Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus

Area of Science:

• Genomics
• Plant Science
• Molecular Biology

Background:

• Mitochondrial DNA (mtDNA) is crucial for understanding plant evolution and population genetics.
• Developing genetic markers for non-model plant species like *Pinus sylvestris* and *Pinus mugo* is challenging due to limited genomic resources.

Purpose of the Study:

• To recover novel mitochondrial genome sequences from *Pinus sylvestris* and the *Pinus mugo* species complex.
• To develop a cost-effective method for generating mitochondrial DNA (mtDNA) markers for population genetics in conifers.

Main Methods:

• Whole-genome-shotgun (WGS) sequencing of total genomic DNA from megagametophyte tissue.
• Bioinformatic identification of candidate mtDNA sequences and novel variants.
• Development and trial of SNP primers on a European sample set of *Pinus* individuals.

Main Results:

• Approximately 1 Mbp of novel mitochondrial (mtDNA) sequence was recovered from *Pinus sylvestris* and *Pinus mugo*.
• 31 single nucleotide polymorphism (SNP) loci were successfully developed and resequenced.
• 15 unique mtDNA haplotypes were characterized across 28 individuals.

Conclusions:

• Whole-genome-shotgun (WGS) sequencing is an effective strategy for recovering mtDNA sequences in plants lacking reference genomes.
• The developed SNP markers provide valuable resources for population genetic studies in *Pinus* species.
• This method offers a scalable and cost-effective approach for marker development in other plant species.