Rose genome reveals its complexities

A rose may be a rose may be a rose (to paraphrase Gertrude Stein) but genetically roses (like many plant species) are wickedly complex. The genus Rosa comprises about 200 species, although only 8-20 species are thought to have contributed to modern rose cultivars. Rose genomic complexity is expressed, inter alia, in their chromosome structures, which is a genetic patchwork of sequences from a large number of cultivars, and as with many plants a significant percentage of Rosa species (about half) are polyploid. 

The evolutionary history of these species has involved reticulate evolution, interspecific hybridization, introgression and polyploidization, which has contributed to the genetic variability and chromosome structure.  This provides broad phenotypic variability, in flower size, color, fragrance, medicinal properties, and other features selected for not (just) naturally but by generations of plant breeders. 

For example, one of the first hybrids, "La France," produced in Europe beginning in the 18th Century, combined "growth vigor" characteristic of European rose varieties with the propensity for current blooming characteristic of Chinese roses (as well as color and scent signatures).  And this genetic complexity has made determining the rose genomic DNA sequence particularly difficult, despite its relatively small size (560 Mb).

Last spring (appropriately) a team of scientists revealed the first compilation of the rose genome in a paper published in Nature Genetics entitled "The Rosa genome provides new insights into the domestication of modern roses." 

Relevant to the genetic mosaicism referenced above, these authors needed to produce a "homozygous" genotype from one of the heterozygous diploid rose progenitors, Rosa chinensis "Old Blush," in order to produce a reliable genomic rose sequence.  Upon sequencing, these scientists were able to produce 7 "pseudo chromosomes" corresponding to a homozygous genome; in nature roses have 7, 14, 28, 35, or 42 chromosomes.  The sequenced data suggested there are 36,377 protein-coding genes and almost 4,000 long noncoding RNA sequences in the rose genome.  Transposable elements comprised almost 68% of the rose genome, with long terminal repeat retrotransposons representing about half of these sequences.  Comparisons between related species permitted these researchers to identify an ancestral karyotype having 9 protochromosomes and 8,861 protogenes, with the ancestral strawberry and rose genomes were modeled into 8 protochromosomes comprising 13,060 protogenes, produced by two ancestral chromosomes fusions and one chromosome fission; the authors report that the strawberry ancestral genome experienced an extra fusion resulting in the modern genome, where the rose genome experienced one fission and two fusions, independently of strawberry.

Click here to read the complete article.

Photo credit: Max Pixel, CC0 Public Domain.

03/13/2019 - JD Supra

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