scholarly journals Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 827 ◽  
Author(s):  
Syed Ahmad ◽  
Worapong Singchat ◽  
Maryam Jehangir ◽  
Thitipong Panthum ◽  
Kornsorn Srikulnath
Keyword(s):  
Paradigm Shift ◽  
Evolutionary Dynamics ◽  
Genomic Structure ◽  
Chromosomal Rearrangements ◽  
Genomic Diversity ◽  
Repeat Elements ◽  
Satellite Sequences ◽  
Karyotype Variability ◽  
Genome Scale ◽  
Reptilian Species

Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the “repeatome”, remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro- and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution.

Molecular and Cytological Analyses of Large Tracks of Centromeric DNA Reveal the Structure and Evolutionary Dynamics of Maize Centromeres

Genetics ◽  
2003 ◽  
Vol 163 (2) ◽  
pp. 759-770 ◽  
Author(s):  
Kiyotaka Nagaki ◽  
Junqi Song ◽  
Robert M Stupar ◽  
Alexander S Parokonny ◽  
Qiaoping Yuan ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Artificial Chromosome ◽  
Grass Species ◽  
Sequence Motifs ◽  
Long Terminal Repeats ◽  
Satellite Repeat ◽  
Sequence Comparisons ◽  
Centromeric Dna ◽  
Conserved Sequence ◽  
Satellite Sequences

Abstract We sequenced two maize bacterial artificial chromosome (BAC) clones anchored by the centromere-specific satellite repeat CentC. The two BACs, consisting of ∼200 kb of cytologically defined centromeric DNA, are composed exclusively of satellite sequences and retrotransposons that can be classified as centromere specific or noncentromere specific on the basis of their distribution in the maize genome. Sequence analysis suggests that the original maize sequences were composed of CentC arrays that were expanded by retrotransposon invasions. Seven centromere-specific retrotransposons of maize (CRM) were found in BAC 16H10. The CRM elements inserted randomly into either CentC monomers or other retrotransposons. Sequence comparisons of the long terminal repeats (LTRs) of individual CRM elements indicated that these elements transposed within the last 1.22 million years. We observed that all of the previously reported centromere-specific retrotransposons in rice and barley, which belong to the same family as the CRM elements, also recently transposed with the oldest element having transposed ∼3.8 million years ago. Highly conserved sequence motifs were found in the LTRs of the centromere-specific retrotransposons in the grass species, suggesting that the LTRs may be important for the centromere specificity of this retrotransposon family.

scholarly journals Population Diversity and Collective Interactions during Influenza Virus Infection

2017 ◽  
Vol 91 (22) ◽  
Author(s):  
Christopher B. Brooke
Keyword(s):  
Genome Organization ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Influenza Virus Infection ◽  
Population Diversity ◽  
Genomic Diversity ◽  
Global Public Health ◽  
Public Health Threat ◽  
Genetic Makeup ◽  
Collective Interactions

ABSTRACT Influenza A virus (IAV) continues to pose an enormous and unpredictable global public health threat, largely due to the continual evolution of escape from preexisting immunity and the potential for zoonotic emergence. Understanding how the unique genetic makeup and structure of IAV populations influences their transmission and evolution is essential for developing more-effective vaccines, therapeutics, and surveillance capabilities. Owing to their mutation-prone replicase and unique genome organization, IAV populations exhibit enormous amounts of diversity both in terms of sequence and functional gene content. Here, I review what is currently known about the genetic and genomic diversity present within IAV populations and how this diversity may shape the replicative and evolutionary dynamics of these viruses.

scholarly journals Molecular Phylogenetics and Evolutionary Analysis of a Highly Recombinant Begomovirus, Cotton Leaf Curl Multan Virus and Associated Satellites

2021 ◽  
Author(s):  
Tahir Farooq ◽  
Muhammad Umar ◽  
Xiaoman She ◽  
Yafei Tang ◽  
Zifu He
Keyword(s):  
Molecular Phylogenetics ◽  
Management Strategies ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Cotton Leaf ◽  
Evolutionary Analysis ◽  
Cotton Production ◽  
Evolutionary Patterns ◽  
Satellite Sequences ◽  
Leaf Curl

Abstract Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite’s virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite (CLCuMuA) and Cotton leaf curl Multan betasatellite (CLCuMuB) populations arising from distinct regions exhibit high mutation rates. Though evolutionary linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.

