scholarly journals Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks

Heredity ◽  
2009 ◽  
Vol 104 (6) ◽  
pp. 543-551 ◽  
Author(s):  
M Plohl ◽  
V Petrović ◽  
A Luchetti ◽  
A Ricci ◽  
E Šatović ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Sequence Divergence ◽  
Bivalve Mollusks ◽  
High Sequence Divergence

scholarly journals Structural characterization and duplication modes of pseudogenes in plants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Flavia Mascagni ◽  
Gabriele Usai ◽  
Andrea Cavallini ◽  
Andrea Porceddu
Keyword(s):  
Evolutionary Rate ◽  
Populus Trichocarpa ◽  
Sequence Divergence ◽  
Strand Break ◽  
Whole Genome ◽  
Flanking Sequence ◽  
Plant Genomes ◽  
High Sequence Divergence ◽  
Flanking Regions

AbstractWe identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

Strong genetic subdivision in Leptobrachium hendricksoni (Anura: Megophryidae) in Southeast Asia

2018 ◽  
Vol 39 (1) ◽  
pp. 99-111
Author(s):  
Gordon Draškić ◽  
Sansareeya Wangkulangkul ◽  
Iñigo Martínez-Solano ◽  
Judit Vörös
Keyword(s):  
Southeast Asia ◽  
Sequence Divergence ◽  
Population Divergence ◽  
Geological History ◽  
Base Pairs ◽  
Sea Levels ◽  
Phylogenetic Studies ◽  
High Sequence Divergence ◽  
Southern Thailand ◽  
Rising Sea Levels

Many biodiversity hotspots are located in areas with a complex geological history, like Southeast Asia, where species diversity may still be far underestimated, especially in morphologically conservative groups like amphibians. Recent phylogenetic studies on the frog genusLeptobrachiumfrom Southeast Asia revealed the presence of deeply divergent mitochondrial clades inLeptobrachium hendricksonifrom Malaysia and Sumatra but populations from Thailand have not been studied so far. In this study, we re-evaluate patterns of intraspecific genetic diversity inL. hendricksonibased on the analysis of combined sequences of mitochondrial 12S and 16S genes (1310 base pairs) including for the first time samples from southern Thailand. Thai populations ofL. hendricksoniformed a distinct clade with respect to populations from central and southern Malaysia and Sumatra. High sequence divergence between lineages from Thailand, Malaysia and Sumatra suggests the possible presence of cryptic species inL. hendricksoni. Divergence withinL. hendricksonidates back to the late Miocene, around 6 Mya, when lineages from Thailand, north Malaysia and Sumatra split from a lineage in south Malaysia, at about the same time as rising sea levels isolated the Thai-Malay peninsula. Subsequent splits took place later in the Pliocene, around 4.5 and 2.6 Mya. Our results highlight the role of geological history in promoting population divergence and speciation.

Morphological and molecular evidence for the recognition of Caloglossa fonticola sp. nov. (Delesseriaceae, Rhodophyta) from an underground spring in Guangxi, China

Phytotaxa ◽  
2021 ◽  
Vol 522 (1) ◽  
pp. 15-26
Author(s):  
KUN-PENG FANG ◽  
FANG-RU NAN ◽  
JIA FENG ◽  
QI LIU ◽  
XU-DONG LIU ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Molecular Evidence ◽  
Unique Combination ◽  
High Sequence Divergence ◽  
Molecular Phylogenetic ◽  
Freshwater Habitats ◽  
Globally Distributed ◽  
Lateral Axis

Caloglossa (Ceramiales, Rhodophyta) is a globally distributed euryhaline red macroalgal genus. However, only a few Caloglossa species have been documented in permanent freshwater habitats. Here, a new Caloglossa species, Caloglossa fonticola sp. nov., is described and illustrated from an underground spring in Bama County, Guangxi, China, based on morphological observations and molecular phylogenetic analysis. The new species is morphologically distinguishable from other species in the genus by a unique combination of character states, including thallus internodal blades linear, hardly or slightly constricted at nodes, adventitious branches and endogenous branches both absent, and unicellular rhizoids forming from clusters of wing cells arising from the first three axial cells of the main axis and lateral axis. Phylogenetic analysis based on rbcL and LSU rRNA DNA sequences indicated that Caloglossa fonticola was nested in a well-supported clade with Caloglossa bengalensis (Bootstrap supports for ML/posterior probabilities for BI: rbcL-98/1.00, LSU-100/1.00), with high sequence divergence between these two species (8.2–8.4% for rbcL and 3.2% for LSU), supporting its specific status. This is the first species of the genus Caloglossa reported in spring water habitats. The description of C. fonticola expands the known diversity of Caloglossa.

scholarly journals Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin

2020 ◽  
Vol 12 (11) ◽  
pp. 2125-2138
Author(s):  
Isidoro Feliciello ◽  
Željka Pezer ◽  
Dušan Kordiš ◽  
Branka Bruvo Mađarić ◽  
Đurđica Ugarković
Keyword(s):  
Satellite Dna ◽  
Evolutionary History ◽  
Genomic Sequence ◽  
Sequence Divergence ◽  
Dna Repeats ◽  
Alpha Satellite ◽  
Alpha Satellite Dna ◽  
Satellite Repeats ◽  
Number Variation ◽  
History Of

