Molecular Polymorphism in the <scp>MTA</scp> and <scp>MTB</scp> Mating Type Genes of Tetrahymena thermophila and Related Asexual Species

Booth, Laurie; Wolfe, Benjamin E.; Doerder, F. Paul

doi:10.1111/jeu.12233

Cited by 3 publications

(3 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An evolutionary study of selected segments of macronuclear mtGPs of T. thermophila cell lines from different geographical locations has been reported (7). These investigators sequenced the entire transmembrane exons (∼1,200 bp and ∼1,400 bp) and the largest exons (LX) (∼750 bp and ∼1,050 bp, roughly one half), respectively, of mating type-specific MTA and MTB gene pair sequences.…”

Section: Mating Type System Evolution In Tetrahymenine Ciliatesmentioning

confidence: 99%

Genetics and Epigenetics of Mating Type Determination in Paramecium and Tetrahymena

Orias

Singh

Meyer

2017

Annu. Rev. Microbiol.

View full text Add to dashboard Cite

While sex is an ancient and highly conserved eukaryotic invention, self-incompatibility systems such as mating types or sexes appear to be derived limitations that show considerable evolutionary plasticity. Within a single class of ciliates, Paramecium and Tetrahymena species have long been known to present a wide variety of mating type numbers and modes of inheritance, but only recently have the genes involved been identified. Although similar transmembrane proteins mediate self/nonself recognition in both ciliates, the mechanisms of mating type determination differ widely, ranging from Mendelian systems to developmental nuclear differentiation, either stochastic or maternally inherited. The non-Mendelian systems rely on programmed editing of the germline genome that occurs during differentiation of the somatic nucleus, and they have co-opted different DNA recombination mechanisms-some previously unknown. Here we review the recent molecular advances and some remaining unsolved questions and discuss the possible implications of these diverse mechanisms for inbreeding/outbreeding balance regulation.

show abstract

Section: Mating Type System Evolution In Tetrahymenine Ciliatesmentioning

confidence: 99%

Genetics and Epigenetics of Mating Type Determination in Paramecium and Tetrahymena

Orias

Singh

Meyer

2017

Annu. Rev. Microbiol.

View full text Add to dashboard Cite

show abstract

“…The ENC was used to quantify the CUB in one specific gene ( Wright, 1990 ). ENC-GC 3 was used to analyze the influence of the GC 3 content on codon usage, the expected ENC value for each GC 3 was calculated using the following formula ( Booth et al, 2015 ), and the expected fitting curve of ENC values was drawn with GraphPad Prism 8.0. 2…”

Section: Methodsmentioning

confidence: 99%

The Codon Usage Bias Analysis of Free-Living Ciliates’ Macronuclear Genomes and Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Vector Construction of Stylonychia lemnae

et al. 2022

View full text Add to dashboard Cite

Ciliates represent higher unicellular animals, and several species are also important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome in ciliates can not only promote a better understanding of the genetic mode and evolution history of these organisms but also help optimize codons to improve the gene editing efficiency of model ciliates. In this study, macronuclear genome sequences of nine free-living ciliates were analyzed with CodonW software to calculate the following indices: the guanine-cytosine content (GC); the frequency of the nucleotides U, C, A, and G at the third position of codons (U3s, C3s, A3s, G3s); the effective number of codons (ENC); the correlation between GC at the first and second positions (GC12); the frequency of the nucleotides G + C at the third position of synonymous codons (GC3s); the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, neutrality plot analysis, and correlation analysis were performed to explore the factors that influence codon preference. The results showed that the GC contents in nine ciliates’ MAC genomes were lower than 50% and appeared AT-rich. The base compositions of GC12 and GC3s are markedly distinct and the codon usage pattern and evolution of ciliates are affected by genetic mutation and natural selection. According to the synonymous codon analysis, the codons of most ciliates ended with A or U and eight codons were the general optimal codons of nine ciliates. A clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) expression vector of Stylonychia lemnae was constructed by optimizing the macronuclear genome codon and was successfully used to knock out the Adss gene. This is the first such extensive investigation of the MAC genome CUB of ciliates and the initial successful application of the CRISPR/Cas9 technique in free-living ciliates.

show abstract

“…Optimal codons definition referred to the analytical method of Liu et al [43]. Gene expression levels were determined by CAI values.…”

Section: Determination Of Optimal Codonsmentioning

confidence: 99%

Comprehensive analysis of codon usage pattern of whole genome in protozoa, Stylonychia lemnae

Wang

Lin

Fan

et al. 2019

Preprint

View full text Add to dashboard Cite

Background: Codon usage pattern is an important evolutionary feature in genomes widely observed in many organisms. Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: a germline micronucleus and a vegetative macronucleus. Analysis of codon usage pattern of S. lemnae macronucleus genome helps in understanding evolution at molecular level and acquires signiﬁcance in mRNA translation, design of transgenic and new gene discovery. Results: The codons of the macronucleus genome sequence of S. lemnae were analyzed and 20,750 coding sequences (CDS) were screened. The overall codon usage of S. lemnae is similar and slightly biased. The value of effective number of codons (ENC) showed that the overall extent of codon usage bias in S. lemnae is relatively high. Nucleotide analysis showed that the overall codon usage is biased toward A- and U-ending codons. The phylogenetic analysis indicated that ciliate is independent evolutionary origins from a common ancestor. The RSCU analysis showed that the codon usage pattern of S. lemnae is more similar to that of Thtrahymana thermophila and Paramecium caudatum . Correlation analysis, ENC-GC 3S plot, and PR2 plot indicated that the codon usage patterns of S. lemnae are influenced by both mutational pressure and natural selection, neutrality plot analysis showed that those two factors play major roles. C onclusions : Codon usage patterns in eukaryotes are not determined by translational efficiency, but also are determined by the genome. Our study is the ﬁrst attempt to evaluate the codon usage pattern of S.lemnae macronucleus genome to better understand the evolutionary changes. These results built the base for further research on the molecular evolution of S. lemnae .

show abstract

Molecular Polymorphism in the MTA and MTB Mating Type Genes of Tetrahymena thermophila and Related Asexual Species

Cited by 3 publications

References 22 publications

Genetics and Epigenetics of Mating Type Determination in Paramecium and Tetrahymena

Genetics and Epigenetics of Mating Type Determination in Paramecium and Tetrahymena

The Codon Usage Bias Analysis of Free-Living Ciliates’ Macronuclear Genomes and Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Vector Construction of Stylonychia lemnae

Comprehensive analysis of codon usage pattern of whole genome in protozoa, Stylonychia lemnae

Contact Info

Product

Resources

About