Isozyme evidence for independently derived, duplicate G3PDH loci among squamate reptiles

1991 ◽  
Vol 69 (9) ◽  
pp. 2381-2396 ◽  
Author(s):  
Jack W. Sites Jr. ◽  
Robert W. Murphy
Keyword(s):  
Specific Gene ◽  
Gene Duplications ◽  
Lizard Species ◽  
Genetic Studies ◽  
Fixed Heterozygosity ◽  
Squamate Reptiles ◽  
Independent Gene ◽  
Sceloporus Grammicus ◽  
Glycerol 3 Phosphate Dehydrogenase ◽  
Almost All

We report evidence for several independent gene duplications for the locus encoding the enzyme glycerol-3-phosphate dehydrogenase (G3PDH) in squamate reptiles. Evidence for the duplication comes from population genetic studies demonstrating "fixed" heterozygosity in all members of some lizard species, the documentation of independent allelic heterozygosity at each of the two G3PDH loci in these same species, and tissue-specific gene expression surveys in a taxonomically diverse array of groups. The duplicated condition is present at both low and high taxonomic levels (selected populations of the phrynosomatid lizard Sceloporus grammicus, and almost all snakes, respectively), and appears to represent the derived condition in most of these groups. One notable exception is the colubrid snake genus Masticophis, which appears to be characterized by an apomorphic secondary silencing event. Evolutionary implications of the duplication and silencing events within squamates are discussed, and we suggest that the overall phylogenetic utility of this marker is low in this radiation as a result of extensive homoplasy.

scholarly journals The morphology of the inner ear of squamate reptiles and its bearing on the origin of snakes

2017 ◽  
Vol 4 (8) ◽  
pp. 170685 ◽  
Author(s):  
Alessandro Palci ◽  
Mark N. Hutchinson ◽  
Michael W. Caldwell ◽  
Michael S. Y. Lee
Keyword(s):  
Geometric Morphometrics ◽  
Inner Ear ◽  
Phylogenetic Signal ◽  
Three Dimensional ◽  
Lizard Species ◽  
Squamate Reptiles ◽  
Strong Affinity ◽  
Ear Morphology

The inner ear morphology of 80 snake and lizard species, representative of a range of ecologies, is here analysed and compared to that of the fossil stem snake Dinilysia patagonica , using three-dimensional geometric morphometrics. Inner ear morphology is linked to phylogeny (we find here a strong phylogenetic signal in the data that can complicate ecological correlations), but also correlated with ecology, with Dinilysia resembling certain semi-fossorial forms ( Xenopeltis and Cylindrophis ), consistent with previous reports. We here also find striking resemblances between Dinilysia and some semi-aquatic snakes, such as Myron (Caenophidia, Homalopsidae). Therefore, the inner ear morphology of Dinilysia is consistent with semi-aquatic as well as semi-fossorial habits: the most similar forms are either semi-fossorial burrowers with a strong affinity to water ( Xenopeltis and Cylindrophis ) or amphibious, intertidal forms which shelter in burrows ( Myron). Notably, Dinilysia does not cluster as closely with snakes with exclusively terrestrial or obligate burrowing habits (e.g. scolecophidians and uropeltids). Moreover, despite the above similarities, Dinilysia also occupies a totally unique morphospace, raising issues with linking it with any particular ecological category.

scholarly journals Partitioning of gene expression among zebrafish photoreceptor subtypes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yohey Ogawa ◽  
Joseph C. Corbo
Keyword(s):  
Gene Expression ◽  
Genome Duplication ◽  
Bright Light ◽  
Transcriptional Regulators ◽  
Specific Gene ◽  
Gene Duplications ◽  
Rna Seq ◽  
Rods And Cones ◽  
Molecular Features ◽  
Photoreceptor Development

AbstractVertebrate photoreceptors are categorized into two broad classes, rods and cones, responsible for dim- and bright-light vision, respectively. While many molecular features that distinguish rods and cones are known, gene expression differences among cone subtypes remain poorly understood. Teleost fishes are renowned for the diversity of their photoreceptor systems. Here, we used single-cell RNA-seq to profile adult photoreceptors in zebrafish, a teleost. We found that in addition to the four canonical zebrafish cone types, there exist subpopulations of green and red cones (previously shown to be located in the ventral retina) that express red-shifted opsin paralogs (opn1mw4 or opn1lw1) as well as a unique combination of cone phototransduction genes. Furthermore, the expression of many paralogous phototransduction genes is partitioned among cone subtypes, analogous to the partitioning of the phototransduction paralogs between rods and cones seen across vertebrates. The partitioned cone-gene pairs arose via the teleost-specific whole-genome duplication or later clade-specific gene duplications. We also discovered that cone subtypes express distinct transcriptional regulators, including many factors not previously implicated in photoreceptor development or differentiation. Overall, our work suggests that partitioning of paralogous gene expression via the action of differentially expressed transcriptional regulators enables diversification of cone subtypes in teleosts.

