gene expansion
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Author(s):  
Damien M O’Halloran

Abstract Glutamate Gated Chloride (GluCl) channels belong to the Cys-loop receptor superfamily. GluCl channels are activated by glutamate (Glu) and form substrates for the anti-parasitic drugs from the avermectin family. GluCl channels are pentameric, and each subunit contains an N-terminal extracellular domain that binds Glu and four helical transmembrane domains (TMs), which contain binding sites for avermectin drugs. In order to provide more insight into phylum-wide patterns of GluCl subunit gene expansion and sequence diversity across nematodes, we have developed a database of predicted GluCl subunit genes from 125 nematode species. Our analysis into this dataset described assorted patterns of species-specific GluCl gene counts across different nematodes as well as sequence diversity in key residues thought to be involved in avermectin binding.


2021 ◽  
Vol 9 ◽  
Author(s):  
Nicolas Montagné ◽  
Muriel Jager ◽  
Thomas Chertemps ◽  
Emma Persyn ◽  
Yan Jaszczyszyn ◽  
...  

Insects astoundingly dominate Earth’s land ecosystems and have a huge impact on human life. Almost every aspect of their life relies upon their highly efficient and adaptable chemosensory system. In the air, most chemical signals that are detected at long range are hydrophobic molecules, which insects detect using proteins encoded by multigenic families that emerged following land colonization by insect ancestors, namely the odorant-binding proteins (OBPs) and the odorant receptors (ORs). However, land-to-freshwater transitions occurred in many lineages within the insect tree of life. Whether chemosensory gene repertoires of aquatic insects remained essentially unchanged or underwent more or less drastic modifications to cope with physico-chemical constraints associated with life underwater remains virtually unknown. To address this issue, we sequenced and analyzed the transcriptome of chemosensory organs of the diving beetle Rhantus suturalis (Coleoptera, Dytiscidae). A reference transcriptome was assembled de novo using reads from five RNA-seq libraries (male and female antennae, male and female palps, and wing muscle). It contained 47,570 non-redundant unigenes encoding proteins of more than 50 amino acids. Within this reference transcriptome, we annotated sequences coding 53 OBPs, 48 ORs, 73 gustatory receptors (GRs), and 53 ionotropic receptors (IRs). Phylogenetic analyses notably revealed a large OBP gene expansion (35 paralogs in R. suturalis) as well as a more modest OR gene expansion (9 paralogs in R. suturalis) that may be specific to diving beetles. Interestingly, these duplicated genes tend to be expressed in palps rather than in antennae, suggesting a possible adaptation with respect to the land-to-water transition. This work provides a strong basis for further evolutionary and functional studies that will elucidate how insect chemosensory systems adapted to life underwater.


2021 ◽  
Vol 17 (S6) ◽  
Author(s):  
Rebecca Kjærgaard Hendel ◽  
Marie Nathalie Nickelsen Hellem ◽  
Lena Elisabeth Hjermind ◽  
Jørgen Erik Nielsen ◽  
Asmus Vogel

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Wenbing Chen ◽  
Changling Zuo ◽  
Chundi Wang ◽  
Tengteng Zhang ◽  
Liping Lyu ◽  
...  

Abstract Background Ciliated protists are a widely distributed, morphologically diverse, and genetically heterogeneous group of unicellular organisms, usually known for containing two types of nuclei: a transcribed polyploid macronucleus involved in gene expression and a silent diploid micronucleus responsible for transmission of genetic material during sexual reproduction and generation of the macronucleus. Although studies in a few species of culturable ciliated protists have revealed the highly dynamic nature of replicative and recombination events relating the micronucleus to the macronucleus, the broader understanding of the genomic diversity of ciliated protists, as well as their phylogenetic relationships and metabolic potential, has been hampered by the inability to culture numerous other species under laboratory conditions, as well as the presence of symbiotic bacteria and microalgae which provide a challenge for current sequencing technologies. Here, we optimized single-cell sequencing methods and associated data analyses, to effectively remove contamination by commensal bacteria, and generated high-quality genomes for a number of Euplotia species. Results We obtained eight high-quality Euplotia genomes by using single-cell genome sequencing techniques. The genomes have high genomic completeness, with sizes between 68 and 125 M and gene numbers between 14K and 25K. Through comparative genomic analysis, we found that there are a large number of gene expansion events in Euplotia genomes, and these expansions are closely related to the phenotypic evolution and specific environmental adaptations of individual species. We further found four distinct subgroups in the genus Euplotes, which exhibited considerable genetic distance and relative lack of conserved genomic syntenies. Comparative genomic analyses of Uronychia and its relatives revealed significant gene expansion associated with the ciliary movement machinery, which may be related to the unique and strong swimming ability. Conclusions We employed single-cell genomics to obtain eight ciliate genomes, characterized the underestimated genomic diversity of Euplotia, and determined the divergence time of representative species in this subclass for the first time. We also further investigated the extensive duplication events associated with speciation and environmental adaptation. This study provides a unique and valuable resource for understanding the evolutionary history and genetic diversity of ciliates.


