DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai

Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan’s Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.

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Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

BioTech ◽

10.3390/biotech10040023 ◽

2021 ◽

Vol 10 (4) ◽

pp. 23

Author(s):

Oxana Khapilina ◽

Ainur Turzhanova ◽

Alevtina Danilova ◽

Asem Tumenbayeva ◽

Vladislav Shevtsov ◽

...

Keyword(s):

Genetic Diversity ◽

Endemic Species ◽

Biological Diversity ◽

Natural Populations ◽

Subsequent Development ◽

Dna Profiling ◽

Primer Binding Site ◽

Anthropogenic Factors ◽

Habitat Specificity ◽

Interspersed Repeats

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

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AUTOCHTHONOUS BREEDS OF DOMESTIC ANIMALS AND CONSERVATION MEASURES

AGROFOR ◽

10.7251/agreng2101127m ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Zoran MALETIC

Keyword(s):

Genetic Diversity ◽

Biological Diversity ◽

Domestic Animals ◽

Conservation Strategy ◽

Ex Situ ◽

Animal Genetic Resources ◽

Diversity Preservation ◽

The Republic ◽

International Conventions

Recently, highly productive breeds of various species of domestic animals have been used in livestock production, which has resulted in the destruction of indigenous breeds of domestic animals around the world, even in our area. This is the first reason why indigenous races and strains have been endangered. Another reason is that domestic, indigenous breeds were crossed with specialized breeds, which were imported, and in that way their genetic diversity was negatively affected. Resistance is lost, adaptation to the conditions in which they were created, the ability to survive in nature. Indigenous breeds of different species of domestic animals, which are recognized in the Republic of Srpska (BiH) are gatačko cattle and buša (cattle), Vlašić pramenka, Podveleška pramenka, Kupres pramenka (sheep), domestic Balkan horned goat (goats), Bosnian mountain horse (horses), mangulica (pigs) and pogrmuša hen or živičarka hen (poultry). By acceding to international conventions, BiH /Republic of Srpska has committed itself to establishing a system of measures that will enable the conservation of biological diversity and the protection of indigenous and endangered breeds of domestic animals. The choice of a strategy for the conservation of diversity, the establishment of an adequate conservation scheme, and the implementation of a conservation strategy are some of the key elements of any process for the conservation of genetic diversity. Preservation of autochthonous and protected breeds of domestic animals is possible through preservation in the original environment (in situ) and preservation outside the original environment (ex situ). There is a possibility of combining these models of conservation of animal genetic resources.

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High Prevalence and Genetic Diversity of Large phiCD211 (phiCDIF1296T)-Like Prophages inClostridioides difficile

Applied and Environmental Microbiology ◽

10.1128/aem.02164-17 ◽

2017 ◽

Vol 84 (3) ◽

Cited By ~ 6

Author(s):

Julian R. Garneau ◽

Ognjen Sekulovic ◽

Bruno Dupuy ◽

Olga Soutourina ◽

Marc Monot ◽

...

Keyword(s):

Genetic Diversity ◽

Mobile Genetic Elements ◽

Large Chromosome ◽

Comparative Genomic ◽

Content Type ◽

Genetic Elements ◽

Clostridioides Difficile ◽

A Genome ◽

Depth Analysis ◽

High Prevalence

ABSTRACTClostridioides difficile(formerlyClostridium difficile) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified inC. difficileso far, with a genome of 131 kbp. It shares morphological and genomic similarity with other large siphophages, like phage 949, infectingLactococcus lactis, and phage c-st, infectingClostridium botulinum. A PhageTerm analysis indicated the presence of 378-bp direct terminal repeats at the phiCD211 genome termini. Among striking features of phiCD211, the presence of several transposase and integrase genes suggests past recombination events with other mobile genetic elements. Several gene products potentially influence the bacterial lifestyle and fitness, including a putative AcrB/AcrD/AcrF multidrug resistance protein, an EzrA septation ring formation regulator, and a spore protease. We also identified a CRISPR locus and acas3gene. We screened 2,584C. difficilegenomes available and detected 149 prophages sharing ≥80% nucleotide identity with phiCD211 (5% prevalence). Overall, phiCD211-like phages were detected inC. difficilestrains corresponding to 21 different multilocus sequence type groups, showing their high prevalence. Comparative genomic analyses revealed the existence of several clusters of highly similar phiCD211-like phages. Of note, large chromosome inversions were observed in some members, as well as multiple gene insertions and module exchanges. This highlights the great plasticity and gene coding potential of the phiCD211/phiCDIF1296T genome. Our analyses also suggest active evolution involving recombination with other mobile genetic elements.IMPORTANCEClostridioides difficileis a clinically important pathogen representing a serious threat to human health. Our hypothesis is that genetic differences between strains caused by the presence of integrated prophages could explain the apparent differences observed in the virulence of differentC. difficilestrains. In this study, we provide a full characterization of phiCD211, also known as phiCDIF1296T, the largest phage known to infectC. difficileso far. Screening 2,584C. difficilegenomes revealed the presence of highly similar phiCD211-like phages in 5% of the strains analyzed, showing their high prevalence. Multiple-genome comparisons suggest that evolution of the phiCD211-like phage community is dynamic, and some members have acquired genes that could influence bacterial biology and fitness. Our study further supports the relevance of studying phages inC. difficileto better understand the epidemiology of this clinically important human pathogen.

