Natural selection and recombination interact to structure genome-wide variation in pines

Area of Science:

• Genomics
• Evolutionary Biology
• Population Genetics

Background:

• Genetic differentiation varies across genomes due to selection and recombination, creating heterogeneous landscapes.
• Genomic valleys (low-differentiation regions) and their evolutionary drivers are poorly understood, especially in non-flowering plants like conifers.
• Genome-wide studies in conifers are limited compared to flowering plants.

Purpose of the Study:

• To investigate the genomic landscape of genetic differentiation in three pine species.
• To understand the role of recombination and selection in shaping genomic valleys.
• To explore the evolution of exceptionally long genes in conifers.

Main Methods:

• Whole-genome sequencing of 100 individuals from Pinus banksiana, Pinus contorta, and Pinus nigra.
• Analysis of recombination rate variation across the genome.
• Genomic scans to identify regions under selection and their association with recombination rates.

Main Results:

• Significant genome-wide variation in recombination rates was observed, with higher rates in intergenic regions and decreasing rates with distance from genes.
• Recombination rate negatively correlated with gene length, particularly intron length, potentially explaining long genes in conifers.
• Genomic valleys are maintained by balancing, background, or parallel selection, strongly associated with local recombination rate variation.

Conclusions:

• Recombination plays a crucial role in shaping genomic differentiation patterns in pines.
• Allopatric selection in low-recombination regions is a major factor structuring genomic variation in these conifer species.
• Findings offer new insights into the evolution and maintenance of extremely long genes in conifers.