The Validity of the DSM-IV Subtypes of Attention-Deficit/Hyperactivity Disorder

2005 ◽  
Vol 39 (5) ◽  
pp. 344-353 ◽  
Author(s):  
Bernardine S. C. Woo ◽  
Joseph M. Rey
Keyword(s):  
Attention Deficit Hyperactivity Disorder ◽  
Attention Deficit ◽  
Age Distribution ◽  
The Other ◽  
Genetic Studies ◽  
Main Research ◽  
Hyperactivity Disorder ◽  
Dsm Iv ◽  
Almost All ◽  
All Treatment

Objective: To examine the validity of the three subtypes of ADHD defined by DSM-IV. Method: Studies published in English were identified through searches of literature databases. Results: Estimates of the prevalence of ADHD have increased as a result of the introduction of DSM-IV criteria. Factor analytical and genetic studies provide some support for the validity of the distinction between the three subtypes. However, diagnosis of the combined subtype seems more reliable than the other two subtypes, although reliability is largely unknown for the latter. The hyperactive-impulsive subtype, the least common, differs from the other two subtypes in age distribution, association with other factors and neuropsychological parameters. Almost all treatment trials are based on participants with the combined type. Conclusion: Data supporting the validity of the inattentive and hyperactive-impulsive subtypes of ADHD a decade after the publication of DSM-IV are still scarce. Given that inattention is the hypothesized core ADHD symptom, it remains to be demonstrated that hyperactive-impulsive children who are not inattentive have the same condition. One of the main research deficits refers to data on treatment of the inattentive and hyperactive impulsive subtypes.

scholarly journals Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream

2019 ◽  
Author(s):  
Jaume Pérez-Sánchez ◽  
Fernando Naya-Català ◽  
Beatriz Soriano ◽  
M. Carla Piazzon ◽  
Ahmed Hafez ◽  
...  
Keyword(s):  
Genome Size ◽  
Transcriptional Analysis ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Gene Duplications ◽  
Dna Transposons ◽  
Species Specific

AbstractGilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding towards more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds (∼732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreambrowser. Homology-based functional annotation, supported by RNA-seq transcripts, identified 55,423 actively transcribed genes corresponding to 21,275 unique descriptions with more than 55% of duplicated genes. The mobilome accounts for the 75% of the full genome size and it is mostly constituted by introns (599 Mb), whereas the rest is represented by low complexity repeats, RNA retrotransposons, DNA transposons and non-coding RNAs. This mobilome also contains a large number of chimeric/composite genes (i. e. loci presenting fragments or exons mostly surrounded by LINEs and Tc1/mariner DNA transposons), whose analysis revealed an enrichment in immune-related functions and processes. Analysis of synteny and gene phylogenies uncovered a high rate of species-specific duplications, resulting from recent independent duplications rather than from genome polyploidization (2.024 duplications per gene; 0.385 excluding gene expansions). These species-specific duplications were enriched in gene families functionally related to genome transposition, immune response and sensory responses. Additionally, transcriptional analysis of liver, skeletal muscle, intestine, gills and spleen supported a high number of functionally specialized paralogs under tissue-exclusive regulation. Altogether, these findings suggest a role of recent large-scale gene duplications coupled to tissue expression diversification in the evolution of gilthead sea bream genome during its successful adaptation to a changing and pathogen-rich environment. This issue also underscores a role of evolutionary routes for rapid increase of the gene repertoire in teleost fish that are independent of polyploidization. Since gilthead sea bream has a well-recognized plasticity, the current study will advance our understanding of fish biology and how organisms of this taxon interact with the environment.

scholarly journals Localization of genes modulating the predisposition to schizophrenia: a revision

2000 ◽  
Vol 23 (3) ◽  
pp. 549-556 ◽  
Author(s):  
E.Z. Lopes-Machado ◽  
F.A.M. Duarte
Keyword(s):  
Dna Marker ◽  
Molecular Level ◽  
Association Studies ◽  
Bipolar Affective Disorder ◽  
Molecular Genetic ◽  
Specific Gene ◽  
Chromosome 6 ◽  
Genetic Studies ◽  
Multiple Loci ◽  
Specific Allele