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How important is CRISPR-Cas for protecting natural populations of bacteria against infections by mobile genetic elements?

10.1101/2020.02.05.935965 ◽

2020 ◽

Cited By ~ 1

Author(s):

Edze Westra ◽

Bruce Levin

Keyword(s):

Computer Simulation ◽

Immune System ◽

Natural Populations ◽

Adaptive Immune System ◽

Simulation Models ◽

Mobile Genetic Elements ◽

Genetic Elements ◽

Adaptive Immune ◽

Computer Simulation Models

AbstractArticles on CRISPR commonly open with some variant of the phrase ‘these short-palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements’. There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes, and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea and the mobile genetic elements that infect them.SignificanceThere is no question about the importance and utility of CRISPR-Cas for editing and modifying genomes. On the other hand, the mechanisms responsible for the evolution and maintenance of these systems and the magnitude of their importance to the ecology and evolution of bacteria, archaea and their infectious DNAs, are not at all clear. With the aid of heuristic mathematical – computer simulation models and reviews of the existing literature, we raise questions that have to be answered to elucidate the contribution of selection – mediated by phage and plasmids – to the evolution and maintenance of this adaptive immune system and its consequences for the ecology and evolution of prokaryotes and their viruses and plasmids.

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Cyanogenic polymorphism as an indicator of genetic diversity in the rarespecies Eucalyptus yarraensis (Myrtaceae)

Functional Plant Biology ◽

10.1071/fp02027 ◽

2002 ◽

Vol 29 (12) ◽

pp. 1445 ◽

Cited By ~ 19

Author(s):

Jason Q. D. Goodger ◽

Ian E. Woodrow

Keyword(s):

Genetic Diversity ◽

Effective Means ◽

Natural Populations ◽

Population Variation ◽

Conservation Strategy ◽

Narrow Sense Heritability ◽

Specialist Herbivores ◽

Cyanogenic Plants ◽

Physical And Chemical ◽

First Time

The rare Australian tree Eucalyptus yarraensis Maiden & Cambage is cyanogenic, a quantitative trait potentially indicative of genetic diversity. Cyanogenic plants are capable of releasing cyanide from endogenous cyanide-containing compounds. Cyanide is toxic or deterrent to generalist or non-adapted specialist herbivores. Consequently, cyanogenic plants are afforded an effective means of chemical defense. In this paper we characterize quantitative variation in cyanogenic capability, known as cyanogenic polymorphism, in E. yarraensis for the first time. We show that the cyanogenic glucoside prunasin (R-mandelonitrile-β-D-glucoside) is the only cyanogenic compound in E. yarraensis foliage. We also show that two natural populations of E. yarraensis display extensive intra- and inter-population variation in foliar prunasin concentration. The high prunasin concentrations reported in this paper represent the highest yet recorded for mature eucalypt leaves. The cyanogenic variation could not be attributed to measured physical and chemical parameters, supporting the hypothesis that the variation is genetically based. A preliminary progeny trial also supports this hypothesis, with narrow sense heritability estimated at 1.17 from three half-sibling families. The variation in cyanogenic capability may be a useful tool in the development of a conservation strategy for the species.

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Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

Canadian Journal of Plant Science ◽

10.4141/cjps07015 ◽

2008 ◽

Vol 88 (1) ◽

pp. 179-186 ◽

Cited By ~ 2

Author(s):

Chu-Chuan Fan ◽

Nicola Pecchioni ◽

Long-Qing Chen

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Genetic Distance ◽

Gene Diversity ◽

Genetic Relationships ◽

Natural Populations ◽

Population Level ◽

Conservation Strategy ◽

Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

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It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1915966117 ◽

2020 ◽

Vol 117 (45) ◽

pp. 27777-27785

Author(s):

Edze R. Westra ◽

Bruce R. Levin

Keyword(s):

A Priori ◽

Natural Populations ◽

Adaptive Immune System ◽

Simulation Models ◽

Mobile Genetic Elements ◽

Genetic Elements ◽

Adaptive Immune ◽

Different Types ◽

Computer Simulation Models

Articles on CRISPR commonly open with some variant of the phrase “these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements.” There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical–computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.

