Exome capture from the spruce and pine giga-genomes

Area of Science:

• Genomics
• Forest Ecology
• Molecular Biology

Background:

• Massive genomes in conifer species pose challenges for genetic research.
• Reduced representation libraries are crucial for efficient genomic analysis.
• Sequence capture offers a flexible approach for targeting specific genomic regions.

Purpose of the Study:

• To apply exome capture for sequencing the gene space of interior spruce and lodgepole pine.
• To design and validate sequence capture baits for conifer genomes.
• To generate a rich resource of genetic variants for adaptation studies.

Main Methods:

• Designed sequence capture baits targeting over 26,000 genes for pine and 28,000 for spruce.
• Utilized RNA-sequencing and draft genome assemblies for bait design.
• Sequenced 579 spruce and 631 pine samples, including related species.

Main Results:

• Achieved >10× sequencing depth in over 50% of targeted regions for both species.
• Demonstrated successful cross-species capture in related conifer congeners.
• Identified approximately 10 million single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) per species.

Conclusions:

• Sequence capture is highly effective for resequencing complex conifer genomes.
• Developed guidelines for improving sequence capture efficiency in non-model organisms.
• The generated genetic variants provide a valuable resource for evolutionary and ecological studies.