scholarly journals Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

2020 ◽  
Author(s):  
Natalia Sawka-Gądek ◽  
Alexey Potekhin ◽  
Deepankar Pratap Singh ◽  
Inessa Grevtseva ◽  
Olivier Arnaiz ◽  
...  
Keyword(s):  
Mating Type ◽  
Sibling Species ◽  
Common Ancestor ◽  
Genome Duplication ◽  
Transmembrane Protein ◽  
Type Systems ◽  
Regulation Mechanism ◽  
Additional Species ◽  
Evolutionary Transitions ◽  
Genetic Determination

Abstract The Paramecium aurelia complex, a group of morphologically similar but sexually incompatible sibling species, is a unique example of the evolutionary plasticity of mating-type systems. Each species has two mating types, O (Odd) and E (Even). Although O and E types are homologous in all species, three different modes of determination and inheritance have been described: genetic determination by Mendelian alleles, stochastic developmental determination, and maternally inherited developmental determination. Previous work in three species of the latter kind have revealed the key roles of the E-specific transmembrane protein mtA and its highly specific transcription factor mtB: type O clones are produced by maternally inherited genome rearrangements that inactivate either mtA or mtB during development. Here we show, through transcriptome analyses in 5 additional species representing the three determination systems, that mtA expression specifies type E in all cases. We further show that the Mendelian system depends on functional and non-functional mtA alleles, and identify novel developmental rearrangements in mtA and mtB which now explain all cases of maternally inherited mating-type determination. Epistasis between these genes likely evolved from less specific interactions between paralogs in the P. aurelia common ancestor, after a whole-genome duplication, but the mtB gene was subsequently lost in three P. aurelia species which appear to have returned to an ancestral regulation mechanism. These results suggest a model accounting for evolutionary transitions between determination systems, and highlight the diversity of molecular solutions explored among sibling species to maintain an essential mating-type polymorphism in cell populations.

scholarly journals Mechanism for Restoration of Fertility in Hybrid Zygosaccharomyces rouxii Generated by Interspecies Hybridization

2017 ◽  
Vol 83 (21) ◽  
Author(s):  
Jun Watanabe ◽  
Kenji Uehara ◽  
Yoshinobu Mogi ◽  
Yuichiro Tsukioka
Keyword(s):  
Mating Type ◽  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Draft Genome ◽  
Content Type ◽  
Zygosaccharomyces Rouxii ◽  
Interspecies Hybridization ◽  
Random Gene Loss ◽  
Interspecies Hybrid

ABSTRACT The mechanism of whole-genome duplication (WGD) in yeast has been intensively studied because it has a large impact on yeast evolution. WGD has shaped the genomic architecture of modern Saccharomyces cerevisiae; however, the mechanism for restoring fertility after interspecies hybridization, which would be involved in the process of WGD, has not been thoroughly elucidated. In this study, we obtained a draft genome sequence of the salt-tolerant yeast Zygosaccharomyces rouxii NBRC110957 and revealed that it is a hybrid lineage of Z. rouxii (allodiploid) with two subgenomes equivalent to NBRC1876. Because this allodiploid yeast can mate with other allodiploid strains and form spores, it can be a good model of restoring fertility after interspecies hybridization. We observed that NBRC110957 and NBRC1876 contain six mating-type-like (MTL) loci. There are no large deletions or deleterious mutations in MTL loci, except for several-base-pair deletions in the X region in certain MTL loci. We also assigned only one mating-type (MAT) locus that exclusively determines mating types from six MTL loci. These results suggest that it is possible to recover mating competence regardless of whether cells lose one MAT locus through random gene loss by mitotically dividing after interspecies hybridization. Moreover, we propose that perturbation of gene expression and substantial breakdown of MAT heterozygosity caused by chromosomal rearrangement at MTL loci play roles in restoring the mating competence of allodiploids. This scenario can provide a mechanism for restoring fertility after interspecies hybridization that is compatible with random gene loss models and suggests genomic plasticity during WGD in yeast. IMPORTANCE A whole-genome duplication occurred in an ancestor of the baker's yeast Saccharomyces cerevisiae. The origins of this complex and multifaceted process, which requires intra- or interspecies hybridization followed by dysfunction of one mating-type (MAT) locus to regain mating competence, has not been thoroughly elucidated. In this study, we provide a mechanism for regaining fertility in an interspecies hybrid, Zygosaccharomyces rouxii. The draft genome sequence analysis and mating test showed that the Z. rouxii strain used in this study is an intact interspecies hybrid, suggesting that it is possible to recover fertility regardless of whether cells lose one MAT locus.

