scholarly journals Origins and Evolutionary Patterns of the 1.688 Satellite DNA Family in Drosophila Phylogeny

2020 ◽  
Vol 10 (11) ◽  
pp. 4129-4146
Author(s):  
Leonardo G. de Lima ◽  
Stacey L. Hanlon ◽  
Jennifer L. Gerton
Keyword(s):  
Repetitive Sequences ◽  
Specific Pattern ◽  
Evolutionary Patterns ◽  
Satellite Dnas ◽  
Evolutionary Pattern ◽  
Functional Roles ◽  
Drosophila Phylogeny ◽  
Species Specific ◽  
Future Work ◽  
Eukaryotic Genomes

Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The 1.688 satDNA, also known as the 359 bp satellite, is one of the most abundant repetitive sequences in Drosophila melanogaster and has been linked to several different biological functions. We investigated the presence and evolution of the 1.688 satDNA in 16 Drosophila genomes. We find that the 1.688 satDNA family is much more ancient than previously appreciated, being shared among part of the melanogaster group that diverged from a common ancestor ∼27 Mya. We found that the 1.688 satDNA family has two major subfamilies spread throughout Drosophila phylogeny (∼360 bp and ∼190 bp). Phylogenetic analysis of ∼10,000 repeats extracted from 14 of the species revealed that the 1.688 satDNA family is present within heterochromatin and euchromatin. A high number of euchromatic repeats are gene proximal, suggesting the potential for local gene regulation. Notably, heterochromatic copies display concerted evolution and a species-specific pattern, whereas euchromatic repeats display a more typical evolutionary pattern, suggesting that chromatin domains may influence the evolution of these sequences. Overall, our data indicate the 1.688 satDNA as the most perduring satDNA family described in Drosophila phylogeny to date. Our study provides a strong foundation for future work on the functional roles of 1.688 satDNA across many Drosophila species.

scholarly journals Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes

2018 ◽  
Author(s):  
Huitong Zhou ◽  
Tina Visnovska ◽  
Hua Gong ◽  
Sebastian Schmeier ◽  
Jon Hickford ◽  
...  
Keyword(s):  
Concerted Evolution ◽  
Purifying Selection ◽  
Gene Families ◽  
Specific Protein ◽  
Common Mechanism ◽  
Dna Repeats ◽  
Coding Region ◽  
Evolutionary Patterns ◽  
Evolutionary Pattern ◽  
Species Specific

AbstractDNA repeats are common elements in eukaryotic genomes, and their multi-copy nature provides the opportunity for genetic exchange. This exchange can produce altered evolutionary patterns, including concerted evolution where within genome repeat copies are more similar to each other than to orthologous repeats in related species. Here we investigated the genetic architecture of the keratin-associated protein (KAP) gene family, KRTAP1. This family encodes proteins that are important components of hair and wool in mammals, and the genes are present in tandem copies. Comparison of KRTAP1 gene repeats from species across the mammalian phylogeny shows strongly contrasting evolutionary patterns between the coding regions, which have a concerted evolution pattern, and the flanking regions, which have a normal, radiating pattern of evolution. This dichotomy in evolutionary pattern transitions abruptly at the start and stop codons, and we show it is not the result of purifying selection acting to maintain species-specific protein sequences, nor of codon adaptation or reverse transcription of KRTAP1-n mRNA. Instead, the results are consistent with short-tract gene conversion events coupled with selection for these events in the coding region driving the contrasting evolutionary patterns found in the KRTAP1 repeats. Our work shows the power that repeat recombination has to complement selection and finely tune the sequences of repetitive genes. Interplay between selection and recombination may be a more common mechanism than currently appreciated for achieving specific adaptive outcomes in the many eukaryotic multi-gene families, and our work argues for greater emphasis on exploring the sequence structures of these families.

