Vanreusel, A. | bioRxiv Science

bioRxiv2024

Gibberellic acid and light effects on seed germination in the seagrass Zostera marina

O_LISeagrass meadows have been heavily affected by human activities, with Zostera marina being one of the most impacted species. Seed-based methods are currently the preferred approach for their restoration. However, low germination rates and seedling establishment often affect the success rate and feasibility of restoration projects. C_LIO_LIWe tested, for the first time, the combined effect of light spectra (white and red light and darkness), photoperiod, and gibberellic acid (GA3) on seed germination rates in Z. marina, by means of an incubation experiment with a fully crossed design, employing penalised logistic regression and Cox proportional hazards analysis. Seedling development was subsequently monitored to assess the potential side-effects of the priming agents on morphometric growth. C_LIO_LILight priming positively affects germination, with germination probability being substantially increased when red light and darkness treatments were combined with GA3. Time to germination was reduced at mid- to high- GA3 concentrations. Morphometric analysis of the cotyledonary and leaf tissue development did not indicate a posteriori side-effects of seed priming on growth. C_LIO_LILight and GA3 priming favour germination probability and release from dormancy in Z. marina seeds. Seed priming can reduce stress- or manipulation-induced dormancy and can be considered in contexts where on-demand germination is required. C_LI

plant biology↗

bioRxiv2021

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

genomics↗