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Sequence Analysis of Bitter Taste Receptor Gene Repertoires in Different Ruminant Species.

Monteiro Ferreira A, Tomás Marques A, Bhide M, Cubric-Curik V, Hollung K, Knight CH, Raundrup K, Lippolis J, Palmer M, Sales-Baptista E, Araújo SS, de Almeida AM - PLoS ONE (2015)

Bottom Line: We describe the first partial repertoires of T2R gene sequences for these species obtained by direct sequencing.We then consider the homology and evolutionary history of these receptors within this ruminant group, and whether it relates to feeding type classification, using MEGA software.Our results suggest that phylogenetic proximity of T2R genes corresponds more to the traditional taxonomic groups of the species rather than reflecting a categorization by feeding strategy.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, 7006-554 Évora, Portugal; Plant Cell Biotechnology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB-UNL), Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.

ABSTRACT
Bitter taste has been extensively studied in mammalian species and is associated with sensitivity to toxins and with food choices that avoid dangerous substances in the diet. At the molecular level, bitter compounds are sensed by bitter taste receptor proteins (T2R) present at the surface of taste receptor cells in the gustatory papillae. Our work aims at exploring the phylogenetic relationships of T2R gene sequences within different ruminant species. To accomplish this goal, we gathered a collection of ruminant species with different feeding behaviors and for which no genome data is available: American bison, chamois, elk, European bison, fallow deer, goat, moose, mouflon, muskox, red deer, reindeer and white tailed deer. The herbivores chosen for this study belong to different taxonomic families and habitats, and hence, exhibit distinct foraging behaviors and diet preferences. We describe the first partial repertoires of T2R gene sequences for these species obtained by direct sequencing. We then consider the homology and evolutionary history of these receptors within this ruminant group, and whether it relates to feeding type classification, using MEGA software. Our results suggest that phylogenetic proximity of T2R genes corresponds more to the traditional taxonomic groups of the species rather than reflecting a categorization by feeding strategy.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree built using MEGA software for the sequenced T2R genes in the different ruminant species.The evolutionary history was inferred using the Neighbor-Joining method [22]. The bootstrap consensus tree inferred from 500 replicates [21] is taken to represent the evolutionary history of the taxa analyzed [21]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The evolutionary distances were computed using the JTT matrix-based method [23] and are in the units of the number of base substitutions per site. The analysis involved 55 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 96 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [20].
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pone.0124933.g001: Phylogenetic tree built using MEGA software for the sequenced T2R genes in the different ruminant species.The evolutionary history was inferred using the Neighbor-Joining method [22]. The bootstrap consensus tree inferred from 500 replicates [21] is taken to represent the evolutionary history of the taxa analyzed [21]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The evolutionary distances were computed using the JTT matrix-based method [23] and are in the units of the number of base substitutions per site. The analysis involved 55 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 96 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [20].

Mentions: A phylogenetic tree was built with the protein sequences for the obtained intact genes, using Neighbor-joining statistical method of analysis, with a bootstrap value of 500 (Fig 1). There is evident clustering by receptor genes. We also observe that some receptors are closer to each other than others. For instance, T2R4 and T2R16 originate from the same branch, which is separated from the other branch in the root of two other sub-branches, one for receptors T2R3, T2R10, T2R67, and another for T2R13 and T2R12. The phylogenetic relations between species are not constant for every gene, nevertheless, there is a clear trend for phylogenetic distance or divergence of T2R genes to correspond to the traditional taxonomic groups of the species, rather than to feeding types (grazers, browsers or intermediate feeders). Species of the Bovidae family/Caprinae sub-family (sheep, mouflon, muskox, goat and chamois) form a cluster separated from species of the Bovidae family/Bovinae sub-family (American bison, European bison) and the Cervidae family (deer, elk, white tailed deer, reindeer, fallow deer and moose). Analyzing each receptor separately we can see different phylogenetic patterns, with the Cervidade family closer to the root of the branch, and Bovidae further away. However, some interesting exceptions are observed. For T2R10 species of the subfamily Bovinae are closer to the Cervidae family than to the Caprinae sub-family of their own family (Bovidae), and for T2R67, there appears to exist a divergence for each species at a time, not in clusters, albeit keeping the same taxonomic proximities. Finally, O. aries, does not cluster with O. ammon musimon for every gene even though they are of the same genus. For example, in T2R10, O. aries is closer to C. hircus, or even to O. moschatus for receptor gene T2R16. Another interesting finding was that for T2R13 we were only able to find intact genes in the Cervidae samples. We could successfully amplify and sequence PCR fragments for other species but the resulting sequences have premature stop codons, indicatig pseudogenezation of this gene for those species.


