Catching up for the Lack of Functional Knowledge and Molecular Markers in a Large and Complex Conifer Genome Using mRNAseq and RADseq

The recent advances in Next Generation Sequencing (NGS) technologies are accelerating the development of genomic resources and allowing a comparative understanding of the genome structure of forest trees. Sequencing a reduced snapshot of the genome is an alternative to the full genome sequencing, particularly interesting for non-model conifer tree species where full sequencing is still hardly feasible.

In the framework of NGS, we applied two genome complexity reduction methods: mRNAseq and RADseq (Restriction site Associated DNA sequencing) in a Pinaceae species with a challenging large and complex genome that has hindered the development of molecular markers so far: Cedrus atlantica Manetti. This study was a first tentative of applying RADseq in a coniferous tree. The PstIhypomethylation sensitive enzyme was used.

Sequence similarity and functional annotation analyses showed comparable redundancy proportions and coding-like sequences fractions between the mRNAseq and RADseq assemblies. It gave insights about the methylation profile and confirmed the ability of the RADseq to generate a redundancy-reduced filtrate of the genome, enriched by coding sequences in conifers. RADseq generated thousands of Single Nucleotide Polymorphism (SNP) markers from which we selected a high-quality subgroup and evaluated the ascertainment bias due to our choice criteria.

Key words: Conifers, genome complexity, genome methylation, coding sequences, SNPs, ascertainment bias.