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Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.

Gavranović H, Chauve C, Salse J, Tannier E - Bioinformatics (2011)

Bottom Line: We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration.We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content.Upon request to the authors. haris.gavranovic@gmail.com; eric.tannier@inria.fr.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Natural Sciences, University of Sarajevo, Bosnia and Herzegovina. haris.gavranovic@gmail.com

ABSTRACT

Motivation: Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these methods, such as the proto-monocotyledon whose evolution involved massive gene loss following a whole genome duplication.

Results: We propose a mapping approach based on the combinatorial notion of 'sandwich consecutive ones matrix', which explicitly takes gene losses into account. We introduce combinatorial optimization problems related to this concept, and propose a heuristic solver and a lower bound on the optimal solution. We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration. We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content.

Availability: Upon request to the authors.

Contact: haris.gavranovic@gmail.com; eric.tannier@inria.fr.

Show MeSH
Four ohnologous chromosomes (bold lines) and the ohnolog pairs of genes (thin lines).
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Figure 4: Four ohnologous chromosomes (bold lines) and the ohnolog pairs of genes (thin lines).

Mentions: Two paralogous chromosomes or genes arising from a whole genome duplication are called ohnologous. Ohnologous chromosomes and chromosome segments were identified in Murat et al. (2010), and we use the gene homologies computed in the same study. For example, Rice chromosomes 1 and 5 are ohnologous, as well as Sorghum chromosomes 3 and 9. As all four arise from the whole genome duplication (Rice 1 is orthologous to Sorghum 3 and Rice 5 to Sorghum 9, due to a speciation posterior to the whole genome duplication), Rice 1 and Sorghum 9 are ohnologous, as well as Rice 5 and Sorghum 3. This gives four ohnologous relations on these four chromosomes summarized in Figure 4, where ohnology relationships between genes are drawn with gene positions in chromosomes. In the present work, we define a relation between genes as follows: an ohnologous pair of genes is a pair of paralogous genes that are located on two ohnologous segments. All ohnologous pairs on Rice chromosomes 1 and 5 and Sorghum chromosomes 3 and 9 are drawn in Figure 4. Genes are grouped into families defined by the transitive closure of the relation, and each family defines an ancestral marker.Fig. 4.


Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.

Gavranović H, Chauve C, Salse J, Tannier E - Bioinformatics (2011)

Four ohnologous chromosomes (bold lines) and the ohnolog pairs of genes (thin lines).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3117370&req=5

Figure 4: Four ohnologous chromosomes (bold lines) and the ohnolog pairs of genes (thin lines).
Mentions: Two paralogous chromosomes or genes arising from a whole genome duplication are called ohnologous. Ohnologous chromosomes and chromosome segments were identified in Murat et al. (2010), and we use the gene homologies computed in the same study. For example, Rice chromosomes 1 and 5 are ohnologous, as well as Sorghum chromosomes 3 and 9. As all four arise from the whole genome duplication (Rice 1 is orthologous to Sorghum 3 and Rice 5 to Sorghum 9, due to a speciation posterior to the whole genome duplication), Rice 1 and Sorghum 9 are ohnologous, as well as Rice 5 and Sorghum 3. This gives four ohnologous relations on these four chromosomes summarized in Figure 4, where ohnology relationships between genes are drawn with gene positions in chromosomes. In the present work, we define a relation between genes as follows: an ohnologous pair of genes is a pair of paralogous genes that are located on two ohnologous segments. All ohnologous pairs on Rice chromosomes 1 and 5 and Sorghum chromosomes 3 and 9 are drawn in Figure 4. Genes are grouped into families defined by the transitive closure of the relation, and each family defines an ancestral marker.Fig. 4.

Bottom Line: We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration.We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content.Upon request to the authors. haris.gavranovic@gmail.com; eric.tannier@inria.fr.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Natural Sciences, University of Sarajevo, Bosnia and Herzegovina. haris.gavranovic@gmail.com

ABSTRACT

Motivation: Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these methods, such as the proto-monocotyledon whose evolution involved massive gene loss following a whole genome duplication.

Results: We propose a mapping approach based on the combinatorial notion of 'sandwich consecutive ones matrix', which explicitly takes gene losses into account. We introduce combinatorial optimization problems related to this concept, and propose a heuristic solver and a lower bound on the optimal solution. We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration. We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content.

Availability: Upon request to the authors.

Contact: haris.gavranovic@gmail.com; eric.tannier@inria.fr.

Show MeSH