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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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Ka/Ks distribution. The figure presents comparison of F. pratensis against L. temulentum, L.m. westerwoldicum, L. multiflorum and L. perenne. The frequency distributions of Ka/Ks rates (x-axis) shown here are based on protein and nucleotide alignments of orthologous genes.
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Fig5: Ka/Ks distribution. The figure presents comparison of F. pratensis against L. temulentum, L.m. westerwoldicum, L. multiflorum and L. perenne. The frequency distributions of Ka/Ks rates (x-axis) shown here are based on protein and nucleotide alignments of orthologous genes.

Mentions: We can identify two types of changes in the coding sequences - non synonymous (dN) substitutions, leading to change in the amino acid sequence, and synonymous (dS) substitutions, which are neutral for the amino acid sequence. The ratio of non-synonymous substitution rate (Ka) and synonymous substitution rate (Ks) is a parameter widely used to assess whether there is any directional selection acting on a protein coding gene. A ratio < 1 indicates that the protein is under purifying selection, whereas a ratio of > 1 is a good indication of positive selection pressure [59,60]. In such a closely related clade, only a small amount of genes can be expected to be responsible for phenotypical differences [61]. We undertook pairwise comparison of transcriptome datasets. Putative orthologous genes have been then classified according to the best bi-directional blast criteria (see Methods), and for every comparison we selected transcript pairs with a Ka/Ks ratio above 1. We have focused on comparing the F. pratensis with the other analyzed species, as it has various features that are important from an agricultural perspective, which include superior biotic and abiotic stress tolerance, good persistency and perenniality. The sequence identity distribution is very uniform among the pairwise comparison, with it’s peak around 95% (Figure 4). We focused our analysis towards genes involved in stress resistance, cell cycle and development related proteins, with the most relevant ones identified listed for every comparison. The overall distribution of Ka/Ks ratio of all pairwise comparisons is very similar, with almost every pair of proteins showing signs of purifying selection (Figure 5). The median ratio was very consistent, between 0.1741 for L. multiflorum and 0.1883 for L. perenne.Figure 4


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)

Ka/Ks distribution. The figure presents comparison of F. pratensis against L. temulentum, L.m. westerwoldicum, L. multiflorum and L. perenne. The frequency distributions of Ka/Ks rates (x-axis) shown here are based on protein and nucleotide alignments of orthologous genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Ka/Ks distribution. The figure presents comparison of F. pratensis against L. temulentum, L.m. westerwoldicum, L. multiflorum and L. perenne. The frequency distributions of Ka/Ks rates (x-axis) shown here are based on protein and nucleotide alignments of orthologous genes.
Mentions: We can identify two types of changes in the coding sequences - non synonymous (dN) substitutions, leading to change in the amino acid sequence, and synonymous (dS) substitutions, which are neutral for the amino acid sequence. The ratio of non-synonymous substitution rate (Ka) and synonymous substitution rate (Ks) is a parameter widely used to assess whether there is any directional selection acting on a protein coding gene. A ratio < 1 indicates that the protein is under purifying selection, whereas a ratio of > 1 is a good indication of positive selection pressure [59,60]. In such a closely related clade, only a small amount of genes can be expected to be responsible for phenotypical differences [61]. We undertook pairwise comparison of transcriptome datasets. Putative orthologous genes have been then classified according to the best bi-directional blast criteria (see Methods), and for every comparison we selected transcript pairs with a Ka/Ks ratio above 1. We have focused on comparing the F. pratensis with the other analyzed species, as it has various features that are important from an agricultural perspective, which include superior biotic and abiotic stress tolerance, good persistency and perenniality. The sequence identity distribution is very uniform among the pairwise comparison, with it’s peak around 95% (Figure 4). We focused our analysis towards genes involved in stress resistance, cell cycle and development related proteins, with the most relevant ones identified listed for every comparison. The overall distribution of Ka/Ks ratio of all pairwise comparisons is very similar, with almost every pair of proteins showing signs of purifying selection (Figure 5). The median ratio was very consistent, between 0.1741 for L. multiflorum and 0.1883 for L. perenne.Figure 4

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