scholarly journals Centromere Repeats: Hidden Gems of the Genome

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 223 ◽  
Author(s):  
Gabrielle Hartley ◽  
Rachel O’Neill
Keyword(s):  
Transposable Elements ◽  
De Novo ◽  
Chromosomal Rearrangements ◽  
Repetitive Sequences ◽  
Chromosomal Evolution ◽  
Satellite Dnas ◽  
Integral Role ◽  
Chromosomal Breakpoints ◽  
Karyotypic Variation ◽  
Species Specific

Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’.

scholarly journals Signatures of conserved and unique molecular features in Afrotheria

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arangasamy Yazhini ◽  
Narayanaswamy Srinivasan ◽  
Sankaran Sandhya
Keyword(s):  
Ribosomal Proteins ◽  
Individual Species ◽  
Functional Domain ◽  
Nucleic Acid Binding ◽  
Uncharacterized Protein ◽  
Homologous Proteins ◽  
Functional Roles ◽  
Molecular Features ◽  
Specific Proteins ◽  
Species Specific

AbstractAfrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.

Comparative Cytogenetics in Four Leptodactylus Species (Amphibia, Anura, Leptodactylidae): Evidence of Inner Chromosomal Diversification in Highly Conserved Karyotypes

2021 ◽  
pp. 1-11
Author(s):  
David S. da Silva ◽  
Heriberto F. da Silva Filho ◽  
Marcelo B. Cioffi ◽  
Edivaldo H.C. de Oliveira ◽  
Anderson J.B. Gomes
Keyword(s):  
18S Rdna ◽  
Repetitive Sequences ◽  
Molecular Cytogenetics ◽  
Comparative Cytogenetics ◽  
The Family ◽  
Agnor Staining ◽  
Dna Elements ◽  
Conventional Cytogenetics ◽  
Species Specific ◽  
Repetitive Dna Elements

With 82 species currently described, the genus <i>Leptodactylus</i> is the most diverse and representative one in the family Leptodactylidae. Concerning chromosomal organization, this genus represents an interesting and underexplored group since data from molecular cytogenetics are incipient, and little is known about the organization and distribution of repetitive DNA elements in the karyotypes. In this sense, this study aimed at providing a comparative analysis in 4 <i>Leptodactylus</i> species (<i>L. macrosternum, L. pentadactylus, L. fuscus,</i> and <i>Leptodactylus</i> cf<i>. podicipinus</i>), combining conventional cytogenetics (Giemsa staining, C-banding, and AgNOR staining) and mapping of molecular markers (18S rDNA, telomeric and microsatellite probes), to investigate mechanisms underlying their karyotype differentiation process. The results showed that all species had karyotypes with 2n = 22 and FN = 44, except for <i>Leptodactylus</i> cf. <i>podicipinus</i> which presented FN = 36. The 18S rDNA was observed in pair 8 of all analyzed species (corresponding to pair 4 in <i>L. pentadactylus</i>), coinciding with the secondary constrictions and AgNOR staining. FISH with microsatellite DNA probes demonstrated species-specific patterns, as well as an association of these repetitive sequences with constitutive heterochromatin blocks and ribosomal DNA clusters, revealing the dynamics of microsatellites in the genome of the analyzed species. In summary, our data demonstrate an ongoing process of genomic divergence inside species with almost similar karyotype, driven most likely by a series of pericentric inversions, followed by differential accumulation of repetitive sequences.

scholarly journals Analysis of substitution rates showed that TLR5 is evolving at different rates among mammalian groups

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ana Pinheiro ◽  
Ana Águeda-Pinto ◽  
José Melo-Ferreira ◽  
Fabiana Neves ◽  
Joana Abrantes ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Relative Rate ◽  
Purifying Selection ◽  
Genetic Distances ◽  
Major Protein ◽  
Substitution Rates ◽  
Evolutionary Pattern ◽  
Branch Model ◽  
Rate Test ◽  
Species Specific

