scholarly journals Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1258
Author(s):  
Dan Yao ◽  
Lei Cheng ◽  
Lianming Du ◽  
Meijin Li ◽  
Maurycy Daroch ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Gc Content ◽  
Phylogenetic Groups ◽  
Coding Regions ◽  
Genome Wide ◽  
Evolutionary Advantage ◽  
Fast Adaptation ◽  
Almost All ◽  
Insight Into ◽  
Simple Sequence

Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in genomes of Leptolyngbya-like strains. The results disclosed diversified patterns of distribution, abundance, density, and diversity of SSRs and CSSRs in genomes, indicating that they may be subject to rapid evolutionary change. The numbers of SSRs and CSSRs were extremely unevenly distributed among genomes, ranging from 11,086 to 24,000 and from 580 to 1865, respectively. Dinucleotide SSRs were the most abundant category in 31 genomes, while the other 15 genomes followed the pattern: mono- > di- > trinucleotide SSRs. The patterns related to SSRs and CSSRs showed differences among phylogenetic groups. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly positively correlated with genome size (p < 0.01) and negatively correlated with GC content (p < 0.05). Moreover, the motif (A/C)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 39 genomes. This study provides the first insight into SSRs and CSSRs in genomes of Leptolyngbya-like strains and will be useful to understanding their distribution, predicting their function, and tracking their evolution. Additionally, the identified SSRs may provide an evolutionary advantage of fast adaptation to environmental changes and may play an important role in the cosmopolitan distribution of Leptolyngbya strains to globally diverse niches.

scholarly journals Genome-wide investigation and analysis of microsatellites and compound microsatellites in Leptolyngbya species, Cyanobacteria

2021 ◽  
Author(s):  
Dan Yao ◽  
Lian-Ming Du ◽  
Meijin Li ◽  
Maurycy Daroch ◽  
Jie Tang
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeats ◽  
Gc Content ◽  
The Other ◽  
Closely Related Species ◽  
Coding Regions ◽  
Genome Wide ◽  
Almost All ◽  
Insight Into ◽  
Simple Sequence

Abstract Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in 36 genomes of Leptolyngbya. The results disclosed diversified patterns of distribution, abundance, density and diversity of SSRs and CSSRs in Leptolyngbya genomes. The numbers of SSRs and CSSRs were extremely uneven distributed among genomes, ranging from 11,086 to 27,292 and from 286 to 1,102, respectively. Mononucleotide SSRs were the most abundant category in 14 genomes, while the other 22 genomes followed the pattern: di- > mono- > trinucleotide SSRs. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly correlated with genome size (P < 0.01) and but not closely correlated with GC content (P > 0.05). Moreover, the motif (A/T)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 33 genomes. This study provides the first insight into SSRs and CSSRs in Leptolyngbya genomes and will be useful to contribute to future use as molecular markers in closely-related species.

scholarly journals Global Phylogeographic and Admixture Patterns in Grey Wolves and Genetic Legacy of An Ancient Siberian Lineage

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Małgorzata Pilot ◽  
Andre E. Moura ◽  
Innokentiy M. Okhlopkov ◽  
Nikolay V. Mamaev ◽  
Abdulaziz N. Alagaili ◽  
...  
Keyword(s):  
Environmental Change ◽  
Environmental Changes ◽  
Phylogeographic Structure ◽  
Evolutionary Relationships ◽  
Clustering Methods ◽  
Species Response ◽  
Genome Wide ◽  
Response To Environmental Change ◽  
Ambiguous Position ◽  
Insight Into

