Pra-GE-ATLAS: Empowering Pinus radiata stress and breeding research through a multi-omics database

Area of Science:

• Plant Science
• Genomics
• Bioinformatics

Background:

• Model organism research in plant science has limitations due to narrow phylogenetic scope.
• Gymnosperms, particularly conifers, are vital yet underrepresented in molecular research.
• Lack of community resources hinders conifer investigation.

Purpose of the Study:

• To develop the Pinus radiata-Gene Expression (Pra-GE)-ATLAS database for conifers.
• To centralize transcriptomic and proteomic data for Pinus radiata.
• To provide insights into gene regulation and evolutionary features in pines.

Main Methods:

• Development of the Pra-GE-ATLAS database with transcriptomics and proteomics modules.
• Integration of regulatory layers across tissues and stressors.
• Analysis of intron retention and alternative splicing.

Main Results:

• Stress influences intron retention, favoring smaller introns.
• Genes with large introns in conifers are constitutively regulated.
• Proteomic responses show distinct convergence across stressors, even with intergenerational tolerance.

Conclusions:

• The Pra-GE-ATLAS database bridges the resource gap between angiosperms and gymnosperms.
• The findings deepen the understanding of conifer gene regulation and evolution.
• The database facilitates new biological insights into characteristic pine traits.