title: Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus.
abstract: Whole-genome-shotgun (WGS) sequencing of total genomic DNA was used to recover ~1 Mbp of novel mitochondrial (mtDNA) sequence from Pinus sylvestris (L.) and three members of the closely related Pinus mugo species complex. DNA was extracted from megagametophyte tissue from six mother trees from locations across Europe, and 100-bp paired-end sequencing was performed on the Illumina HiSeq platform. Candidate mtDNA sequences were identified by their size and coverage characteristics, and by comparison with published plant mitochondrial genomes. Novel variants were identified, and primers targeting these loci were trialled on a set of 28 individuals from across Europe. In total, 31 SNP loci were successfully resequenced, characterizing 15 unique haplotypes. This approach offers a cost-effective means of developing marker resources for mitochondrial genomes in other plant species where reference sequences are unavailable.
authors.affiliation: NERC Centre for Ecology and Hydrology, Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.|Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK.
authors.forename: Kevin
authors.identifier: http://orcid.org/0000-0001-7633-9113
authors.initials: K
authors.lastname: Donnelly
authors.affiliation: Forest Research, Northern Research Station, Roslin, Midlothian, EH25 9SY, UK.
authors.forename: Joan
authors.initials: J
authors.lastname: Cottrell
authors.affiliation: Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Ennos
authors.affiliation: Institute of Biosciences and BioResources, Division of Florence, National Research Council, Via Madonna del Piano, 10, 50019, Sesto Fiorentino (Firenze), Italy.
authors.forename: Giovanni Giuseppe
authors.initials: GG
authors.lastname: Vendramin
authors.affiliation: Forest Research, Northern Research Station, Roslin, Midlothian, EH25 9SY, UK.
authors.forename: Stuart
authors.initials: S
authors.lastname: A'Hara
authors.affiliation: NERC Centre for Ecology and Hydrology, Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.
authors.forename: Sarah
authors.initials: S
authors.lastname: King
authors.affiliation: NERC Centre for Ecology and Hydrology, Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.
authors.forename: Annika
authors.initials: A
authors.lastname: Perry
authors.affiliation: NERC Centre for Ecology and Hydrology, Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.|Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland.
authors.forename: Witold
authors.initials: W
authors.lastname: Wachowiak
authors.affiliation: NERC Centre for Ecology and Hydrology, Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.
authors.forename: Stephen
authors.identifier: http://orcid.org/0000-0003-2139-9236
authors.initials: S
authors.lastname: Cavers
mesh_terms: D019295:Computational Biology; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D005060:Europe; D054629:Genome, Mitochondrial; D006239:Haplotypes; D008928:Mitochondria / Q000235:genetics*; D028223:Pinus / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D000073336:Whole Genome Sequencing
chemical_list: D004272:DNA, Mitochondrial; D018744:DNA, Plant
keywords: Pinus; high-throughput sequencing; marker discovery; mitochondrion; phylogeography