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

Abstract

Sequencing technologies and bioinformatic approaches are now available to resolve the challenges associated with complex and heterozygous genomes. Increased access to less expensive and more effective instrumentation will contribute to a wealth of high‐quality plant genomes in the next few years. In the meantime, more than 370 tree species are associated with public projects in primary repositories that are interrogating expression profiles, identifying variants, or analyzing targeted capture without a high‐quality reference genome. Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes. These data contribute to forest tree biology, but the associated sequence remains trapped in supplemental files that are poorly integrated in plant community databases and comparative genomic platforms. Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non‐model plant species. Unique to forest trees with large populations that are long‐lived, outcrossing, and genetically diverse, the phenotypic and environmental metrics associated with georeferenced populations are just as important as the genomic data sampled for each individual. To address questions related to forest health and productivity, cyberinfrastructure must keep pace with the magnitude of genomic and phenomic sampling of larger populations. This review examines the current landscape of cyberinfrastructure, with an emphasis on best practices and resources to align community data with the Findable, Accessible, Interoperable, and Reusable (FAIR) guidelines.

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

“…Transcriptomic resources have been particularly important for research in conifers and other non-model species, as a strategy to compensate for the challenges associated with efficient genome assembly and annotation ( Cañas et al, 2019 ; Wegrzyn et al, 2020 ). As the biological functions can not be directly inferred from nucleotide sequences, reference transcriptomes and gene expression studies are useful in the identification and annotation of genes ( Raherison et al, 2012 ; Wegrzyn et al, 2014 ; Merino et al, 2016 ; Little et al, 2016 ; Cañas et al, 2017 ).…”

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

“…In order to inform adaptive forest management strategies such as assisted gene flow and to increase their likelihood of success, species-specific adaptive genetic heterogeneity should be documented to look for future optimal genetic composition 15 , 36 , 60 , 62 . Nowadays, baseline genetic data and/or genomic resources (including tools) are available for more than 2000 tree species and this number is increasing 63 ( https://treegenesdb.org/ ). This information, or at least a part of it, can be used and/or translated into applications and/or adapted to assess mitigation potential of different forest strategies across different tree species 15 , 36 .…”

Genomics studies for trait improvement in four important tree species: Current status and future prospects

“…In addition, there are other tree genomic databases like TropGeneDB, TropiTree, PGP Repository, Plantgenie, etc. (Wegrzyn et al, 2020), which are striving to enhance the data generated by the researchers to store, submit and analyze forest tree data improving forest health and productivity.…”