scholarly journals On the origin of degeneracy in the genetic code

2019 ◽  
Vol 9 (6) ◽  
pp. 20190038 ◽  
Author(s):  
D. L. Gonzalez ◽  
S. Giannerini ◽  
R. Rosa
Keyword(s):  
Genetic Code ◽  
Common Ancestor ◽  
Mathematical Framework ◽  
Last Universal Common Ancestor ◽  
Evolutionary Transitions ◽  
Genetic Codes ◽  
Mitochondrial Genetic Code ◽  
Symmetry Principles ◽  
Universal Common Ancestor ◽  
New Perspective

The degeneracy of amino acid coding is one of the most crucial and enigmatic aspects of the genetic code. Different theories about the origin of the genetic code have been developed. However, to date, there is no comprehensive hypothesis on the mechanism that might have generated the degeneracy as we observe it. Here, we provide a new theory that explains the origin of the degeneracy based only on symmetry principles. The approach allows one to describe exactly the degeneracy of the early code (progenitor of the genetic code of LUCA, the last universal common ancestor) which is hypothesized to have the same degeneracy as the present vertebrate mitochondrial genetic code. The theory is based upon the tessera code, that fits as the progenitor of the early code. Moreover, we describe in detail the possible evolutionary transitions implied by our theory. The approach is supported by a unified mathematical framework that accounts for the degeneracy properties of both nuclear and mitochondrial genetic codes. Our work provides a new perspective to the understanding of the origin of the genetic code and the roles of symmetry principles in the organization of genetic information.

scholarly journals Polyploidy and the Evolution of Complex Traits

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Lukasz Huminiecki ◽  
Gavin C. Conant
Keyword(s):  
Complex Traits ◽  
Genome Duplication ◽  
Single Gene ◽  
Whole Genome ◽  
Gene Duplications ◽  
Evolutionary Potential ◽  
Evolutionary Transitions ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Modern Evolutionary Theory

We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers’ yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.

scholarly journals Regulation Mechanism for the movement of BP180, A transmembrane protein of the hemidesmosome.

1999 ◽  
Vol 39 (supplement) ◽  
pp. S42
Author(s):  
K. Murase ◽  
Y. Hirako ◽  
K. Owaribe ◽  
A. Kusumi
Keyword(s):  
Transmembrane Protein ◽  
Regulation Mechanism

scholarly journals Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Sibo Wang ◽  
Hongping Liang ◽  
Yan Xu ◽  
Linzhou Li ◽  
Hongli Wang ◽  
...  
Keyword(s):  
Small Rna ◽  
Stress Responses ◽  
Small Rnas ◽  
Common Ancestor ◽  
Regulation Of Gene Expression ◽  
Mirna Biogenesis ◽  
Last Common Ancestor ◽  
Evolutionary Transitions ◽  
Genome Wide ◽  
Post Transcriptional Regulation

AbstractSmall RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small RNA (miRNA & siRNA) biosynthetic and degradation pathways. The results suggest that Viridiplantae started to evolve plant-like miRNA biogenesis and degradation after the divergence of the Mesostigmatophyceae in the streptophyte algae. We identified two major evolutionary transitions in small RNA metabolism in streptophyte algae; during the first transition, the origin of DCL-New, DCL1, AGO1/5/10 and AGO4/6/9 in the last common ancestor of Klebsormidiophyceae and all other streptophytes could be linked to abiotic stress responses and evolution of multicellularity in streptophytes. During the second transition, the evolution of DCL 2,3,4, and AGO 2,3,7 as well as DRB1 in the last common ancestor of Zygnematophyceae and embryophytes, suggests their possible contribution to pathogen defense and antibacterial immunity. Overall, the origin and diversification of DICER and AGO along with several other small RNA pathway-related genes among streptophyte algae suggested progressive adaptations of streptophyte algae during evolution to a subaerial environment.

scholarly journals Comparative Genomics of Six Juglans Species Reveals Patterns of Disease-associated Gene Family Contractions

2019 ◽  
Author(s):  
Alex Trouern-Trend ◽  
Taylor Falk ◽  
Sumaira Zaman ◽  
Madison Caballero ◽  
David B. Neale ◽  
...  
Keyword(s):  
Gene Family ◽  
Whole Genome Duplication ◽  
Common Ancestor ◽  
Genome Duplication ◽  
Gene Prediction ◽  
Gene Families ◽  
Whole Genome ◽  
High Quality ◽  
Gene Models ◽  
Genome Annotations