2021 ◽  
Vol 34 (4) ◽  
pp. 295-302
Author(s):  
Rebecca K. Hendel ◽  
Marie N.N. Hellem ◽  
Lena E. Hjermind ◽  
Jørgen E. Nielsen ◽  
Asmus Vogel

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ao Li ◽  
He Dai ◽  
Ximing Guo ◽  
Ziyan Zhang ◽  
Kexin Zhang ◽  
...  

AbstractUnderstanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology and important for assessing adaptive potential of species under climate change. Analysis of a chromosome-level assembly and resequencing of individuals across wide latitude distribution in the estuarine oyster (Crassostrea ariakensis) revealed unexpectedly low genomic diversity and population structures shaped by historical glaciation, geological events and oceanographic forces. Strong selection signals were detected in genes responding to temperature and salinity stress, especially of the expanded solute carrier families, highlighting the importance of gene expansion in environmental adaptation. Genes exhibiting high plasticity showed strong selection in upstream regulatory regions that modulate transcription, indicating selection favoring plasticity. Our findings suggest that genomic variation and population structure in marine bivalves are heavily influenced by climate history and physical forces, and gene expansion and selection may enhance phenotypic plasticity that is critical for the adaptation to rapidly changing environments.


2021 ◽  
Author(s):  
Alexander J Lowe ◽  
Filipe B Rodrigues ◽  
Marzenna Arridge ◽  
Eileanoir B Johnson ◽  
Rachel I Scahill ◽  
...  

Magnetic resonance spectroscopy (MRS) is a non-invasive method of exploring cerebral metabolism. In Huntingtons disease, altered MRS-determined concentrations of several metabolites have been described; however, findings are often discrepant and longitudinal studies of metabolite trajectory are lacking. MRS metabolites may represent a valuable source of biomarkers, thus their relationship with established biofluid and structural imaging markers of disease progression require further exploration to assess prognostic value and elucidate biochemical pathways associated with neurodegeneration. In a prospective single-site controlled cohort study with standardised collection of CSF, blood, phenotypic and imaging data, we used MRS to evaluate metabolic profiles in the putamen of 56 participants at baseline (15 healthy controls, 15 premanifest and 26 manifest gene expansion carriers) and at 2-year follow-up. Intergroup differences and associations with established measures were assessed cross-sectionally using generalized linear models and partial correlation, controlling for age and CAG repeat length. We report no significant groupwise differences in metabolite concentration but found several metabolites to be associated with measures of disease progression; however, only two relationships were replicated across both time points, with total Creatine (creatine + phosphocreatine) and myo-inositol displaying significant associations with reduced caudate volume. Although relationships were observed between MRS metabolites and biofluid measures, these were not consistent across time points. To further assess prognostic value of the metabolites, we examined whether baseline MRS values, or rate of change, predicted subsequent change in established measures of disease progression. Several associations were found but were inconsistent across known indicators of disease progression. Finally, longitudinal mixed effects models, controlling for age, revealed no significant change in metabolite concentration over time in gene expansion carriers. Altogether, our findings show some interesting cross-sectional associations between select metabolites, namely total creatine and myo-inositol, and markers of disease progression, potentially highlighting the proposed roles of neuroinflammation and metabolic dysfunction in disease pathogenesis. However, the absence of group differences, inconsistency between baseline and follow-up, and lack of clear longitudinal change over two years suggests that MRS metabolites have limited potential as biomarkers in Huntingtons disease.


2021 ◽  
Vol 22 (17) ◽  
pp. 9167
Author(s):  
Xiaonan Zhao ◽  
Karen Usdin

Fragile X-related disorders (FXDs), also known as FMR1 disorders, are examples of repeat expansion diseases (REDs), clinical conditions that arise from an increase in the number of repeats in a disease-specific microsatellite. In the case of FXDs, the repeat unit is CGG/CCG and the repeat tract is located in the 5′ UTR of the X-linked FMR1 gene. Expansion can result in neurodegeneration, ovarian dysfunction, or intellectual disability depending on the number of repeats in the expanded allele. A growing body of evidence suggests that the mutational mechanisms responsible for many REDs share several common features. It is also increasingly apparent that in some of these diseases the pathologic consequences of expansion may arise in similar ways. It has long been known that many of the disease-associated repeats form unusual DNA and RNA structures. This review will focus on what is known about these structures, the proteins with which they interact, and how they may be related to the causative mutation and disease pathology in the FMR1 disorders.


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