Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Solà, Eduard; Álvarez‐Presas, Marta; Frías-López, Cristina; Littlewood, D. Timothy J.; Rozas, Julio; Riutort, Marta

doi:10.1371/journal.pone.0120081

Cited by 52 publications

(65 citation statements)

References 57 publications

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“…This content is similar to those observed in other Platyhelminthes (Solà et al. ). The negative AT skew (−0.095) indicated the occurrence of more Ts than As.…”

Section: Resultssupporting

confidence: 91%

“…While it has been generally assumed that the atp8 gene has been lost from the mitochondrial genome of Platyhelminthes (Solà et al. ), we report the presence of a highly divergent putative atp8 gene, similar to the one found in other invertebrates.…”

Section: Introductionsupporting

confidence: 63%

“…; Solà et al. ). The atp8 gene is not detected, in S. leucops, using conventional tools for mitogenome gene search in.…”

Section: Discussionmentioning

confidence: 96%

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Characterization of the first mitochondrial genome of a catenulid flatworm:Stenostomum leucops(Platyhelminthes)

Rosa

Oliveira²,

Loreto

2017

J Zool Syst Evol Res

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The first complete mitochondrial genome of a catenulid, Stenostomum leucops, was characterized. Illumina sequencing and 90 813 reads were utilized in the assembly, producing one contig with an average coverage of 1118×. The length of this genome is 15 742 bp with 12 protein‐coding, two rRNA and 22 tRNA genes. Although the atp8 gene is absent in other Platyhelminthes, a highly divergent putative atp8 gene was found in S. leucops. In contrast to other Platyhelminthes, the mitochondrial genes of S. leucops are encoded on both strands. The gene order in the S. leucops mitogenome is very divergent from those observed in other Platyhelminthes, showing only small blocks of synteny. With AAA as the codon for lysine S. leucops shows the probable plesiomorphic condition, whereas Rhabditophora possess the derived GAA. This evolutionary transition is correlated with changes in the respective anticodons in trnK. It remains unclear whether the absence of the D arm and loop in trnS1 is a convergence in Catenulida and Neodermata.

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“…This content is similar to those observed in other Platyhelminthes (Solà et al. ). The negative AT skew (−0.095) indicated the occurrence of more Ts than As.…”

Section: Resultssupporting

confidence: 91%

Section: Introductionsupporting

confidence: 63%

See 1 more Smart Citation

Characterization of the first mitochondrial genome of a catenulid flatworm:Stenostomum leucops(Platyhelminthes)

Rosa

Oliveira²,

Loreto

2017

J Zool Syst Evol Res

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“…Planarians are found worldwide in a variety of habitats, ranging from humid, terrestrial ecosystems to freshwater and marine saltwater environments (Alvarez-Presas et al, 2008; Solà et al, 2015). Freshwater planarians are metazoan flatworms which are bilaterally symmetrical.…”

Section: Introductionmentioning

confidence: 99%

Physiological evaluation of the behavior and epidermis of freshwater planarians (Girardia tigrina and Girardia sp.) exposed to stressors

et al. 2018

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Planarians are metazoan freshwater flatworms which are free-living organisms. Their body has pluripotent stem cell promoters of tissue regeneration capacity. The water temperature and the potential of hydrogen (pH) of lentic ecosystems are important factors involved in the distribution and abundance of these animals. Although the pH factor is directly related to the physiology and behavior of planarians, their adaptive and regenerating capacities still remain unknown. The Critical Thermal Maximum (CTM) is a very widespread method used in the evaluation of thermal tolerance. In this study, Girardia tigrina (Girard, 1850) and Girardia sp., a species found in Brazil, which is under study as a new species, had their epidermis assessed by scanning electron microscopy (SEM) to analyze their physiological structures before and after exposure to different stressors. SEM was used as a method to evaluate the planarians' epidermis as a result of the increasing temperature (CTM) and pH alterations, the latter with the use of a new methodology defined as Critical Hydrogen ion concentration Maximum (CHM). In increasing temperatures from 20°C to 37°C, both Girardia tigrina and Girardia sp. proved to be adaptable to thermal stress. Girardia sp. was shown to be more resistant to higher temperatures. However, Girardia tigrina was more resistant to extreme pH conditions (4.0 to 10.0). SEM analysis showed morphological differences among planarian species, such as the arrangement of the structures and cell types of the dorsal epidermis. Moreover, planarians demonstrated the ability to change the surrounding pH of their external environment in order to maintain the function of their physiological mechanisms, suggesting that these animals have a complex survival system, possibly related to protonephridia, flame cells and excretory pores..

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“…Indeed, ribosomal proteins were among the most common hidden orthologs recovered from our data set (Supplemental Table S2). These findings suggest that mitochondrial genes show accelerated evolutionary rates (Solà et al 2015), which might be causing nuclear-encoded proteins that are exported to the mitochondrion to adapt to this change (Barreto and Burton 2013).…”

Section: The Possible Mechanisms Driving Hidden Orthology In Platyhelmentioning

confidence: 96%

Increased taxon sampling reveals thousands of hidden orthologs in flatworms

et al. 2017

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Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages-mistakenly considered new genes-but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify putative hidden orthologs in large transcriptomic databases by transitive homology. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3427 putative hidden orthologs, some unidentified by OrthoFinder and HaMStR, two common orthogroup inference algorithms. Unexpectedly, we do not observe a correlation between the number of putative hidden orthologs in a lineage and its "average" evolutionary rate. Hidden orthologs do not show unusual sequence composition biases that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g., planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution.

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Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Cited by 52 publications

References 57 publications

Characterization of the first mitochondrial genome of a catenulid flatworm:Stenostomum leucops(Platyhelminthes)

Characterization of the first mitochondrial genome of a catenulid flatworm:Stenostomum leucops(Platyhelminthes)

Physiological evaluation of the behavior and epidermis of freshwater planarians (Girardia tigrina and Girardia sp.) exposed to stressors

Increased taxon sampling reveals thousands of hidden orthologs in flatworms

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