Sequence Analysis of Bitter Taste Receptor Gene Repertoires in Different Ruminant Species.

Monteiro Ferreira A, Tomás Marques A, Bhide M, Cubric-Curik V, Hollung K, Knight CH, Raundrup K, Lippolis J, Palmer M, Sales-Baptista E, Araújo SS, de Almeida AM - PLoS ONE (2015)

Phylogenetic tree built using MEGA software for the sequenced T2R genes in the different ruminant species.The evolutionary history was inferred using the Neighbor-Joining method [22]. The bootstrap consensus tree inferred from 500 replicates [21] is taken to represent the evolutionary history of the taxa analyzed [21]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The evolutionary distances were computed using the JTT matrix-based method [23] and are in the units of the number of base substitutions per site. The analysis involved 55 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 96 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [20].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4465170&req=5

pone.0124933.g001: Phylogenetic tree built using MEGA software for the sequenced T2R genes in the different ruminant species.The evolutionary history was inferred using the Neighbor-Joining method [22]. The bootstrap consensus tree inferred from 500 replicates [21] is taken to represent the evolutionary history of the taxa analyzed [21]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The evolutionary distances were computed using the JTT matrix-based method [23] and are in the units of the number of base substitutions per site. The analysis involved 55 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 96 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [20].
Mentions: A phylogenetic tree was built with the protein sequences for the obtained intact genes, using Neighbor-joining statistical method of analysis, with a bootstrap value of 500 (Fig 1). There is evident clustering by receptor genes. We also observe that some receptors are closer to each other than others. For instance, T2R4 and T2R16 originate from the same branch, which is separated from the other branch in the root of two other sub-branches, one for receptors T2R3, T2R10, T2R67, and another for T2R13 and T2R12. The phylogenetic relations between species are not constant for every gene, nevertheless, there is a clear trend for phylogenetic distance or divergence of T2R genes to correspond to the traditional taxonomic groups of the species, rather than to feeding types (grazers, browsers or intermediate feeders). Species of the Bovidae family/Caprinae sub-family (sheep, mouflon, muskox, goat and chamois) form a cluster separated from species of the Bovidae family/Bovinae sub-family (American bison, European bison) and the Cervidae family (deer, elk, white tailed deer, reindeer, fallow deer and moose). Analyzing each receptor separately we can see different phylogenetic patterns, with the Cervidade family closer to the root of the branch, and Bovidae further away. However, some interesting exceptions are observed. For T2R10 species of the subfamily Bovinae are closer to the Cervidae family than to the Caprinae sub-family of their own family (Bovidae), and for T2R67, there appears to exist a divergence for each species at a time, not in clusters, albeit keeping the same taxonomic proximities. Finally, O. aries, does not cluster with O. ammon musimon for every gene even though they are of the same genus. For example, in T2R10, O. aries is closer to C. hircus, or even to O. moschatus for receptor gene T2R16. Another interesting finding was that for T2R13 we were only able to find intact genes in the Cervidae samples. We could successfully amplify and sequence PCR fragments for other species but the resulting sequences have premature stop codons, indicatig pseudogenezation of this gene for those species.

Bottom Line: We describe the first partial repertoires of T2R gene sequences for these species obtained by direct sequencing.We then consider the homology and evolutionary history of these receptors within this ruminant group, and whether it relates to feeding type classification, using MEGA software.Our results suggest that phylogenetic proximity of T2R genes corresponds more to the traditional taxonomic groups of the species rather than reflecting a categorization by feeding strategy.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, 7006-554 Évora, Portugal; Plant Cell Biotechnology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB-UNL), Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.

ABSTRACT
Bitter taste has been extensively studied in mammalian species and is associated with sensitivity to toxins and with food choices that avoid dangerous substances in the diet. At the molecular level, bitter compounds are sensed by bitter taste receptor proteins (T2R) present at the surface of taste receptor cells in the gustatory papillae. Our work aims at exploring the phylogenetic relationships of T2R gene sequences within different ruminant species. To accomplish this goal, we gathered a collection of ruminant species with different feeding behaviors and for which no genome data is available: American bison, chamois, elk, European bison, fallow deer, goat, moose, mouflon, muskox, red deer, reindeer and white tailed deer. The herbivores chosen for this study belong to different taxonomic families and habitats, and hence, exhibit distinct foraging behaviors and diet preferences. We describe the first partial repertoires of T2R gene sequences for these species obtained by direct sequencing. We then consider the homology and evolutionary history of these receptors within this ruminant group, and whether it relates to feeding type classification, using MEGA software. Our results suggest that phylogenetic proximity of T2R genes corresponds more to the traditional taxonomic groups of the species rather than reflecting a categorization by feeding strategy.

No MeSH data available.


Related in: MedlinePlus