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Genetic diversity among natural populations of Agathis borneensis (Araucariaceae), a tropical rain forest conifer from Brunei Darussalam, Borneo, Southeast Asia

Canadian Journal of Botany ◽

10.1139/b92-242 ◽

1992 ◽

Vol 70 (10) ◽

pp. 1945-1949 ◽

Cited By ~ 9

Author(s):

Keiko Kitamura ◽

Mohamad Yusof Bin Abdul Rahman

Keyword(s):

Genetic Diversity ◽

Southeast Asia ◽

Rain Forest ◽

Tropical Rain Forest ◽

Natural Populations ◽

Conservation Strategy ◽

Restricted Gene Flow ◽

Isozyme Electrophoresis ◽

Brunei Darussalam ◽

Population Component

Agathis is a genus of tropical conifers that occurs mainly in Southeast Asia. Because of its production of good softwood, many stands of Agathis have been harvested. We provide an estimate of genetic variation within and among populations of Agathis borneensis in Brunei Darussalam, Southeast Asia. Five populations were investigated using isozyme electrophoresis. We investigated a total of 17 putative loci, five of which were polymorphic. Estimated total heterozygosity was 0.122. Heterozygosity within populations was 0.106. The population structure did not deviate significantly from Hardy–Weinberg expectations. Nei's coefficient of gene differentiation indicated that the among-population component of genetic diversity represents 14% of the total population component. The low level of genetic diversity and the large diversity among populations were the opposite of that for conifers in the temperate zone, because of the small size of each population. The large diversity among populations indicated the restricted gene flow resulting from the asynchronous flowering of this species. The genetic distance indicated that A. borneensis in Brunei could be classified in two groups, with one isolated population considerably different from the others both genetically and ecologically. The conservation strategy is discussed from the viewpoint of genetic resources. Key words: Agathis borneensis, Araucariaceae, Brunei Darussalam, genetic diversity, isozyme, tropical rain forest.

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Discovering complete quasispecies in bacterial genomes

10.1101/119743 ◽

2017 ◽

Author(s):

Frederic Bertels ◽

Chaitanya S. Gokhale ◽

Arne Traulsen

Keyword(s):

Natural Populations ◽

Mobile Genetic Elements ◽

Small Range ◽

Mutational Load ◽

Bacterial Strains ◽

Bacterial Genomes ◽

Genetic Elements ◽

Quasispecies Model ◽

A Genome ◽

Almost All

ABSTRACTMobile genetic elements can be found in almost all genomes. Possibly the most common non-autonomous mobile genetic elements in bacteria are REPINs that can occur hundreds of times within a genome. The sum of all REPINs within a genome are an evolving populations because they replicate and mutate. We know the exact composition of this population and the sequence of each member of a REPIN population, in contrast to most other biological populations. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to ten different REPIN populations from ten different bacterial strains and estimate duplication rates. We find that our estimated duplication rates range from about 5 × 10−9to 37 × 10−9duplications per generation per genome. The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. The REPIN populations we investigated also possess features typical of other natural populations. One population shows hallmarks of a population that is going extinct, another population seems to be growing in size and we also see an example of competition between two REPIN populations.

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Clonal Reproduction and Low Genetic Diversity in Northern Australian Santalum lanceolatum (Santalaceae) Populations Highlights the Need for Genetic Rescue of This Commercially Significant Species

Forests ◽

10.3390/f12060741 ◽

2021 ◽

Vol 12 (6) ◽

pp. 741

Author(s):

Aaron Brunton ◽

David J. Lee ◽

Gabriel Conroy ◽

Steven Ogbourne

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Life History Strategy ◽

Conservation Strategy ◽

Regional Differentiation ◽

Genetic Rescue ◽

Environmental Pressures ◽

Northern Margin ◽

Low Genetic Diversity ◽

Wild Harvesting

Genetic diversity and the extent of clonality in a plant species can significantly influence its reproductive success. Whilst clonality can be an effective life-history strategy, in harsh environments it can lead to low levels of diversity and sexual reproductive failure. Santalum lanceolatum (Santalaceae) is a hemi-parasitic shrub endemic to the monsoonal dry tropics of northern Australia, which was harvested for its oil-rich heartwood from natural populations in Cape York, Australia. Despite wild harvesting ending over 70 years ago, populations in the region are currently declining. The aims of this study were to examine genetic variation, population genetic structure, inbreeding and clonality of six S. lanceolatum populations from this northern margin of the species range. Analyses of twelve microsatellite markers showed S. lanceolatum had low genetic diversity (AR = 2.776, HE = 0.409), evidence of regional differentiation (FST = 0.307–0.424) and negligible inbreeding levels (F = −0.052). Clonality investigations revealed 135 genets among 200 samples, suggesting that the clonal structure of S. lanceolatum may be limiting the potential for sexual reproduction and natural recruitment. We recommend a conservation strategy involving genetic rescue to prevent the further decline and potential local extinction from a variety of environmental pressures and human activities.

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