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Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies.

Jung S, Cestaro A, Troggio M, Main D, Zheng P, Cho I, Folta KM, Sosinski B, Abbott A, Celton JM, Arús P, Shulaev V, Verde I, Morgante M, Rokhsar D, Velasco R, Sargent DJ - BMC Genomics (2012)

Bottom Line: However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor.Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae.The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA. sook_jung@wsu.edu

ABSTRACT

Background: Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes.

Results: Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes.

Conclusion: Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.

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The Concentric circle of Rosaceae genomes. The innermost circle represents the putative nine chromosomes of Rosaceae ancestral genome. Next sets of circles represent eight, 17 and seven chromosomes of Prunus, Malus and Fragaria, respectively. The regions originated from each Rosaceae ancestral chromosome are highlighted with corresponding color in Figure S3. The Data were plotted using Circos [42].
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Figure 5: The Concentric circle of Rosaceae genomes. The innermost circle represents the putative nine chromosomes of Rosaceae ancestral genome. Next sets of circles represent eight, 17 and seven chromosomes of Prunus, Malus and Fragaria, respectively. The regions originated from each Rosaceae ancestral chromosome are highlighted with corresponding color in Figure S3. The Data were plotted using Circos [42].

Mentions: To show how the genomes of the three taxa have evolved since they diverged from this common ancestral karyotypes, the nine ancestral chromosomes, A1 through A9, along with genomes of three species, colored by the ancestral chromosomal origin, were constructed (Additional file 4: Figure S3). In this figure, the 24 CARs in Figure 4 were reassigned with colors based on which of the nine ancestral chromosomes they reside in. The orthologous relationships amongst the three Rosaceae genomes are shown in the Rosaceae concentric circle with the putative nine chromosomes of Rosaceae ancestral genome as the innermost circle (Figure 5). This allows the identification of orthologous regions between the three genomes that have a common ancestral origin.


Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies.

Jung S, Cestaro A, Troggio M, Main D, Zheng P, Cho I, Folta KM, Sosinski B, Abbott A, Celton JM, Arús P, Shulaev V, Verde I, Morgante M, Rokhsar D, Velasco R, Sargent DJ - BMC Genomics (2012)

The Concentric circle of Rosaceae genomes. The innermost circle represents the putative nine chromosomes of Rosaceae ancestral genome. Next sets of circles represent eight, 17 and seven chromosomes of Prunus, Malus and Fragaria, respectively. The regions originated from each Rosaceae ancestral chromosome are highlighted with corresponding color in Figure S3. The Data were plotted using Circos [42].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368713&req=5

Figure 5: The Concentric circle of Rosaceae genomes. The innermost circle represents the putative nine chromosomes of Rosaceae ancestral genome. Next sets of circles represent eight, 17 and seven chromosomes of Prunus, Malus and Fragaria, respectively. The regions originated from each Rosaceae ancestral chromosome are highlighted with corresponding color in Figure S3. The Data were plotted using Circos [42].
Mentions: To show how the genomes of the three taxa have evolved since they diverged from this common ancestral karyotypes, the nine ancestral chromosomes, A1 through A9, along with genomes of three species, colored by the ancestral chromosomal origin, were constructed (Additional file 4: Figure S3). In this figure, the 24 CARs in Figure 4 were reassigned with colors based on which of the nine ancestral chromosomes they reside in. The orthologous relationships amongst the three Rosaceae genomes are shown in the Rosaceae concentric circle with the putative nine chromosomes of Rosaceae ancestral genome as the innermost circle (Figure 5). This allows the identification of orthologous regions between the three genomes that have a common ancestral origin.

Bottom Line: However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor.Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae.The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA. sook_jung@wsu.edu

ABSTRACT

Background: Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes.

Results: Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes.

Conclusion: Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.

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