The genetics of schizophrenia or bipolar affective disorder has advanced greatly at the molecular level since the introduction of probes for the localization of specific genes. Research on gene candidates for susceptibility to schizophrenia can broadly be divided into two types, i.e., linkage studies, where a gene is found near a specific DNA marker on a specific chromosome, and association studies, when a condition is associated with a specific allele of a specific gene. This review covers a decade of publications in this area, from the 1988 works of Bassett et al. and Sherrington et al. on a gene localized on the long arm of chromosome 5 at the 5q11-13 loci, to the 1997 work of Lin et al. pointing to the 13q14.1-q32 loci of chromosome 13 and to the 1998 work of Wright et al. on an HLA DRB1 gene locus on chromosome 6 at 6p21-3. The most replicated loci were those in the long arm of chromosome 22 (22q12-q13.1) and on the short arm of chromosome 6 (6p24-22). In this critical review of the molecular genetic studies involved in the localization of genes which modulate the predisposition to schizophrenia the high variability in the results obtained by different workers suggests that multiple loci are involved in the predisposition to this illness.

scholarly journals Diurnal.plant.tools: comparative transcriptomic and co-expression analyses of diurnal gene expression of the Archaeplastida kingdom

2019 ◽  
Author(s):  
Jonathan Wei Xiong Ng ◽  
Qiao Wen Tan ◽  
Camilla Ferrari ◽  
Marek Mutwil
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Species Comparisons ◽  
Gene Modules ◽  
Time Specific ◽  
Almost All ◽  
User Friendly ◽  
Diurnal Regulation

ABSTRACTAlmost all organisms coordinate some aspects of their biology through the diurnal cycle. Photosynthetic organisms, and plants especially, have established complex programs that coordinate physiological, metabolic and developmental processes with the changing light. The diurnal regulation of the underlying transcriptional processes is observed when groups of functionally related genes (gene modules) are expressed at a specific time of the day. However, studying the diurnal regulation of these gene modules in the plant kingdom was hampered by the large amount of data required for the analyses. To meet this need, we used gene expression data from 17 diurnal studies spanning the whole Archaeplastida kingdom (Plantae kingdom in the broad sense) to make an online diurnal database. We have equipped the database with tools that allow user-friendly cross-species comparisons of gene expression profiles, entire co-expression networks, co-expressed clusters (involved in specific biological processes), time-specific gene expression, and others. We exemplify how these tools can be used by studying three important biological questions: (i) the evolution of cell division, (ii) the diurnal control of gene modules in algae and (iii) the conservation of diurnally-controlled modules across species. The database is freely available at http://diurnal.plant.tools/.

scholarly journals Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology

2021 ◽  
Vol 12 ◽  
Author(s):  
Revuru Bharadwaj ◽  
Sarma R. Kumar ◽  
Ashutosh Sharma ◽  
Ramalingam Sathishkumar
Keyword(s):  
Synthetic Biology ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Gene Clustering ◽  
Specific Gene ◽  
Gene Duplications ◽  
Ecological Functions ◽  
Specialized Metabolites ◽  
Coordinated Expression

Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.

scholarly journals Evolutionary Variability of W-Linked Repetitive Content in Lacertid Lizards

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 531
Author(s):  
Grzegorz Suwala ◽  
Marie Altmanová ◽  
Sofia Mazzoleni ◽  
Emmanouela Karameta ◽  
Panayiotis Pafilis ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Phylogenetic Signal ◽  
Z Chromosome ◽  
Specific Gene ◽  
W Chromosome ◽  
Squamate Reptiles ◽  
Lacertid Lizards ◽  
Species Specific

Lacertid lizards are a widely radiated group of squamate reptiles with long-term stable ZZ/ZW sex chromosomes. Despite their family-wide homology of Z-specific gene content, previous cytogenetic studies revealed significant variability in the size, morphology, and heterochromatin distribution of their W chromosome. However, there is little evidence about the accumulation and distribution of repetitive content on lacertid chromosomes, especially on their W chromosome. In order to expand our knowledge of the evolution of sex chromosome repetitive content, we examined the topology of telomeric and microsatellite motifs that tend to often accumulate on the sex chromosomes of reptiles in the karyotypes of 15 species of lacertids by fluorescence in situ hybridization (FISH). The topology of the above-mentioned motifs was compared to the pattern of heterochromatin distribution, as revealed by C-banding. Our results show that the topologies of the examined motifs on the W chromosome do not seem to follow a strong phylogenetic signal, indicating independent and species-specific accumulations. In addition, the degeneration of the W chromosome can also affect the Z chromosome and potentially also other parts of the genome. Our study provides solid evidence that the repetitive content of the degenerated sex chromosomes is one of the most evolutionary dynamic parts of the genome.

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