Abstract
BackgroundThe 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.ResultsA 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2069-4) contains supplementary material, which is available to authorized users.
Highlights
The Rosaceae family encompasses numerous genera exhibiting morphological diversification in fruit types and plant habit as well as a wide variety of chromosome numbers
genotyping by sequencing (GBS) and BLAST analysis A total of 94,558,351 reads were produced from sequencing of the GBS library and the average number of reads per genotype used in map construction was 1,170,375
The linkage groups contained a total of 332 molecular markers—222 SNP markers developed through GBS, 96 RAPDs, nine AFLPs, four gene specific markers and one SSR—and the two phenotypic traits mapped previously and the map spanned a total of 413.7 cM
Summary
The Rosaceae family encompasses numerous genera exhibiting morphological diversification in fruit types and plant habit as well as a wide variety of chromosome numbers. The subsequent release of genome sequences for three Rosaceous species, in Fragaria, Malus, and Prunus [4,5,6] permitted synteny studies to be performed at higher resolution and with greater precision than had been possible using linkage mapping alone. While these studies supported the hypothesis of an ancestral genome containing nine chromosomes they provided further insights into the mechanisms that have shaped the evolution of the genomes of the various genera within the family that encompass such diversity in traits important to man [7, 8].
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