scholarly journals Comparative genomics analysis reveals high levels of differential DNA transposition among primates

2019 ◽  
Author(s):  
Wanxiangfu Tang ◽  
Ping Liang
Keyword(s):  
Comparative Genomics ◽  
Gene Function ◽  
Large Scale ◽  
Primate Evolution ◽  
Mobile Elements ◽  
Activity Level ◽  
Genome Sequences ◽  
Dna Transposition ◽  
Dominant Class ◽  
Macaque Genome

ABSTRACTMobile elements generated via DNA transposition constitute ∼50% of the primate genomes. As a result of past and ongoing activity, DNA transposition is responsible for generating inter- and intra-species genomic variations, and it plays important roles in shaping genome evolution and impacting gene function. While limited analysis of mobile elements has been performed in many primate genomes, a large-scale comparative genomic analysis examining the impact of DNA transposition on primate evolution is still missing.Using a bioinformatics comparative genomics approach, we performed analysis of species-specific mobile elements (SS-MEs) in eight primate genomes, which include human, chimpanzee, gorilla, orangutan, green monkey, crab-eating macaque, rhesus monkey, and baboon. These species have good representations for the top two primate families, Hominidae (great apes) and the Cercopithecidae (old world monkeys), for which draft genome sequences are available.Our analysis identified a total of 230,855 SS-MEs from the eight primate genomes, which collectively contribute to ∼82 Mbp genome sequences, ranging from 14 to 25 Mbp for individual genomes. Several new interesting observations were made based on these SS-MEs. First, the DNA transposition activity level reflected by the numbers of SS-MEs was shown to be drastically different across species with the highest (baboon genome) being more than 30 times higher than the lowest (crab-eating macaque genome). Second, the compositions of SS-MEs, as well as the top active ME subfamilies, also differ significantly across genomes. By the copy numbers of SS-MEs divided into major ME classes, SINE represents the dominant class in all genomes, but more so in the Cercopithecidae genomes than in the Hominidae genomes in general with the orangutan genome being the outliner of this trend by having LINE as the dominant class. While AluY represents the major SINE groups in the Hominidae genomes, AluYRa1 is the dominant SINE in the Cercopithecidae genomes. For LINEs, each Hominidae genome seems to have a unique most active L1 subfamily, but all Cercopithecidae genomes have L1RS2 as the most active LINEs. While genomes with a high number of SS-MEs all have one or more very active ME subfamilies, the crab-eating macaque genome, being the one with an extremely low level of DNA transposition, has no single ME class being very active, suggesting the existence of a genome-wide mechanism suppressing DNA transposition. Third, DNA transposons, despite being considered dead in primate genomes, were in fact shown to have a certain level of activity in all genomes examined with a total of ∼2,400 entries as SS-MEs. Among these SS-MEs, at least 23% locate to genic regions, including exons and regulatory elements, presenting significant potentials for their impact on gene function. Very interestingly, our data demonstrate that, among the eight primates included in this study, the human genome is shown to be the most actively evolving genome via DNA transposition as having the highest most recent activity of many ME subfamilies, notably the AluYa5/Yb8/Yb9, L1HS, and SVA-D subfamilies.Representing the first of its kind, our large-scale comparative genomics study has shown that mobile elements evolved quite differently among different groups and species of primates, indicating that differential DNA transposition has served as an important mechanism in primate evolution.

scholarly journals Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families

2019 ◽  
Vol 11 (11) ◽  
pp. 3309-3325 ◽  
Author(s):  
Wanxiangfu Tang ◽  
Ping Liang
Keyword(s):  
Comparative Genomics ◽  
Gene Function ◽  
Mobile Elements ◽  
Protein Coding ◽  
Dominant Class ◽  
Highly Active ◽  
Macaque Genome ◽  
A Genome ◽  
Orangutan Genome ◽  
Species Specific

Abstract Mobile elements (MEs), making ∼50% of primate genomes, are known to be responsible for generating inter- and intra-species genomic variations and play important roles in genome evolution and gene function. Using a bioinformatics comparative genomics approach, we performed analyses of species-specific MEs (SS-MEs) in eight primate genomes from the families of Hominidae and Cercopithecidae, focusing on retrotransposons. We identified a total of 230,855 SS-MEs, with which we performed normalization based on evolutionary distances, and we also analyzed the most recent SS-MEs in these genomes. Comparative analysis of SS-MEs reveals striking differences in ME transposition among these primate genomes. Interesting highlights of our results include: 1) the baboon genome has the highest number of SS-MEs with a strong bias for SINEs, while the crab-eating macaque genome has a sustained extremely low transposition for all ME classes, suggesting the existence of a genome-wide mechanism suppressing ME transposition; 2) while SS-SINEs represent the dominant class in general, the orangutan genome stands out by having SS-LINEs as the dominant class; 3) the human genome stands out among the eight genomes by having the largest number of recent highly active ME subfamilies, suggesting a greater impact of ME transposition on its recent evolution; and 4) at least 33% of the SS-MEs locate to genic regions, including protein coding regions, presenting significant potentials for impacting gene function. Our study, as the first of its kind, demonstrates that mobile elements evolve quite differently among these primates, suggesting differential ME transposition as an important mechanism in primate evolution.