Abstract Major human alpha satellite DNA repeats are preferentially assembled within (peri)centromeric regions but are also dispersed within euchromatin in the form of clustered or short single repeat arrays. To study the evolutionary history of single euchromatic human alpha satellite repeats (ARs), we analyzed their orthologous loci across the primate genomes. The continuous insertion of euchromatic ARs throughout the evolutionary history of primates starting with the ancestors of Simiformes (45–60 Ma) and continuing up to the ancestors of Homo is revealed. Once inserted, the euchromatic ARs were stably transmitted to the descendant species, some exhibiting copy number variation, whereas their sequence divergence followed the species phylogeny. Many euchromatic ARs have sequence characteristics of (peri)centromeric alpha repeats suggesting heterochromatin as a source of dispersed euchromatic ARs. The majority of euchromatic ARs are inserted in the vicinity of other repetitive elements such as L1, Alu, and ERV or are embedded within them. Irrespective of the insertion context, each AR insertion seems to be unique and once inserted, ARs do not seem to be subsequently spread to new genomic locations. In spite of association with (retro)transposable elements, there is no indication that such elements play a role in ARs proliferation. The presence of short duplications at most of ARs insertion sites suggests site-directed recombination between homologous motifs in ARs and in the target genomic sequence, probably mediated by extrachromosomal circular DNA, as a mechanism of spreading within euchromatin.

scholarly journals Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

2021 ◽  
Author(s):  
Manu Kumar Gundappa ◽  
Thu-Hien To ◽  
Lars Grønvold ◽  
Samuel A M Martin ◽  
Sigbjørn Lien ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Meiotic Pairing ◽  
Genome Wide ◽  
A Genome ◽  
Clock Analysis ◽  
Multiple Species ◽  
Genomic Regions ◽  
Genome Assemblies

The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent 'explosion' of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial 'wave' of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained in a tetraploid state. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Finally, using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. Overall, this study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.

scholarly journals Characteristics and evolution of satellite DNA sequences in bivalve mollusks

2018 ◽  
Vol 85 (1) ◽  
pp. 94-103 ◽  
Author(s):  
E. Šatović ◽  
T. Vojvoda Zeljko ◽  
M. Plohl
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Bivalve Mollusks

scholarly journals Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

2015 ◽  
Author(s):  
Mark Lipson ◽  
Po-Ru Loh ◽  
Sriram Sankararaman ◽  
Nick Patterson ◽  
Bonnie Berger ◽  
...  
Keyword(s):  
Mutation Rate ◽  
De Novo ◽  
Sequence Divergence ◽  
Great Apes ◽  
Human Populations ◽  
De Novo Mutations ◽  
Essential Parameter ◽  
Human Mutation ◽  
Rate Of Accumulation

The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Most notably, recent approaches based on counting de novo mutations in family pedigrees have yielded significantly smaller values than classical methods based on sequence divergence. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.61 +/- 0.13 x 10^(-8) mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.

scholarly journals Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil’s Disease

2021 ◽  
Vol 22 (24) ◽  
pp. 13434
Author(s):  
Eric Olo Ndela ◽  
François Enault ◽  
Ariane Toussaint
Keyword(s):  
Gene Transfer ◽  
Genomic Organization ◽  
Sequence Divergence ◽  
Specific Gene ◽  
Diverse Group ◽  
High Sequence Divergence ◽  
Causative Agents ◽  
Weil’S Disease ◽  
Weil's Disease ◽  
Model Strain

The virome associated with the corkscrew shaped bacterium Leptospira, responsible for Weil’s disease, is scarcely known, and genetic tools available for these bacteria remain limited. To reduce these two issues, potential transposable prophages were searched in Leptospiraceae genomes. The 236 predicted transposable prophages were particularly abundant in the most pathogenic leptospiral clade, being potentially involved in the acquisition of virulent traits. According to genomic similarities and phylogenies, these prophages are distantly related to known transposable phages and are organized into six groups, one of them encompassing prophages with unusual TA-TA ends. Interestingly, structural and transposition proteins reconstruct different relationships between groups, suggesting ancestral recombinations. Based on the baseplate phylogeny, two large clades emerge, with specific gene-contents and high sequence divergence reflecting their ancient origin. Despite their high divergence, the size and overall genomic organization of all prophages are very conserved, a testimony to the highly constrained nature of their genomes. Finally, similarities between these prophages and the three known non-transposable phages infecting L. biflexa, suggest gene transfer between different Caudovirales inside their leptospiral host, and the possibility to use some of the transposable prophages in that model strain.

Nucleotide Sequence of Bovine 1.723 Satellite DNA

1985 ◽  
Vol 40 (3-4) ◽  
pp. 242-246 ◽  
Author(s):  
G. Plucienniczak ◽  
J. Skowronski ◽  
A. Plucienniczak ◽  
J. Jaworski
Keyword(s):  
Nucleotide Sequence ◽  
Satellite Dna ◽  
Repetitive Sequences ◽  
Sequence Divergence ◽  
Satellite Dnas ◽  
Long Period ◽  
Repeated Unit ◽  
Periodical Structure ◽  
Sequence Similarities

The nucleotide sequence of the bovine 1.723 satellite DNA repeated unit was determined. The 680 bp long period of this satellite DNA does not show any significant sequence similarities with the known bovine satellite DNAs. Short repetitive sequences which are parts of 680 bp long repeated units do not form any orderly periodical structure. It seems, however, that the basic repeated unit of the 1.723 bovine satellite DNA has been formed by successive duplications of two, about 100 bp long sequences. The sequence divergence between different copies of the 680 bp repeated unit was also analyzed.

Sign in / Sign up

Export Citation Format

Share Document