ABSTRACTJuglans (walnuts), the most speciose genus in the walnut family (Juglandaceae) represents most of the family’s commercially valuable fruit and wood-producing trees and includes several species used as rootstock in agriculture for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional in-house developed tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multiexonic and monoexonic putative genes to yield between 27,000 and 44,000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 89.6%. We utilized these high quality annotations to assess gene family evolution within Juglans and among Juglans and selected Eurosid species, which revealed significant contractions in several gene families in J. hindsii including disease resistance-related Wall-associated Kinase (WAK) and Catharanthus roseus Receptor-like Kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.SIGNIFICANCEHigh-quality full genome annotations for six species of walnut (Juglans) and a wingnut (Pterocarya) outgroup were constructed using semi-unsupervised gene prediction followed by gene model filtering and functional characterization. These annotations represent the most comprehensive set for any hardwood genus to date. Comparative analyses based on the gene models uncovered rapid evolution in multiple gene families related to disease-response and a whole genome duplication in a Juglandaceae common ancestor.

scholarly journals MUTATIONAL ANALYSIS OF MATING TYPE INHERITANCE IN SYNGEN 4 OF PARAMECIUM AURELIA

Genetics ◽  
1973 ◽  
Vol 74 (1) ◽  
pp. 63-80
Author(s):  
Bruce C Byrne
Keyword(s):  
Mating Type ◽  
Mutational Analysis ◽  
Type Systems ◽  
Mutant Gene ◽  
Mating Types ◽  
Mutant Genes

ABSTRACT Six genic mutations restricting clones to mating type VII (O) were isolated in syngen 4, Paramecium aurelia. The only three extensively tested were neither allelic nor closely linked. A second type of mutation, allelic to one of the O restricted mutants, was also found. Clones homozygous for this mutant gene were selfers, producing both O and E (VIII) mating types, but only when they were progeny of mating type E parental clones. While all seven mutant genes behaved as recessives in monohybrid crosses, clones heterozygous at two different loci often demonstrated an unanticipated phenotype: selfing. The significance of the findings is discussed in relation to mating type determination and the evolution of mating type systems.

scholarly journals Carbonic Anhydrases: An Ancient Tool in Calcareous Sponge Biomineralization

2021 ◽  
Vol 12 ◽  
Author(s):  
Oliver Voigt ◽  
Benedetta Fradusco ◽  
Carolin Gut ◽  
Charalampos Kevrekidis ◽  
Sergio Vargas ◽  
...  
Keyword(s):  
Gene Family ◽  
Common Ancestor ◽  
Last Common Ancestor ◽  
Gene Duplications ◽  
Carbonic Anhydrases ◽  
Temporal Expression ◽  
Additional Species ◽  
Calcareous Sponges ◽  
Membrane Bound

Enzymes of the α-carbonic anhydrase gene family (CAs) are essential for the deposition of calcium carbonate biominerals. In calcareous sponges (phylum Porifera, class Calcarea), specific CAs are involved in the formation of calcite spicules, a unique trait and synapomorphy of this class. However, detailed studies on the CA repertoire of calcareous sponges exist for only two species of one of the two Calcarea subclasses, the Calcaronea. The CA repertoire of the second subclass, the Calcinea, has not been investigated so far, leaving a considerable gap in our knowledge about this gene family in Calcarea. Here, using transcriptomic analysis, phylogenetics, and in situ hybridization, we study the CA repertoire of four additional species of calcareous sponges, including three from the previously unsampled subclass Calcinea. Our data indicate that the last common ancestor of Calcarea had four ancestral CAs with defined subcellular localizations and functions (mitochondrial/cytosolic, membrane-bound, and secreted non-catalytic). The evolution of membrane-bound and secreted CAs involved gene duplications and losses, whereas mitochondrial/cytosolic and non-catalytic CAs are evidently orthologous genes. Mitochondrial/cytosolic CAs are biomineralization-specific genes recruited for biomineralization in the last common ancestor of calcareous sponges. The spatial–temporal expression of these CAs differs between species, which may reflect differences between subclasses or be related to the secondary thickening of spicules during biomineralization that does not occur in all species. With this study, we extend the understanding of the role and the evolution of a key biomineralization gene in calcareous sponges.

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