AbstractThe evolutionary relationships between extinct and extant lineages provide important insight into species’ response to environmental change. The grey wolf is among the few Holarctic large carnivores that survived the Late Pleistocene megafaunal extinctions, responding to that period’s profound environmental changes with loss of distinct lineages and phylogeographic shifts, and undergoing domestication. We reconstructed global genome-wide phylogeographic patterns in modern wolves, including previously underrepresented Siberian wolves, and assessed their evolutionary relationships with a previously genotyped wolf from Taimyr, Siberia, dated at 35 Kya. The inferred phylogeographic structure was affected by admixture with dogs, coyotes and golden jackals, stressing the importance of accounting for this process in phylogeographic studies. The Taimyr lineage was distinct from modern Siberian wolves and constituted a sister lineage of modern Eurasian wolves and domestic dogs, with an ambiguous position relative to North American wolves. We detected gene flow from the Taimyr lineage to Arctic dog breeds, but population clustering methods indicated closer similarity of the Taimyr wolf to modern wolves than dogs, implying complex post-divergence relationships among these lineages. Our study shows that introgression from ecologically diverse con-specific and con-generic populations was common in wolves’ evolutionary history, and could have facilitated their adaptation to environmental change.

scholarly journals The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens”

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Geng Zou ◽  
Bernardo Bello-Orti ◽  
Virginia Aragon ◽  
Alexander W. Tucker ◽  
Rui Luo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Simple Sequence Repeats ◽  
Potential Role ◽  
Gc Content ◽  
Nucleotide Metabolism ◽  
Coding Regions ◽  
Purine Nucleotide Metabolism ◽  
Go Terms ◽  
Simple Sequence

Abstract Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like “vampire pathogens” (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3 and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation.

scholarly journals Genome-wide characterization and analysis of microsatellite sequences in camelid species

2019 ◽  
Vol 65 (2) ◽  
pp. 359-373
Author(s):  
Manee M. Manee ◽  
Abdulmalek T. Algarni ◽  
Sultan N. Alharbi ◽  
Badr M. Al-Shomrani ◽  
Mohanad A. Ibrahim ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gc Content ◽  
Paternity Testing ◽  
Breeding Programs ◽  
Coding Regions ◽  
Systemic Analysis ◽  
Genome Wide ◽  
Vicugna Pacos ◽  
Arabian Camel ◽  
Genome Assemblies

AbstractMicrosatellites or simple sequence repeats (SSRs) are among the genetic markers most widely utilized in research. This includes applications in numerous fields such as genetic conservation, paternity testing, and molecular breeding. Though ordered draft genome assemblies of camels have been announced, including for the Arabian camel, systemic analysis of camel SSRs is still limited. The identification and development of informative and robust molecular SSR markers are essential for marker assisted breeding programs and paternity testing. Here we searched and compared perfect SSRs with 1–6 bp nucleotide motifs to characterize microsatellites for draft genome sequences of the Camelidae. We analyzed and compared the occurrence, relative abundance, relative density, and guanine-cytosine (GC) content in four taxonomically different camelid species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. A total of 546762, 544494, 547974, and 437815 SSRs were mined, respectively. Mononucleotide SSRs were the most frequent in the four genomes, followed in descending order by di-, tetra-, tri-, penta-, and hexanucleotide SSRs. GC content was highest in dinucleotide SSRs and lowest in mononucleotide SSRs. Our results provide further evidence that SSRs are more abundant in noncoding regions than in coding regions. Similar distributions of microsatellites were found in all four species, which indicates that the pattern of microsatellites is conserved in family Camelidae.

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and comparative genome analysis for elucidating the role of CAZymes in cold adaptation

2020 ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Complete Genome ◽  
Cold Adaptation ◽  
Environmental Changes ◽  
Gc Content ◽  
Extreme Environment ◽  
Cold Environments ◽  
Carbohydrate Degradation ◽  
Survival Mechanisms ◽  
Insight Into