scholarly journals Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome

Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2386
Author(s):  
Worapong Singchat ◽  
Syed Farhan Ahmad ◽  
Nararat Laopichienpong ◽  
Aorarat Suntronpong ◽  
Thitipong Panthum ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Evolutionary Dynamics ◽  
Sex Chromosome ◽  
Chromosomal Rearrangements ◽  
Chromosome Analysis ◽  
Chromosome Conformation ◽  
Principal Mechanism ◽  
Squamate Reptiles ◽  
Genomic Landscape ◽  
Heteromorphic Sex Chromosomes

Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.

scholarly journals Impact of insertion sequences on convergent evolution ofShigellaspecies

2019 ◽  
Author(s):  
Jane Hawkey ◽  
Jonathan M. Monk ◽  
Helen Billman-Jacobe ◽  
Bernhard Palsson ◽  
Kathryn E. Holt
Keyword(s):  
Evolutionary Dynamics ◽  
Shigella Flexneri ◽  
Bacterial Species ◽  
Genomic Variation ◽  
Shigella Dysenteriae ◽  
Insertion Sequences ◽  
Single Nucleotide Variants ◽  
Genomic Studies ◽  
Metabolic Reduction ◽  
Genome Scale

AbstractShigellaspecies are specialised lineages ofEscherichia colithat have converged to become human-adapted and cause dysentery by invading human gut epithelial cells. Most studies ofShigellaevolution have been restricted to comparisons of single representatives of each species; and population genomic studies of individualShigellaspecies have focused on genomic variation caused by single nucleotide variants and ignored the contribution of insertion sequences (IS) which are highly prevalent inShigellagenomes. Here, we investigate the distribution and evolutionary dynamics of IS within populations ofShigella dysenteriaeSd1,Shigella sonneiandShigella flexneri. We find that five IS (IS1, IS2, IS4, IS600and IS911) have undergone expansion in allShigellaspecies, creating substantial strain-to-strain variation within each population and contributing to convergent patterns of functional gene loss within and between species. We find that IS expansion and genome degradation are most advanced inS. dysenteriaeand least advanced inS. sonnei; and using genome-scale models of metabolism we show thatShigellaspecies display convergent loss of coreE. colimetabolic capabilities, withS. sonneiandS. flexnerifollowing a similar trajectory of metabolic streamlining to that ofS. dysenteriae. This study highlights the importance of IS to the evolution ofShigellaand provides a framework for the investigation of IS dynamics and metabolic reduction in other bacterial species.

scholarly journals Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations 

2020 ◽  
Author(s):  
Eeva Jansson ◽  
Francois Besnier ◽  
Ketil Malde ◽  
Carl André ◽  
Geir Dahle ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
De Novo ◽  
Genomic Structure ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Full Genome Sequencing ◽  
Population Genomic ◽  
Genome Wide ◽  
Ctenolabrus Rupestris ◽  
Goldsinny Wrasse

Abstract Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse ( Ctenolabrus rupestris ) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 genome wide SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global F ST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence ( F ST >0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. 69 of these SNPs were significantly ( p <0.05) differentiated (mean F ST_173_loci = 0.065, F ST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

scholarly journals Fine scale population structure and extensive gene flow within an Eastern Nearctic snake complex (Pituophis melanoleucus)

2021 ◽  
Author(s):  
Zachary L Nikolakis ◽  
Richard Orton ◽  
Brian I Crother
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Genomic Structure ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Population Genomic ◽  
Isolation By Environment ◽  
Pituophis Melanoleucus ◽  
Lineage Divergence

Understanding the processes and mechanisms that promote lineage divergence is a central goal in evolutionary biology. For instance, studies investigating the spatial distribution of genomic variation often highlight biogeographic barriers underpinning geographic isolation, as well as patterns of isolation by environment and isolation by distance that can also lead to lineage divergence. However, the patterns and processes that shape genomic variation and drive lineage divergence may be taxa-specific, even across closely related taxa co-occurring within the same biogeographic region. Here, we use molecular data in the form of ultra-conserved elements (UCEs) to infer the evolutionary relationships and population genomic structure of the Eastern Pinesnake complex (Pituophis melanoleucus) – a polytypic wide-ranging species that occupies much of the Eastern Nearctic. In addition to inferring evolutionary relationships, population genomic structure, and gene flow, we also test relationships between genomic diversity and putative barriers to dispersal, environmental variation, and geographic distance. We present results that reveal shallow population genomic structure and ongoing gene flow, despite an extensive geographic range that transcends geographic features found to reduce gene flow among many taxa, including other squamate reptiles within the Eastern Nearctic. Further, our results indicate that the observed genomic diversity is spatially distributed as a pattern of isolation by distance and suggest that the current subspecific taxonomy do not adhere to independent lineages, but rather, show a significant amount of admixture across the entire P. melanoleucus range.

