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. 2023 Jan 12;8(1):59.
doi: 10.3390/tropicalmed8010059.

Exploring Evolutionary Relationships within Neodermata Using Putative Orthologous Groups of Proteins, with Emphasis on Peptidases

Víctor Caña-Bozada  1 , Mark W Robinson  2 , David I Hernández-Mena  3 , Francisco N Morales-Serna  4
Affiliations

Exploring Evolutionary Relationships within Neodermata Using Putative Orthologous Groups of Proteins, with Emphasis on Peptidases

Víctor Caña-Bozada et al. Trop Med Infect Dis. .

Abstract

The phylogenetic relationships within Neodermata were examined based on putative orthologous groups of proteins (OGPs) from 11 species of Monogenea, Trematoda, and Cestoda. The dataset included OGPs from BUSCO and OMA. Additionally, peptidases were identified and evaluated as phylogenetic markers. Phylogenies were inferred using the maximum likelihood method. A network analysis and a hierarchical grouping analysis of the principal components (HCPC) of orthologous groups of peptidases were performed. The phylogenetic analyses showed the monopisthocotylean monogeneans as the sister-group of cestodes, and the polyopisthocotylean monogeneans as the sister-group of trematodes. However, the sister-group relationship between Monopisthocotylea and Cestoda was not statistically well supported. The network analysis and HCPC also showed a cluster formed by polyopisthocotyleans and trematodes. The present study supports the non-monophyly of Monogenea. An analysis of mutation rates indicated that secreted peptidases and inhibitors, and those with multiple copies, are under positive selection pressure, which could explain the expansion of some families such as C01, C19, I02, and S01. Whilst not definitive, our study presents another point of view in the discussion of the evolution of Neodermata, and we hope that our data drive further discussion and debate on this intriguing topic.

Keywords: Platyhelminthes; cestoda; monogenea; parasites; phylogenomic; trematoda.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic trees of 13 platyhelminth species, based on (A) single-copy BUSCO OGPs and (B) simply OMA OGPs. Values above represent SH-aLRT support (%)/ultrafast bootstrap support (%) and below represent Maximum Likelihood rapid bootstrap support. The free-living platyhelminths Bothrioplana semperi, belonging to the order Bothrioplanida, and Schmidtea mediterranea, belonging to the order Tricladida, were used as outgroups.
Figure 2
Figure 2
Heat map showing the proportion of peptidase and inhibitor families in each platyhelminth species.
Figure 3
Figure 3
Peptidases and inhibitors with predicted signal peptides in the platyhelminth species analysed. (A) The proportion of peptidases and inhibitors with/without predicted signal peptides for secretion. (B) Proportion of secreted protein in the top 20 most abundant peptidase and inhibitor families.
Figure 4
Figure 4
Peptidases and inhibitors of 13 platyhelminth species analysed. (A) Phylogenetic tree with values above representing SH-aLRT support (%)/ultrafast bootstrap support (%) and below representing Maximum Likelihood rapid bootstrap support. The free-living platyhelminths Bothrioplana semperi, belonging to the order Bothrioplanida, and Schmidtea mediterranea, belonging to the order Tricladida, were used as outgroups. (B) Formation of clusters according to their peptidases and inhibitors OGs using hierarchical grouping analysis in principal components.
Figure 5
Figure 5
Circus chart representing the OGs of peptidase and inhibitor families that most contribute to the formation of groups in the HCPC and network analyses.
Figure 6
Figure 6
The distribution of (A) Ka and (B) Ks in single-copy OGs of peptidases and inhibitors of platyhelminths with/without predicted signal peptides. FL indicate the free-living platyhelminths Bothrioplana semperi and Schmidtea mediterranea. * indicates p < 0.05.
Figure 7
Figure 7
The distribution of (A) Ka and (B) Ks in multiple-copy OGs of peptidases and inhibitors of platyhelminths with/without predicted signal peptides. FL indicate the free-living platyhelminths Bothrioplana semperi and Schmidtea mediterranea. * indicate p < 0.05.
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