Cyberinfrastructure and resources to enable an integrative approach to studying forest trees

FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research

The genomes of thousands of individuals are profiled within Dutch healthcare and research each year. However, this valuable genomic data, associated clinical data and consent are captured in different ways and stored across many systems and organizations. This makes it difficult to discover rare disease patients, reuse data for personalized medicine and establish research cohorts based on specific parameters. FAIR Genomes aims to enable NGS data reuse by developing metadata standards for the data descriptions needed to FAIRify genomic data while also addressing ELSI issues. We developed a semantic schema of essential data elements harmonized with international FAIR initiatives. The FAIR Genomes schema v1.1 contains 110 elements in 9 modules. It reuses common ontologies such as NCIT, DUO and EDAM, only introducing new terms when necessary. The schema is represented by a YAML file that can be transformed into templates for data entry software (EDC) and programmatic interfaces (JSON, RDF) to ease genomic data sharing in research and healthcare. The schema, documentation and MOLGENIS reference implementation are available at https://fairgenomes.org .

Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.

Dual activities of ACC synthase: Novel clues regarding the molecular evolution of ACS genes

Ethylene plays profound roles in plant development. The rate-limiting enzyme of ethylene biosynthesis is 1-aminocyclopropane-1-carboxylate (ACC) synthase (ACS), which is generally believed to be a single-activity enzyme evolving from aspartate aminotransferases. Here, we demonstrate that, in addition to catalyzing the conversion of S-adenosyl-methionine to the ethylene precursor ACC, genuine ACSs widely have C_β-S lyase activity. Two N-terminal motifs, including a glutamine residue, are essential for conferring ACS activity to ACS-like proteins. Motif and activity analyses of ACS-like proteins from plants at different evolutionary stages suggest that the ACC-dependent pathway is uniquely developed in seed plants. A putative catalytic mechanism for the dual activities of ACSs is proposed on the basis of the crystal structure and biochemical data. These findings not only expand our current understanding of ACS functions but also provide novel insights into the evolutionary origin of ACS genes.

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.

Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis

The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.

Annual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting

Assisted gene flow between populations has been proposed as an adaptive forest management strategy that could contribute to the sequestration of carbon. Here we provide an assessment of the mitigation potential of assisted gene flow in 46 populations of the widespread boreal conifer Picea mariana, grown in two 42-year-old common garden experiments and established in contrasting Canadian boreal regions. We use a dendroecological approach taking into account phylogeographic structure to retrospectively analyse population phenotypic variability in annual aboveground net primary productivity (NPP). We compare population NPP phenotypes to detect signals of adaptive variation and/or the presence of phenotypic clines across tree lifespans, and assess genotype-by-environment interactions by evaluating climate and NPP relationships. Our results show a positive effect of assisted gene flow for a period of approximately 15 years following planting, after which there was little to no effect. Although not long lasting, well-informed assisted gene flow could accelerate the transition from carbon source to carbon sink after disturbance.

Forest genomics: Advancing climate adaptation, forest health, productivity, and conservation

Forest ecosystems provide important ecological services and resources, from habitat for biodiversity to the production of environmentally friendly products, and play a key role in the global carbon cycle. Humanity is counting on forests to sequester and store a substantial portion of the anthropogenic carbon dioxide produced globally. However, the unprecedented rate of climate change, deforestation, and accidental importation of invasive insects and diseases are threatening the health and productivity of forests, and their capacity to provide these services. Knowledge of genetic diversity, local adaptation, and genetic control of key traits is required to predict the adaptive capacity of tree populations, inform forest management and conservation decisions, and improve breeding for productive trees that will withstand the challenges of the 21st century. Genomic approaches have well accelerated the generation of knowledge of the genetic and evolutionary underpinnings of nonmodel tree species, and advanced their applications to address these challenges. This special issue of Evolutionary Applications features 14 papers that demonstrate the value of a wide range of genomic approaches that can be used to better understand the biology of forest trees, including species that are widespread and managed for timber production, and others that are threatened or endangered, or serve important ecological roles. We highlight some of the major advances, ranging from understanding the evolution of genomes since the period when gymnosperms separated from angiosperms 300 million years ago to using genomic selection to accelerate breeding for tree health and productivity. We also discuss some of the challenges and future directions for applying genomic tools to address long-standing questions about forest trees.