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Evolutionary analysis of mitogenomes from parasitic and free-living flatworms.

Solà E, Álvarez-Presas M, Frías-López C, Littlewood DT, Rozas J, Riutort M - PLoS ONE (2015)

Bottom Line: We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection.Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels.Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

View Article: PubMed Central - PubMed

Affiliation: Institut de Recerca de la Biodiversitat and Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.

ABSTRACT
Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

No MeSH data available.


sAT and sGC values of the protein coding genes (PCG) along the mtDNA molecule.A) sAT of Tricladida; B) sAT of Neodermata; C) sGC of Tricladida; D) sGC of Neodermata.
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pone.0120081.g004: sAT and sGC values of the protein coding genes (PCG) along the mtDNA molecule.A) sAT of Tricladida; B) sAT of Neodermata; C) sGC of Tricladida; D) sGC of Neodermata.

Mentions: In contrast to the A+T and NB values, free-living and parasitic species do not differentiate themselves from one another with respect to sAT or sGT values, either for the total data or for the values estimated at positions with different functional behavior (S9 and S10 Figs.). All sAT values are negative (in all genes and in all species), with the exception of the rrnS gene of Obama sp. and T. sigani where values are slightly positive (Fig. 4A and 4B). Thus, there is a clear prevalence of T over A in the coding strand. Moreover, the general sAT skew varies considerably among species (−0.187 to −0.4 Tricladida; −0.168 to −0.483 Neodermata), but it is consistent across genes; for instance F. hepatica has the highest overall sAT values, a feature exhibited in all of its genes (Fig. 4B). The sAT and A+T content, however, are uncoupled; for instance, Obama sp., the species with highest A+T content, exhibits nearly the lowest sAT values. The general sGC estimates also show important strand skews, ranging from 0.246 to 0.283 in triclads and 0.148 to 0.475 in parasites, which indicate a higher frequency of G than C. Although the sGC values also show some species-specific pattern it is much less consistent across genes. Overall, the analyses uncover a species-specific pattern that (i) is not correlated with the actual A+T content (S9 Fig), (ii) differs between sGC and sAT estimates, and (iii) does not cluster free-living or parasitic species separately.


Evolutionary analysis of mitogenomes from parasitic and free-living flatworms.

Solà E, Álvarez-Presas M, Frías-López C, Littlewood DT, Rozas J, Riutort M - PLoS ONE (2015)

sAT and sGC values of the protein coding genes (PCG) along the mtDNA molecule.A) sAT of Tricladida; B) sAT of Neodermata; C) sGC of Tricladida; D) sGC of Neodermata.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4368550&req=5

pone.0120081.g004: sAT and sGC values of the protein coding genes (PCG) along the mtDNA molecule.A) sAT of Tricladida; B) sAT of Neodermata; C) sGC of Tricladida; D) sGC of Neodermata.
Mentions: In contrast to the A+T and NB values, free-living and parasitic species do not differentiate themselves from one another with respect to sAT or sGT values, either for the total data or for the values estimated at positions with different functional behavior (S9 and S10 Figs.). All sAT values are negative (in all genes and in all species), with the exception of the rrnS gene of Obama sp. and T. sigani where values are slightly positive (Fig. 4A and 4B). Thus, there is a clear prevalence of T over A in the coding strand. Moreover, the general sAT skew varies considerably among species (−0.187 to −0.4 Tricladida; −0.168 to −0.483 Neodermata), but it is consistent across genes; for instance F. hepatica has the highest overall sAT values, a feature exhibited in all of its genes (Fig. 4B). The sAT and A+T content, however, are uncoupled; for instance, Obama sp., the species with highest A+T content, exhibits nearly the lowest sAT values. The general sGC estimates also show important strand skews, ranging from 0.246 to 0.283 in triclads and 0.148 to 0.475 in parasites, which indicate a higher frequency of G than C. Although the sGC values also show some species-specific pattern it is much less consistent across genes. Overall, the analyses uncover a species-specific pattern that (i) is not correlated with the actual A+T content (S9 Fig), (ii) differs between sGC and sAT estimates, and (iii) does not cluster free-living or parasitic species separately.

Bottom Line: We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection.Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels.Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

View Article: PubMed Central - PubMed

Affiliation: Institut de Recerca de la Biodiversitat and Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.

ABSTRACT
Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

No MeSH data available.