Abstract Background: The Arthrobacter group is a known isolate from cold areas, the species of which are highly likely to play diverse roles in low temperatures. However, their role and survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of sixteen strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that adapt and survive life in the cold environment.Results: The genome of Arthrobacter sp. PAMC25564 comprised 4,170,970 bp with 66.74 % GC content, a predicted genomic island, and 3,829 genes. This study provides an insight into the redundancy of CAZymes for potential cold adaptation and suggests that the isolate has glycogen, trehalose, and maltodextrin pathways associated to CAZyme genes. This strain can utilize polysaccharide or carbohydrate degradation as a source of energy. Moreover, this study provides a foundation on which to understand how the Arthrobacter strain produces energy in an extreme environment, and the genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how bacteria adapt and survive in such environments.Conclusions: We characterized the Arthrobacter sp. PAMC25564 complete genome and comparative analysis, provided an insight into the redundancy of CAZymes for potential cold adaptation. This provide a foundation to understand how Arthrobacter strain produces energy in an extreme environment, there are reports on the use of CAZymes in cold environments. Therefore, we suppose that this process has allowed Arthrobacter species to establish a symbiotic relationship with other bacteria in cold environments or live independently thanks to their capacity for adapting to environmental changes.

scholarly journals Evolutionary analysis implicates RNA polymerase II pausing and chromatin structure in nematode piRNA biogenesis

2018 ◽  
Author(s):  
T. Beltran ◽  
C. Barroso ◽  
T.Y. Birkle ◽  
L. Stevens ◽  
H. T. Schwartz ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Core Promoter ◽  
Evolutionary Analysis ◽  
C Elegans ◽  
Comparative Epigenomics ◽  
Genome Wide ◽  
Almost All ◽  
Precursor Transcript ◽  
Insight Into

AbstractPiwi-interacting RNAs (piRNAs) control transposable elements widely across metazoans but have rapidly evolving biogenesis pathways. In Caenorhabditis elegans, almost all piRNA loci are found within two 3Mb clusters on Chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce a ∼28 nt precursor transcript. Here, we use comparative epigenomics across nematodes to gain insight into piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA biogenesis. We describe two alternative modes of piRNA organisation in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, whilst in other species, typified by Pristionchus pacificus, piRNAs are distributed genome-wide within introns of actively transcribed genes. In both groups, piRNA production depends on downstream sequence signals associated with RNA polymerase II pausing, which synergise with the chromatin environment to control piRNA precursor transcription.

scholarly journals Genetic structure of apple accessions maintained ex situ in Bosnia and Herzegovina examined by microsatellite markers

Genetika ◽  
2013 ◽  
Vol 45 (2) ◽  
pp. 467-478 ◽  
Author(s):  
Fuad Gasi ◽  
Maja Zulj-Mihaljevic ◽  
Silvio Simon ◽  
Jasmin Grahic ◽  
Naris Pojskic ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Ottoman Empire ◽  
Ex Situ ◽  
Breeding Programs ◽  
Molecular Variance ◽  
International Reference ◽  
Apple Cultivars ◽  
Almost All ◽  
Insight Into ◽  
Simple Sequence

In order to identify possible mislabeling of the apple accession maintained ex situ in Srebrenik and to gain insight into the genetic structure of the conserved germplasm, 14 accessions from the collection were genotyped using 10 SSR (Simple Sequence Repeats) markers. Obtained SSR profiles were then added to an existing database constructed for previously characterized 24 traditional and 13 international, reference apple cultivars maintained at the same collection. Bayesian analysis implemented in the STRUCTURE program grouped 42 out of 51 analyzed apple accessions (38 traditional and 13 international) into three RPPs (reconstructed panmictic populations) with probability of membership qI higher than 75%. Almost all international, reference cultivars grouped in RPP3, whereas traditional B&H cultivars from the Srebrenik collection grouped in all three RPPs. Large and significant differentiations between all three individual RPPs were detected through the analyses of molecular variance and confirmed with FCA (factorial correspondence analyses). NJ cluster analysis, based on the Bruvo genetic distance, revealed that out of 38 traditional B&H apple cultivars, analyzed in the study, ?Ljepocvjetka?, ?Bobovec? and ?Bobovec J? grouped closest to the international reference cultivars. Available date indicates that unlike a large number of B&H apple cultivars which were introduced during the reign of the Ottoman Empire, ?Ljepocvjetka? and ?Bobovec? were probably introduced at a later date. Cluster analyses also enabled the detection of one synonym and three homonyms within the collection. In four cases, previously conducted identification based on phenotypic analyses was confirmed by genetic analyses. Results of the structure analyses indicate a heterogeneous genetic structure of the analyzed accessions. This characteristic of the B&H apple germplasm could be useful for future breeding programs.

