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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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Comparison of orthologous regions (OR) from two-species analyses and those from the three-species analysis. A. ORs between PC2 and chromosomes of Fragaria and Malus, detected from two separate analyses. B. The same ORs shown in A as well as ORs that are shared by all three species. Blue lines link the ORs shared by all three species, red lines link ORs between Prunus and Fragaria only, and green lines link ORs between Prunus and Malus only. Data were plotted using Circos [42].
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Figure 2: Comparison of orthologous regions (OR) from two-species analyses and those from the three-species analysis. A. ORs between PC2 and chromosomes of Fragaria and Malus, detected from two separate analyses. B. The same ORs shown in A as well as ORs that are shared by all three species. Blue lines link the ORs shared by all three species, red lines link ORs between Prunus and Fragaria only, and green lines link ORs between Prunus and Malus only. Data were plotted using Circos [42].

Mentions: When multiple species are used, as in this analysis, pairwise homology maps can be utilized to build orthology maps for multiple species, as Mercator will find orthologous segments even if some anchors are missing in one of the species. The analysis thus resulted in the detection of additional orthologous regions that were not detected when the taxon pairs were investigated separately (Table 1). The comparison of ORs from the two-species analyses and the comparison of ORs from the three-species analysis are shown in Figure 2. Figure 2A shows ORs between PC2 and chromosomes of Fragaria and Malus, detected by separate taxon pair analyses. Figure 2B shows the same ORs shown in Figure 2A as well as the ORs shared between all three species. Blue lines link the ORs shared by all three species, red lines link ORs between Prunus and Fragaria only, and green lines link ORs between Prunus and Malus only. The figures showing ORs in the other seven Prunus chromosomes are shown in Additional file 1: Figure S1. The presence of red lines and green lines in Figure 2B shows that some ORs remain syntenic only between two species, as expected. The comparison of Figure 2A, B also shows additional ORs, which were not detected by the analyses of single taxon pairs. Most notable were the large numbers of additional ORs between Prunus and Malus that were detected in the three-species analysis. The additional ORs that were detected mostly resided in chromosomes that did not display major orthologous relationships with chromosome PC2 (Figure 2B, Table 2). This result suggests that content and/or order of the genes in ORs that reside on non-orthologous chromosomes went through more rearrangements than those in highly orthologous regions, masking their ancestral origins.


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)

Comparison of orthologous regions (OR) from two-species analyses and those from the three-species analysis. A. ORs between PC2 and chromosomes of Fragaria and Malus, detected from two separate analyses. B. The same ORs shown in A as well as ORs that are shared by all three species. Blue lines link the ORs shared by all three species, red lines link ORs between Prunus and Fragaria only, and green lines link ORs between Prunus and Malus only. 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 2: Comparison of orthologous regions (OR) from two-species analyses and those from the three-species analysis. A. ORs between PC2 and chromosomes of Fragaria and Malus, detected from two separate analyses. B. The same ORs shown in A as well as ORs that are shared by all three species. Blue lines link the ORs shared by all three species, red lines link ORs between Prunus and Fragaria only, and green lines link ORs between Prunus and Malus only. Data were plotted using Circos [42].
Mentions: When multiple species are used, as in this analysis, pairwise homology maps can be utilized to build orthology maps for multiple species, as Mercator will find orthologous segments even if some anchors are missing in one of the species. The analysis thus resulted in the detection of additional orthologous regions that were not detected when the taxon pairs were investigated separately (Table 1). The comparison of ORs from the two-species analyses and the comparison of ORs from the three-species analysis are shown in Figure 2. Figure 2A shows ORs between PC2 and chromosomes of Fragaria and Malus, detected by separate taxon pair analyses. Figure 2B shows the same ORs shown in Figure 2A as well as the ORs shared between all three species. Blue lines link the ORs shared by all three species, red lines link ORs between Prunus and Fragaria only, and green lines link ORs between Prunus and Malus only. The figures showing ORs in the other seven Prunus chromosomes are shown in Additional file 1: Figure S1. The presence of red lines and green lines in Figure 2B shows that some ORs remain syntenic only between two species, as expected. The comparison of Figure 2A, B also shows additional ORs, which were not detected by the analyses of single taxon pairs. Most notable were the large numbers of additional ORs between Prunus and Malus that were detected in the three-species analysis. The additional ORs that were detected mostly resided in chromosomes that did not display major orthologous relationships with chromosome PC2 (Figure 2B, Table 2). This result suggests that content and/or order of the genes in ORs that reside on non-orthologous chromosomes went through more rearrangements than those in highly orthologous regions, masking their ancestral origins.

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