypes in the field, but it may also result in the enhanced absorption conditions ( Fig. 2-3, Supplemental Fig. 3-4).

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Mitochondrial activity is strongly connected to photosynthesis and chloroplasts light-and ethylene-mediated developmental processes and drought stress tolerance. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. Intergovernmental Panel on Climate Change. IPCC. Geneva, Switzerland: IPCC. canopy, sky condition, and solar angle on light quality in a longleaf pine woodland. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/378612 doi: bioRxiv preprint