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Gene co-expression networks (GCNs) are a powerful approach for exploring transcriptional regulation by identifying functionally related genes through their expression patterns across various conditions. The inference of GCNs can be achieved by various computational algorithms, each with distinct merits and limitations. The choice of algorithm can influence the network structure and the biological interpretation derived from it. By using a combination of different methods, biases can be minimised providing more robust and complementary insights. These methodologies are particularly valuable for non-model species, a challenge exemplified by Norway spruce and Scots pine. With ongoing climate change, drought and cold stresses are becoming increasingly important factors shaping the survival of these boreal conifers. Boreal regions are experiencing more frequent and prolonged drought periods, alongside greater variability in early spring, including sudden freeze-thaw events and episodes of extreme cold. Understanding the genetic regulation through which species such as Norway spruce and Scots pine, perceive, respond to, and potentially recover from drought and cold is therefore of high importance. 

In this thesis I have used an extensive collection of transcriptomic data generated from boreal tree species under abiotic stress conditions to infer GCNs to reveal coordinated patterns of gene expression responses to environmental challenges. In addition, comparative analyses of GCNs enabled the systematic assessment of conservation and divergence of co-expression among these species, identifying both shared regulatory circuits and species-specific adaptations. Analyses uncovered down-regulated modules of developmental processes, up-regulated modules of abiotic stress response, and several candidate transcription factors directly connected to these stress-responsive pathways. Comparison with boreal angiosperms revealed divergent responses in core cold-regulatory processes, most notably in the regulation and representation of C- repeat Binding Factor (CBF) transcription factors. The abiotic stress response patterns of both cold and drought were largely shared between the two conifer species, indicating a high degree of conservation in their transcriptional responses. This conservation extended to the organisation of topologically associated domains, where a subset of highly conserved co-expressed orthologs were found at the same location in the genomes of these conifers. 

Together, these analyses demonstrated the utility of comparative co-expression networks as a tool for understanding both conserved and diverged regulatory mechanisms, while offering new perspectives on the resilience of conifers in the context of environmental change.

Samuttrycksnätverk (GCNs) är ett kraftfullt verktyg för att utforska transkriptionsreglering genom att identifiera funktionellt relaterade gener via deras uttrycksmönster under olika förhållanden. GCNs kan konstrueras med hjälp av olika beräkningsalgoritmer, som var och en har styrkor och begränsningar. Valet av algoritm kan påverka nätverkets struktur och den biologiska tolkning som görs utifrån det. Genom att använda en kombination av olika metoder kan bias minimeras, vilket ger mer robusta och kompletterande insikter. Dessa metoder är särskilt värdefulla för icke-modellorganismer, vilket illustreras av gran och tall. I takt med det pågående klimatförändringarna blir torka och kyla allt viktigare faktorer som påverkar överlevnaden hos dessa boreala barrträd. Boreala regioner upplever nu mer frekventa och långvariga torkperioder, tillsammans med större variationer under tidig vår, inklusive plötsliga frysnings-tiningscykler och perioder av extrem kyla. Att förstå den genetiska regleringen genom vilken arter som gran och tall uppfattar, reagerar på och potentiellt återhämtar sig från torka och kyla är därför av stor betydelse.

I denna avhandling har jag använt en omfattande samling transkriptomdata genererad från boreala trädslag under abiotiska stressförhållanden för att konstruera GCNs och därigenom avslöja koordinerade uttrycksmönster som svar på miljöutmaningar. Dessutom möjliggjorde jämförande analyser av GCNs en systematisk bedömning av bevarande och divergens i samuttryck mellan arterna, vilket identifierade både delade regulatoriska nätverk och artspecifika anpassningar. Analyserna avslöjade nedreglerade moduler kopplade till utvecklingsprocesser, uppreglerade moduler involverade i abiotisk stressrespons, och flera kandidattranskriptionsfaktorer som var direkt kopplade till reglering av dessa stressrespons. Jämförelser mellan boreala angiospermer visade divergerande response i centrala processer reglerade av kyla, mest noterbart i regleringen och representationen av C-repeat Binding Factor (CBF)-transkriptionsfaktorer. Responsmönstren för både kyla och torka var i stor utsträckning delade mellan de två barrträdsarterna, vilket tyder på en hög grad av bevarande i deras transkriptionella svar. Detta bevarande sträckte sig även till organisationen av topologiskt associerade domäner, där en undergrupp av starkt bevarade samuttryckta ortologer hittades på samma position i båda arternas genom.

Sammantaget visar dessa analyser nyttan av att jämföra samuttrycksnätverk som ett verktyg för att förstå både bevarade och divergerade regulatoriska mekanismer, och ger samtidigt nya perspektiv på barrträdens resiliens i en föränderlig miljö.

What makes a tree a tree?

The capacity to form and maintain woody tissue has been key for the ecological success and economic relevance of forest trees. While fundamental cell types and developmental processes are common to most trees, there are significant differences between the two main tree lineages: angiosperms and gymnosperms.

Comparative genomic research has dramatically expanded our understanding of plant genome evolution, with several studies demonstrating that the transcriptional programmes underlying xylogenesis are largely conserved between lineages. Modern research suggests that both speciation and intraspecific variation are often the result, not only of coding sequence mutations, but also of shifts in gene expression regulation.

The aim of this thesis was to elucidate how genomic architecture and regulatory programmes govern wood development and secondary growth evolution. By combining comparative genomics with high-resolution spatial transcriptomics across angiosperm and gymnosperm species, this research establishes a multi-layered regulomic and evolutionary framework for studying wood formation.

The results identified multiple regulatory gene groups linked to wood evolution and development and generated significant genomic resources. In particular, chromosome-scale reference genomes were generated for two conifer species and an "evo-devo" resource for wood was established using a high-resolution comparative regulomic framework across wood differentiation layers in six tree species. Furthermore, a modified DNA Affinity Purification sequencing (DAP-seq) protocol was developed and optimised for mature woody tissues.

These resources can facilitate the identification of conserved and lineage-specific regulators, providing a critical blueprint for precision breeding and targeted genome engineering. Ultimately, these findings can contribute to the development of advanced materials and the transition toward a carbon-neutral bioeconomy.