Molecular Evolutionary Analyses of Euplotes Species Living in Freshwater and Marine Habitats: A Mitogenomic Perspective

Shuo Zhao,Qi Song,Ning Huang,Yan Zhao,Ming He,Shuai Chen,Miao Miao,Lina Hou

doi:10.3389/fmars.2021.627879

Shuo Zhao, Qi Song + Show 6 more

Open Access

https://doi.org/10.3389/fmars.2021.627879

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Abstract

Ciliates are the most complex unicellular eukaryotic organisms, which play important roles in various ecosystems. The Euplotes is a dominant genus in the ciliates Euplotida and consists of approximate one hundred species. They distribute widely in environments with various salinity levels including freshwater, brackish, seawater as well as hypersaline. In this study, we obtained four mitochondrial genomes of Euplotes species, using both high throughput sequencing and Sanger sequencing. Combined with two previously reported Euplotes mitochondrial genomes, we analyzed their gene structure, codon usage pattern as well as phylogenetic relationship. We found that gene rearrangement exists in Euplotes and codon usage bias is different among these species. Phylogenetic analyses based on both mitochondrial and nuclear genes further unveiled that Euplotes spp. living in similar salinity levels tend to be clustered together. Moreover, we found that the dN/dS ratios of two mitochondrial genes, cox1 and cox2, are significantly different between marine and freshwater species, indicating the salinity could act as a barrier for the Euplotes species distribution. We also recommended mitochondrial genes to discriminate the species with highly similarity of Euplotes which could not be easily distinguished by nuclear gene marker and morphological characteristics. This study provides novel resources to improve our understanding of Euplotes evolution and also its adaptation to habitats with different salinity levels.

Highlights

Ciliates play important ecological roles in natural environments and become one of the most prevailing model territory in unicellular eukaryotes (Graziano et al, 2010; Gentekaki et al, 2014)
We found that Euplotes mitochondrial genomes have all proteincoding genes (PCGs) that have been reported in other ciliate mitochondria
Regardless of the open reading frames (ORFs) with unknown function, gene order among E. minuta, E. crassus, E. vannus as well as E. focardii is almost the same with exception of nad6, which is absent in E. crassus

Summary

Introduction

Ciliates play important ecological roles in natural environments and become one of the most prevailing model territory in unicellular eukaryotes (Graziano et al, 2010; Gentekaki et al, 2014). They are more diverse and highly differentiated than multicellular eukaryotes (Graziano et al, 2010) and able to survive in various types of environments (Giuseppe et al, 2011). Mitochondrial genome analyses have been playing a growing important role in phylogenetic and evolutionary studies. The inheritance of mitochondrial DNA occurs in a unique and heritably separate manner that is spatially different from nuclear DNA, which may provide a new perspective for the phylogenetics of the Euplotes. Mitochondrial genomes from only three species have been sequenced in ciliated species (de Graaf et al, 2009; Serra et al, 2019)

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