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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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Orthology map identified between three Rosaceous genera based on whole genome sequence analysis. The lines link one to one orthologous regions, identified using Mercator program [25]. A. Comparison between Prunus and Fragaria, B. Comparison between Prunus and Malus. Data were plotted using Circos [42]. Colors for plots A and B follow the same pattern based on Prunus chromosomes.
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Figure 1: Orthology map identified between three Rosaceous genera based on whole genome sequence analysis. The lines link one to one orthologous regions, identified using Mercator program [25]. A. Comparison between Prunus and Fragaria, B. Comparison between Prunus and Malus. Data were plotted using Circos [42]. Colors for plots A and B follow the same pattern based on Prunus chromosomes.

Mentions: Thus, the evolutionary history of Rosaceous genomes was investigated through the detection of ORs between Prunus and Fragaria or Malus, using Mercator [25]. A total of 1281 ORs were obtained in the comparison between Prunus and Fragaria, with the longest region of 1.7 Mb of PC3 and 1.4 Mb of FC6 (Table 1). The mean number of matching exons in each OR was 17 and the mean lengths of ORs were 98.8 kb in Prunus and 98.4 kb in Fragaria (Table 1). Figure 1 shows the ORs between Prunus and Fragaria (A) and Prunus and Malus (B). In most cases, each peach chromosome showed major orthology to one strawberry chromosome, but to two or more apple chromosomes, clearly indicating that the whole genome duplication (WGD) in apple occurred following the divergence of the three genera. The ortholgous relationships between chromosomes of Fragaria and Prunus were clear, with the majority of ORs on Prunus chromosomes PC2, PC3, PC4, PC5, and PC8 each corresponding to single homologous chromosome in Fragaria, FC7, FC6, FC3, FC5, and FC2, respectively. The majority of ORs on PC7 corresponded to two Fragaria chromosomes, FC1 and FC6, and those on PC6 corresponded to three regions of the Fragaria genome on FC1, FC3 and FC6. The Prunus ORs on PC1 were the most widely distributed within the Fragaria genome, with ORs corresponding to multiple homologous chromosomal regions, but with one major syntenic relationship with FC4 (Figure 1A, Table 2).


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)

Orthology map identified between three Rosaceous genera based on whole genome sequence analysis. The lines link one to one orthologous regions, identified using Mercator program [25]. A. Comparison between Prunus and Fragaria, B. Comparison between Prunus and Malus. Data were plotted using Circos [42]. Colors for plots A and B follow the same pattern based on Prunus chromosomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Orthology map identified between three Rosaceous genera based on whole genome sequence analysis. The lines link one to one orthologous regions, identified using Mercator program [25]. A. Comparison between Prunus and Fragaria, B. Comparison between Prunus and Malus. Data were plotted using Circos [42]. Colors for plots A and B follow the same pattern based on Prunus chromosomes.
Mentions: Thus, the evolutionary history of Rosaceous genomes was investigated through the detection of ORs between Prunus and Fragaria or Malus, using Mercator [25]. A total of 1281 ORs were obtained in the comparison between Prunus and Fragaria, with the longest region of 1.7 Mb of PC3 and 1.4 Mb of FC6 (Table 1). The mean number of matching exons in each OR was 17 and the mean lengths of ORs were 98.8 kb in Prunus and 98.4 kb in Fragaria (Table 1). Figure 1 shows the ORs between Prunus and Fragaria (A) and Prunus and Malus (B). In most cases, each peach chromosome showed major orthology to one strawberry chromosome, but to two or more apple chromosomes, clearly indicating that the whole genome duplication (WGD) in apple occurred following the divergence of the three genera. The ortholgous relationships between chromosomes of Fragaria and Prunus were clear, with the majority of ORs on Prunus chromosomes PC2, PC3, PC4, PC5, and PC8 each corresponding to single homologous chromosome in Fragaria, FC7, FC6, FC3, FC5, and FC2, respectively. The majority of ORs on PC7 corresponded to two Fragaria chromosomes, FC1 and FC6, and those on PC6 corresponded to three regions of the Fragaria genome on FC1, FC3 and FC6. The Prunus ORs on PC1 were the most widely distributed within the Fragaria genome, with ORs corresponding to multiple homologous chromosomal regions, but with one major syntenic relationship with FC4 (Figure 1A, Table 2).

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