Abstract Background Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, the major protein of bacterial flagella. TLR5 has been reported to be under overall purifying selection in mammals, with a small proportion of codons under positive selection. However, the variation of substitution rates among major mammalian groups has been neglected. Here, we studied the evolution of TLR5 in mammals, comparing the substitution rates among groups. Results In this study we analysed the TLR5 substitution rates in Euungulata, Carnivora, Chiroptera, Primata, Rodentia and Lagomorpha, groups. For that, Tajima’s relative rate test, Bayesian inference of evolutionary rates and genetic distances were estimated with CODEML’s branch model and RELAX. The combined results showed that in the Lagomorpha, Rodentia, Carnivora and Chiroptera lineages TLR5 is evolving at a higher substitution rate. The RELAX analysis further suggested a significant relaxation of selective pressures for the Lagomorpha (K = 0.22, p < 0.01), Rodentia (K = 0.58, p < 0.01) and Chiroptera (K = 0.65, p < 0.01) lineages and for the Carnivora ancestral branches (K = 0.13, p < 0.01). Conclusions Our results show that the TLR5 substitution rate is not uniform among mammals. In fact, among the different mammal groups studied, the Lagomorpha, Rodentia, Carnivora and Chiroptera are evolving faster. This evolutionary pattern could be explained by 1) the acquisition of new functions of TLR5 in the groups with higher substitution rate, i.e. TLR5 neofunctionalization, 2) by the beginning of a TLR5 pseudogenization in these groups due to some redundancy between the TLRs genes, or 3) an arms race between TLR5 and species-specific parasites.

scholarly journals SATELLITE DNAs IN THE EMBRYOS OF VARIOUS SPECIES OF THE GENUS DROSOPHILA

Genetics ◽  
1972 ◽  
Vol 72 (3) ◽  
pp. 431-439
Author(s):  
E C Travaglini ◽  
J Petrovic ◽  
J Schultz
Keyword(s):  
Buoyant Density ◽  
Gc Content ◽  
Drosophila Species ◽  
Class I ◽  
Evolutionary Divergence ◽  
Dna Molecules ◽  
Class Iii ◽  
Satellite Dnas ◽  
Evolutionary Pattern ◽  
Gc Composition

ABSTRACT A tentative evolutionary pattern has been found for two classes of the multiple satellite DNA's found in the genus Drosophila. The satellite DNA's from five Drosophila species (D. melanogaster, D. simulans, D. nasuta, D. virilis and D. hydei) were analyzed and found to fall into three arbitrary CsCl buoyant density classes: Class I, ρ = 1.661-1.669 g cm-3, DNA molecules composed of primarily dA and dT moieties; Class II, ρ = 1.685 and ρ = 1.692, DNA molecules of low GC content; and Class III, ρ = 1.711, a DNA of high GC composition. The dAT satellite DNA's appear in all the species studied except D. hydei, the species of most recent evolutionary divergence, whereas the heavy satellite appears only in the two species of most recent divergence, D. virilis and D. hydei.

LINE-1 distribution in six rodent genomes follow a species-specific pattern

2016 ◽  
Vol 95 (1) ◽  
pp. 21-33 ◽  
Author(s):  
A. VIEIRA-DA-SILVA ◽  
F. ADEGA ◽  
H. GUEDES-PINTO ◽  
R. CHAVES
Keyword(s):  
Specific Pattern ◽  
Species Specific

scholarly journals Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion

2012 ◽  
Vol 8 ◽  
pp. EBO.S9758 ◽  
Author(s):  
Dapeng Wang ◽  
Yao Su ◽  
Xumin Wang ◽  
Hongxing Lei ◽  
Jun Yu
Keyword(s):  
Repetitive Sequences ◽  
Intron Size ◽  
Functional Roles

scholarly journals Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 148
Author(s):  
Watcharaporn Thapana ◽  
Nattakan Ariyaraphong ◽  
Parinya Wongtienchai ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Analyses ◽  
Evolutionary Patterns ◽  
Evolutionary Pattern ◽  
Independent Evolution ◽  
Substitution Saturation ◽  
Varanus Salvator ◽  
Monitor Lizards ◽  
Control Regions

Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

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