Op De Beeck, M. | bioRxiv Science

bioRxiv2019

OCTAVVS: A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data

Modern vibrational spectroscopy techniques enable rapid collection of thousands of spectra in a single hyperspectral image, allowing researchers to resolve spatially heterogeneous samples down to a resolution of a few m. A number of algorithms have been developed to correct for effects such as atmospheric absorption, light scattering by cellular structures and varying baseline levels. Following such preprocessing, spectra are commonly decomposed and clustered to reveal informative patterns and subtle spectral changes. Several of these steps are slow, labor-intensive and require programming skills to make use of published algorithms and code. We here present a free and platform-independent graphical toolbox that allows rapid processing of large sets of spectroscopic images, including atmospheric correction and an algorithm for resonant Mie scattering with improved speed and stability. The software includes modules for decomposition into constituent spectra using the popular MCR-ALS algorithm, augmented by region-of-interest selection, as well as clustering and cluster annotation.

biochemistry↗

bioRxiv2019

Adaptive zinc tolerance is supported by extensive gene multiplication and differences in cis-regulation of a CDF transporter in an ectomycorrhizal fungus

Abiotic changes due to anthropogenic activities affect selection regimes for organisms. How trees and their mycorrhizal symbionts adapt to altered environments in heterogeneous landscapes is of great interest. With a global distribution and multiple adaptive phenotypes available, Suillus luteus is an excellent ectomycorrhizal model to study evolutionary dynamics of local adaptation. We assessed pathways of homeostasis and detoxification in S. luteus isolates, displaying contrasting Zn tolerance phenotypes to identify mechanisms underlying adaptive Zn tolerance. Using 30 randomly selected isolates sampled at metal contaminated and control sites, we documented Zn tolerance phenotypes, assessed the link with identified candidate genes and explored its genetic basis via targeted amplicon sequencing and qPCR. Zn tolerance phenotypes covering a continuum from Zn sensitive to hypertolerant were identified and inversely correlate with cellular Zn accumulation. Gene expression of SlZnT2, encoding a putative Zn transporter explains 72% of the observed phenotypic variation. SlZnT2 copy number varies among isolates and different promotor genotypes were identified. Rapid adaptation in this species is supported by the cumulative effect of gene copy number variation and differences in cis-regulation and might be triggered by environmental stress rather than being the result of standing variation.\n\nOriginality - significance statementTo the best of our knowledge, this is the first study linking genotypes to adaptive phenotypes in mycorrhizal fungi. It is unique in the way it combines evolutionary and functional genetics to allow a significant advance in the understanding of responses to environmental stress factors in general and, to soil metal pollution in particular. A better understanding of adaptive tolerance mechanisms in keystone symbiotic fungi is paramount for developing impactful phyto and mycoremediation strategies for metal polluted waste land and to predict the impact of future environmental change on mycorrhizal diversity and ecosystem functioning.

genetics↗