scholarly journals Enzyme promiscuity shapes evolutionary innovation and optimization

2018 ◽  
Author(s):  
Gabriela I. Guzmán ◽  
Troy E. Sandberg ◽  
Ryan A. LaCroix ◽  
Akos Nyerges ◽  
Henrietta Papp ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
High Efficiency ◽  
Scale Model ◽  
Turnover Rates ◽  
Enzyme Promiscuity ◽  
Evolutionary Innovation ◽  
K 12 ◽  
Enzyme Functions ◽  
Genome Scale

AbstractEvidence suggests that novel enzyme functions evolved from low-level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems-level adaptations are poorly understood. Furthermore, it remains untested whether knowledge of an organism’s promiscuous reaction set (‘underground metabolism’) can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates inE. coliK-12 MG1655. After as few as 20 generations, the evolving populations repeatedly acquired the capacity to grow on five predicted novel substrates–D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate–none of which could support growth in wild-type cells. Promiscuous enzyme activities played key roles in multiple phases of adaptation. Altered promiscuous activities not only established novel high-efficiency pathways, but also suppressed undesirable metabolic routes. Further, structural mutations shifted enzyme substrate turnover rates towards the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome-scale model simulations of metabolism with enzyme promiscuity. Computational approaches will be essential to synthesize the complex role of promiscuous activities in applied biotechnology and in models of evolutionary adaptation.

scholarly journals Altered lentiviral infection dynamics follow genetic rescue of the Florida panther

2019 ◽  
Vol 286 (1913) ◽  
pp. 20191689
Author(s):  
Jennifer L. Malmberg ◽  
Justin S. Lee ◽  
Roderick B. Gagne ◽  
Simona Kraberger ◽  
Sarah Kechejian ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Puma Concolor ◽  
Population Expansion ◽  
Genomic Diversity ◽  
Genetic Rescue ◽  
Effective Population ◽  
Florida Panther ◽  
Infection Dynamics ◽  
Lentiviral Infection ◽  
Detailed Assessment

Wildlife translocations are a commonly used strategy in endangered species recovery programmes. Although translocations require detailed assessment of risk, their impact on parasite distribution has not been thoroughly assessed. This is despite the observation that actions that alter host–parasite distributions can drive evolution or introduce new parasites to previously sequestered populations. Here, we use a contemporary approach to amplify viral sequences from archived biological samples to characterize a previously undocumented impact of the successful genetic rescue of the Florida panther ( Puma concolor coryi ). Our efforts reveal transmission of feline immunodeficiency virus (FIV) during translocation of pumas from Texas to Florida, resulting in extirpation of a historic Florida panther FIV subtype and expansion of a genetically stable subtype that is highly conserved in Texas and Florida. We used coalescent theory to estimate viral demography across time and show an exponential increase in the effective population size of FIV coincident with expansion of the panther population. Additionally, we show that FIV isolates from Texas are basal to isolates from Florida. Interestingly, FIV genomes recovered from Florida and Texas demonstrate exceptionally low interhost divergence. Low host genomic diversity and lack of additional introgressions may underlie the surprising lack of FIV evolution over 2 decades. We conclude that modern FIV in the Florida panther disseminated following genetic rescue and rapid population expansion, and that infectious disease risks should be carefully considered during conservation efforts involving translocations. Further, viral evolutionary dynamics may be significantly altered by ecological niche, host diversity and connectivity between host populations.

scholarly journals Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Eeva Jansson ◽  
Francois Besnier ◽  
Ketil Malde ◽  
Carl André ◽  
Geir Dahle ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
De Novo ◽  
Genomic Structure ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Full Genome Sequencing ◽  
Population Genomic ◽  
Cost Efficient ◽  
Ctenolabrus Rupestris ◽  
Goldsinny Wrasse

Abstract Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

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