scholarly journals Genome-wide Identification and Expression Pattern Analysis of BRI1-EMS–suppressor Transcription Factors in Tomato under Abiotic Stresses

2018 ◽  
Vol 143 (1) ◽  
pp. 84-90 ◽  
Author(s):  
Yingmei Gao ◽  
Jingkang Hu ◽  
Tingting Zhao ◽  
Xiangyang Xu ◽  
Jingbin Jiang ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Functional Identification ◽  
Tomato Plants ◽  
Protein Motifs ◽  
Genome Wide ◽  
Polymerase Chain ◽  
Regulated Gene Expression ◽  
Insight Into

BRI1-EMS-suppressor 1 (BES1) is a transcription factor (TF) that functions as a master regulator of brassinosteroid (BR)-regulated gene expression. Here, we provide a complete overview of Solanum lycopersicum BES1 (SLB) genes, including phylogeny, gene structure, protein motifs, chromosome locations and expression characteristics. Through bioinformatic analysis, we compared the sequences of SLB genes, arabidopsis (Arabidopsis thaliana) genes, and chinese cabbage (Brassica pekinensis) genes. All of the gene sequences were divided into three groups by cluster analysis. SLB genes were mapped to the eight tomato (S. lycopersicum) chromosomes. Bioinformatic analysis showed that SLB genes shares similarities with the proteins from other plants, though different species exhibit specific features. The expression patterns of SLB genes in various tissues and under different abiotic conditions were analyzed by quantitative reverse transcription polymerase chain reaction. SLB genes were found to be induced by multiple stresses, particularly salt stress, indicating that SLB genes may have important roles in the response to unfavorable environmental changes. This study provides insight into the evolution of SLB genes and may aid in the further functional identification of BES1 proteins and the response of tomato plants to different stresses.

The Genetics of Human Behavior

2018 ◽  
Author(s):  
Colter Mitchell
Keyword(s):  
Candidate Genes ◽  
Human Behavior ◽  
Social Research ◽  
Genetic Research ◽  
Whole Genome ◽  
High Expectations ◽  
Twin Research ◽  
Genome Wide ◽  
Almost All ◽  
Insight Into

This chapter examines the recent massive expansion of genetic research into human behavior. Based on decades of twin research, there were high expectations of strong genetic effects for almost all behavior. Further work on candidate genes from animal research proved initially exciting. Although that research continues, it now currently receives much less attention, in contrast to whole-genome examinations. This chapter provides insight into the whole-genome era of behavioral research and the extent to which it may or may not be a profitable endeavor. Sociologists are generally unaware of this body of research, but it will likely continue to grow. The methods, strengths, and limitations of genome-wide work are discussed. A discussion of the future of this area and the extent to which this provides any leverage for social research of human behavior concludes the chapter.

scholarly journals The open targets post-GWAS analysis pipeline

2020 ◽  
Vol 36 (9) ◽  
pp. 2936-2937 ◽  
Author(s):  
Gareth Peat ◽  
William Jones ◽  
Michael Nuhn ◽  
José Carlos Marugán ◽  
William Newell ◽  
...  
Keyword(s):  
Drug Targets ◽  
Gene Expression Regulation ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Protein Coding ◽  
Data Resource ◽  
Coding Regions ◽  
Genome Wide ◽  
Causal Genes ◽  
Interactive Data

Abstract Motivation Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data. Results We present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource. Availability and implementation The analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io.

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