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Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation.

Czaban A, Sharma S, Byrne SL, Spannagl M, Mayer KF, Asp T - BMC Genomics (2015)

Bottom Line: Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex.The orthologous genes between the species have a very high %id (91,61%) and the majority of gene families were shared for all of them.It is likely that the knowledge of the genomes will be largely transferable between species within the complex.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark. Adrian.Czaban@mbg.au.dk.

ABSTRACT

Background: The Lolium-Festuca complex incorporates species from the Lolium genera and the broad leaf fescues, both belonging to the subfamily Pooideae. This subfamily also includes wheat, barley, oat and rye, making it extremely important to world agriculture. Species within the Lolium-Festuca complex show very diverse phenotypes, and many of them are related to agronomically important traits. Analysis of sequenced transcriptomes of these non-model species may shed light on the molecular mechanisms underlying this phenotypic diversity.

Results: We have generated de novo transcriptome assemblies for four species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some of the differences between the more stress tolerant Festuca, and the less stress tolerant Lolium species.

Conclusions: Our data presents a comprehensive transcriptome sequence comparison between species from the Lolium-Festuca complex, with the identification of potential candidate genes underlying some important phenotypical differences within the complex (such as VRN2). The orthologous genes between the species have a very high %id (91,61%) and the majority of gene families were shared for all of them. It is likely that the knowledge of the genomes will be largely transferable between species within the complex.

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Extended majority rule consensus tree. A consensus phylogenetic tree, created from 4022 individual trees originating from OrthoMCL groups with one representative per specie. The numbers on the branches indicate the number of times the species have been partitioned into two sets.
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Fig3: Extended majority rule consensus tree. A consensus phylogenetic tree, created from 4022 individual trees originating from OrthoMCL groups with one representative per specie. The numbers on the branches indicate the number of times the species have been partitioned into two sets.

Mentions: In our study we performed the phylogenetic analysis using the orthologous groups identified by OrthoMCL. The clustering output was further filtered for conserved orthologous genes as a representative from each species - that is, having exactly one representative in the cluster for each of the species. 4022 groups fulfilled this criteria. Using these groups we inferred gene trees (using PAML tool) which were then clustered using the Phylip tool to infer a consensus tree (Figure 3). It is important to note that gene trees were calculated based solely on the gene-coding regions obtained from assembled transcriptome sequences only. The numbers on the branches indicate the number of times the species are partitioned into the two sets (out of 4022 groups). This means, that the branch topology has the highest support, or has been represented most commonly in the input trees. However, we find that a high proportion of the original trees have a different topology. This points to a different phylogenetic relationship depending on the group of orthologous proteins analyzed. These findings make sense in light of the fact that some of the species in the complex are interfertile. The fact that introgression of genes is possible within the complex has been utilized in breeding efforts as well as in research [55-57]. The genomes of modern grass species are a result of more complex evolutionary mechanisms, and reticulate evolution in the complex has been previously proposed [58]. The consensus tree (phylogeny) strongly corresponds to the possible phylogeny of the Poaceae family reported in [54].Figure 3


Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation.

Czaban A, Sharma S, Byrne SL, Spannagl M, Mayer KF, Asp T - BMC Genomics (2015)

Extended majority rule consensus tree. A consensus phylogenetic tree, created from 4022 individual trees originating from OrthoMCL groups with one representative per specie. The numbers on the branches indicate the number of times the species have been partitioned into two sets.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4389671&req=5

Fig3: Extended majority rule consensus tree. A consensus phylogenetic tree, created from 4022 individual trees originating from OrthoMCL groups with one representative per specie. The numbers on the branches indicate the number of times the species have been partitioned into two sets.
Mentions: In our study we performed the phylogenetic analysis using the orthologous groups identified by OrthoMCL. The clustering output was further filtered for conserved orthologous genes as a representative from each species - that is, having exactly one representative in the cluster for each of the species. 4022 groups fulfilled this criteria. Using these groups we inferred gene trees (using PAML tool) which were then clustered using the Phylip tool to infer a consensus tree (Figure 3). It is important to note that gene trees were calculated based solely on the gene-coding regions obtained from assembled transcriptome sequences only. The numbers on the branches indicate the number of times the species are partitioned into the two sets (out of 4022 groups). This means, that the branch topology has the highest support, or has been represented most commonly in the input trees. However, we find that a high proportion of the original trees have a different topology. This points to a different phylogenetic relationship depending on the group of orthologous proteins analyzed. These findings make sense in light of the fact that some of the species in the complex are interfertile. The fact that introgression of genes is possible within the complex has been utilized in breeding efforts as well as in research [55-57]. The genomes of modern grass species are a result of more complex evolutionary mechanisms, and reticulate evolution in the complex has been previously proposed [58]. The consensus tree (phylogeny) strongly corresponds to the possible phylogeny of the Poaceae family reported in [54].Figure 3

Bottom Line: Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex.The orthologous genes between the species have a very high %id (91,61%) and the majority of gene families were shared for all of them.It is likely that the knowledge of the genomes will be largely transferable between species within the complex.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark. Adrian.Czaban@mbg.au.dk.

ABSTRACT

Background: The Lolium-Festuca complex incorporates species from the Lolium genera and the broad leaf fescues, both belonging to the subfamily Pooideae. This subfamily also includes wheat, barley, oat and rye, making it extremely important to world agriculture. Species within the Lolium-Festuca complex show very diverse phenotypes, and many of them are related to agronomically important traits. Analysis of sequenced transcriptomes of these non-model species may shed light on the molecular mechanisms underlying this phenotypic diversity.

Results: We have generated de novo transcriptome assemblies for four species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some of the differences between the more stress tolerant Festuca, and the less stress tolerant Lolium species.

Conclusions: Our data presents a comprehensive transcriptome sequence comparison between species from the Lolium-Festuca complex, with the identification of potential candidate genes underlying some important phenotypical differences within the complex (such as VRN2). The orthologous genes between the species have a very high %id (91,61%) and the majority of gene families were shared for all of them. It is likely that the knowledge of the genomes will be largely transferable between species within the complex.

Show MeSH