Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus

Background: The Rosaceae family encompasses numerous genera exhibiting morphological diversification in fruit types and plant habit as well as a wide variety of chromosome numbers. Comparative genomics between various Rosaceous genera has led to the hypothesis that the ancestral genome of the family contained nine chromosomes, however, the synteny studies performed in the Rosaceae to date encompass species with base chromosome numbers x = 7 (Fragaria), x = 8 (Prunus), and x = 17 (Malus), and no study has included species from one of the many Rosaceous genera containing a base chromosome number of x = 9. Results: A genetic linkage map of the species Physocarpus opulifolius (x = 9) was populated with sequence characterised SNP markers using genotyping by sequencing. This allowed for the first time, the extent of the genome diversification of a Rosaceous genus with a base chromosome number of x = 9 to be performed. Orthologous loci distributed throughout the nine chromosomes of Physocarpus and the eight chromosomes of Prunus were identified which permitted a meaningful comparison of the genomes of these two genera to be made. Conclusions: The study revealed a high level of macro-synteny between the two genomes, and relatively few chromosomal rearrangements, as has been observed in studies of other Rosaceous genomes, lending further support for a relatively simple model of genomic evolution in Rosaceae

Predicted Fire Behavior and Societal Benefits in Three Eastern Sierra Nevada Vegetation Types

We investigated potential fire behavior and various societal benefits (air pollution removal, carbon sequestration, and carbon storage) provided by woodlands of pinyon pine (Pinus monophylla) and juniper (Juniperus californica), shrublands of Great Basin sagebrush (Artemisia tridentata) and rabbitbrush (Ericameria nauseosa), and recently burned annual grasslands near a wildland-urban interface (WUI) community in the high desert of the eastern Sierra Nevada Mountains. Fire behavior simulations showed that shrublands had the greatest flame lengths under low wind conditions, and that pinyon-juniper woodlands had the greatest flame lengths when winds exceeded 25 km hr-1 and fire transitioned to the crowns. Air pollution removal capacity (PM10, O3, NO2, etc.) was significantly greater in pinyon-juniper stands, followed by shrublands and grasslands. Carbon storage (trees and burned tree snags only) did not significantly differ between pinyon-juniper and burned stands (~14 000 kg ha-1), but will change as burned snags decompose. Annual C sequestration rates in pinyon-juniper stands averaged 630 kg ha-1 yr-1. A landscape-level assessment showed that total compliance with residential defensible space regulations would result in minimal impact to air pollution removal capacity and carbon sequestration due to a currently low population density. Our methodology provides a practical mechanism to assess how potential management options might simultaneously impact both fire behavior and various environmental services provided by WUI vegetation

MOESM1 of Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus

Additional file 1: Figure S1–S9. Orthology maps of each individual Physocarpus opulifolius linkage group detailing the relationships between each and the eight pseudomolecules of the P. persica genome sequence through the mapping of orthologous markers. Physocarpus linkage groups are shown on the left of the figure and genetic distances are given in cM, whilst Prunus pseudomolecules are given to the right and their physical distances are given in 100,000 bp intervals. Links between linkage groups and pseudomolecules indicate the positions of orthologous markers on the two genomes

MOESM2 of Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus

Additional file 2: Table S1. Positions of orthologous markers mapped in Physocarpus, the linkage group and genetic position of each marker, and their corresponding Prunus chromosome and physical position