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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 chromosomes of Prunus, Fragaria, and Malus, with the colors represent the origin from the 49 contiguous ancestral regions (CARs). The spaces with a black line represent chromosomal regions where the ancestral origin was not assigned. CARs that existed before the split of Prunus, Fragaria and Malus, were detected by MGRA (Multiple Genome Rearrangments and Ancestors) algorithm [32]. The figure was drawn using R program (Hornik 2011).
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Figure 3: The chromosomes of Prunus, Fragaria, and Malus, with the colors represent the origin from the 49 contiguous ancestral regions (CARs). The spaces with a black line represent chromosomal regions where the ancestral origin was not assigned. CARs that existed before the split of Prunus, Fragaria and Malus, were detected by MGRA (Multiple Genome Rearrangments and Ancestors) algorithm [32]. The figure was drawn using R program (Hornik 2011).

Mentions: Reconstruction of a hypothetical ancestral genome for Rosaceae was performed using the MGRA (Multiple Genome Rearrangements and Ancestors) algorithm [32]. The Prunus and Fragaria genomes were used in the analysis with the Vitis genome as an outgroup. The Malus genome was not included in the MGRA analysis due to the fact that the primary assembly of apple did not include all the predicted genes sequenced. MGRA did not predict the number of chromosomes the ancestral genome contained, but it identified 49 CARs (Contiguous Ancestral Regions) that existed before the divergence of the Prunus, Fragaria and Malus genomes from a common ancestor. Each CAR represents a chromosomal region of the genome of the common ancestor of Prunus and Fragaria. The ancestral origins of the extant Malus chromosomes were inferred through a comparison of corresponding ORs in the Malus and Prunus genomes. Figure 3 shows the chromosomes of Prunus, Fragaria, and Malus, in which the 49 CARs are depicted in different colors. The results show that chromosomes of Fragaria are composed of many small chromosomal regions that originated from different ancestral CARs compared to those of Malus and Prunus (Figure 3), suggesting that the Fragaria genome went through a greater number of small scale rearrangements compared to the genomes of the other genera since they diverged from a common ancestor (Figure 3). Table 4 shows that the number of breaks between the chromosomal regions originating from different CARs in Fragaria is over two times greater than that in Malus and over 1.5 times greater than that in Prunus. The genomes of the diploid and the octoploid Fragaria that have been investigated to date through comparative mapping have been shown to be largely collinear [33,34], however, whether the occurrence of small chromosomal rearrangements is common in the entire Fragaria lineage or restricted to species closely related to F. vesca would require further investigation.


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 chromosomes of Prunus, Fragaria, and Malus, with the colors represent the origin from the 49 contiguous ancestral regions (CARs). The spaces with a black line represent chromosomal regions where the ancestral origin was not assigned. CARs that existed before the split of Prunus, Fragaria and Malus, were detected by MGRA (Multiple Genome Rearrangments and Ancestors) algorithm [32]. The figure was drawn using R program (Hornik 2011).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The chromosomes of Prunus, Fragaria, and Malus, with the colors represent the origin from the 49 contiguous ancestral regions (CARs). The spaces with a black line represent chromosomal regions where the ancestral origin was not assigned. CARs that existed before the split of Prunus, Fragaria and Malus, were detected by MGRA (Multiple Genome Rearrangments and Ancestors) algorithm [32]. The figure was drawn using R program (Hornik 2011).
Mentions: Reconstruction of a hypothetical ancestral genome for Rosaceae was performed using the MGRA (Multiple Genome Rearrangements and Ancestors) algorithm [32]. The Prunus and Fragaria genomes were used in the analysis with the Vitis genome as an outgroup. The Malus genome was not included in the MGRA analysis due to the fact that the primary assembly of apple did not include all the predicted genes sequenced. MGRA did not predict the number of chromosomes the ancestral genome contained, but it identified 49 CARs (Contiguous Ancestral Regions) that existed before the divergence of the Prunus, Fragaria and Malus genomes from a common ancestor. Each CAR represents a chromosomal region of the genome of the common ancestor of Prunus and Fragaria. The ancestral origins of the extant Malus chromosomes were inferred through a comparison of corresponding ORs in the Malus and Prunus genomes. Figure 3 shows the chromosomes of Prunus, Fragaria, and Malus, in which the 49 CARs are depicted in different colors. The results show that chromosomes of Fragaria are composed of many small chromosomal regions that originated from different ancestral CARs compared to those of Malus and Prunus (Figure 3), suggesting that the Fragaria genome went through a greater number of small scale rearrangements compared to the genomes of the other genera since they diverged from a common ancestor (Figure 3). Table 4 shows that the number of breaks between the chromosomal regions originating from different CARs in Fragaria is over two times greater than that in Malus and over 1.5 times greater than that in Prunus. The genomes of the diploid and the octoploid Fragaria that have been investigated to date through comparative mapping have been shown to be largely collinear [33,34], however, whether the occurrence of small chromosomal rearrangements is common in the entire Fragaria lineage or restricted to species closely related to F. vesca would require further investigation.

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.

Show MeSH
Related in: MedlinePlus