Limits...
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.

Show MeSH

Related in: MedlinePlus

Hypothetical evolutionary steps from the nine Rosaceae ancestral chromosomes to Fragaria, Prunus and Malus lineage. Each color represent distinct CARs detected by MGRA algorithm. Chromosomal rearrangements specific for Rosoideae (contains Fragaria) and Spireaoideae (contains Malus and Prunus) are depicted. Also shown are chromosomal rearragenments specific for Prunus, Malus, and subgenome of Malus after the WGD.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3368713&req=5

Figure 4: Hypothetical evolutionary steps from the nine Rosaceae ancestral chromosomes to Fragaria, Prunus and Malus lineage. Each color represent distinct CARs detected by MGRA algorithm. Chromosomal rearrangements specific for Rosoideae (contains Fragaria) and Spireaoideae (contains Malus and Prunus) are depicted. Also shown are chromosomal rearragenments specific for Prunus, Malus, and subgenome of Malus after the WGD.

Mentions: Since the genus Fragaria split from the common ancestor of Malus and Prunus before those species diverged, if regions with the same ancestral origin reside in the same chromosome of both Prunus and Fragaria, but in different chromosomes of Malus, we can infer that the those chromosomes of Malus were generated by a fission event. Likewise, if regions with the same ancestral origin reside in the same chromosome of Prunus but in different chromosomes of Malus and Fragaria, we can infer the chromosome of Prunus was generated by a fusion event. In this way, we have constructed a hypothetical ancestral karyotype, consisting of nine chromosomes, using the top 24 CARs identified in this investigation (Figure 4). The orthology maps between the three species, which support the hypothesis, are shown in Additional file 2: Figure S2. Figure 4 shows that the Fragaria lineage went through at least five fission events and seven fusion events, not including intrachromosomal rearrangements, the Prunus lineage went through at least three fission events and four fusion events and the Malus lineage went through seven fission events and nine fusion events. Two fission events occurred after the split of Fragaria and before the split of Malus and Prunus. Two further fission events and three fusion events occurred before the WGD of Malus lineage and the three further fission events occurred after the WGD in only one of the two homeologous chromosomes (Figure 4) of Malus. These data suggest that the Prunus lineage has the most conserved karyotype of the three species investigated and that the Malus lineage went through the most large-scale chromosomal fission/fusion events. It is also clear that intrachromosomal genome rearrangements played an important role in the genome evolution of the genus Fragaria. Additionally, Figure 4 suggests that the karyotypes of the ancestor of Malus existed before the WGD, as M1, M9 and A2 to A8. M1 and M9 were generated from A1 and A9, after four fissions and three fusions, and correspond to the present Malus chromosomes MC5/MC10 and MC3/MC11, respectively. Our result is consistent with previous phylogenetic analyses [21,35] and the analysis of comparative mapping data [2], in suggesting that both the ancestors of Rosaceae and Malus have genomes consisting of nine chromosomes.


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)

Hypothetical evolutionary steps from the nine Rosaceae ancestral chromosomes to Fragaria, Prunus and Malus lineage. Each color represent distinct CARs detected by MGRA algorithm. Chromosomal rearrangements specific for Rosoideae (contains Fragaria) and Spireaoideae (contains Malus and Prunus) are depicted. Also shown are chromosomal rearragenments specific for Prunus, Malus, and subgenome of Malus after the WGD.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Hypothetical evolutionary steps from the nine Rosaceae ancestral chromosomes to Fragaria, Prunus and Malus lineage. Each color represent distinct CARs detected by MGRA algorithm. Chromosomal rearrangements specific for Rosoideae (contains Fragaria) and Spireaoideae (contains Malus and Prunus) are depicted. Also shown are chromosomal rearragenments specific for Prunus, Malus, and subgenome of Malus after the WGD.
Mentions: Since the genus Fragaria split from the common ancestor of Malus and Prunus before those species diverged, if regions with the same ancestral origin reside in the same chromosome of both Prunus and Fragaria, but in different chromosomes of Malus, we can infer that the those chromosomes of Malus were generated by a fission event. Likewise, if regions with the same ancestral origin reside in the same chromosome of Prunus but in different chromosomes of Malus and Fragaria, we can infer the chromosome of Prunus was generated by a fusion event. In this way, we have constructed a hypothetical ancestral karyotype, consisting of nine chromosomes, using the top 24 CARs identified in this investigation (Figure 4). The orthology maps between the three species, which support the hypothesis, are shown in Additional file 2: Figure S2. Figure 4 shows that the Fragaria lineage went through at least five fission events and seven fusion events, not including intrachromosomal rearrangements, the Prunus lineage went through at least three fission events and four fusion events and the Malus lineage went through seven fission events and nine fusion events. Two fission events occurred after the split of Fragaria and before the split of Malus and Prunus. Two further fission events and three fusion events occurred before the WGD of Malus lineage and the three further fission events occurred after the WGD in only one of the two homeologous chromosomes (Figure 4) of Malus. These data suggest that the Prunus lineage has the most conserved karyotype of the three species investigated and that the Malus lineage went through the most large-scale chromosomal fission/fusion events. It is also clear that intrachromosomal genome rearrangements played an important role in the genome evolution of the genus Fragaria. Additionally, Figure 4 suggests that the karyotypes of the ancestor of Malus existed before the WGD, as M1, M9 and A2 to A8. M1 and M9 were generated from A1 and A9, after four fissions and three fusions, and correspond to the present Malus chromosomes MC5/MC10 and MC3/MC11, respectively. Our result is consistent with previous phylogenetic analyses [21,35] and the analysis of comparative mapping data [2], in suggesting that both the ancestors of Rosaceae and Malus have genomes consisting of nine chromosomes.

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