scholarly journals Contribution of mobile elements to the uniqueness of human genome with more than 15,000 human-specific insertions

2016 ◽  
Author(s):  
Wanxiangfu Tang ◽  
Seyoung Mun ◽  
Adiya Joshi ◽  
Kyundong Han ◽  
Ping Liang
Keyword(s):  
Genetic Diversity ◽  
Human Genome ◽  
Genome Evolution ◽  
Gene Function ◽  
Mobile Elements ◽  
Dna Transposition ◽  
Protein Coding ◽  
Human Genome Evolution ◽  
The Impact ◽  
Human Specific

AbstractMobile elements (MEs) collectively constituted to at least 51% of the human genome. Due to their past incremental accumulation and ongoing DNA transposition of members from certain subfamilies, MEs serve as a significant source for both inter- and intra-species genetic diversity during primate and human evolution. Since MEs can exert direct impact on gene function via a plethora of mechanism, it is believed that the ME-derived genetic diversity has contributed to the phenotypic differences between human and non-human primates, as well as among human populations and individuals. To define the specific contribution of MEs in making Human sapiens as a biologically unique species, we aim to compile a complete list of MEs that are only uniquely present in the human genome, i.e., human-specific MEs (HS-MEs).By making use of the most recent reference genome sequences for human and many other primates and a unbiased more robust and integrative multi-way comparative genomic approach, we identified a total of 15,463 HS-MEs. This list of HS-MEs represents a 120% increase from prior studies with over 8,000 being newly identified as HS-MEs. Collectively, these ~15,000 HS-MEs have contributed to a total of 15 million base pair (Mbp) sequence increase through insertion, generation of target site duplications, and transductions, as well as a 0.5 Mbp sequence loss via insertion- mediated deletions, leading to a net total of 14.5 Mbp genome size increase. Other new observations made with these HS-MEs include: 1) identification of several additional ME subfamilies with significant transposition activities not visible with prior smaller datasets (e.g. L1HS, L1PA2, and HERV-K); 2) A clear similarity of the retrotransposition mechanism among L1, Alus, and SVAs that is distinct from HERVs based on the pre- integration site sequence motifs; 3) Y-chromosome as a strikingly hot target for HS-MEs, particularly for LTRs, which showed an insertion rate 15 times higher than the genome average; 4) among the ME types, SVAs seem to show a very strong bias in inserting into existing SVAs. Among the HS-MEs, more than 8,000 elements were integrated into the vicinity of ~4900 unique genes, in regions including CDS, untranslated exon regions, promoters, and introns of protein coding genes, as well as promoters and exons of non- coding RNAs. In seven cases, MEs participate in protein coding. Furthermore, 1,213 HS-MEs contributed to a total of 3,124 experimentally identified binding sites for 146 of the 161 transcriptional factors in association with 622 genes. All these data suggest that these HS-MEs, despite being very young, already showed sufficient sign for their participation in gene function via regulation of transcription, splicing, and protein coding, with more potential for future participation.In conclusion, our results demonstrate that the amount of MEs uniquely occurred in the human genome is much higher than previously known, and we predict that the same is true regarding their impact on human genome evolution and function. The comprehensive list of HS-MEs provides an important reference resource for studying the impact of DNA transposition in human genome evolution and gene function.

scholarly journals Leisure Time Sports Activities and Life Satisfaction: Deeper Insights Based on a Representative Survey from Germany

2020 ◽  
Author(s):  
Michael Mutz ◽  
Anne K. Reimers ◽  
Yolanda Demetriou
Keyword(s):  
Life Satisfaction ◽  
Large Scale ◽  
Leisure Time ◽  
Organizational Context ◽  
Experimental Studies ◽  
Well Being ◽  
Activity Level ◽  
Leisure Satisfaction ◽  
General Life Satisfaction ◽  
Sports Activities

Abstract Observational and experimental studies show that leisure time sporting activity (LTSA) is associated with higher well-being. However, scholars often seem to assume that 1) LTSA fosters “general” life satisfaction, thereby ignoring effects on domain satisfaction; 2) the effect of LTSA on well-being is linear and independent of a person’s general activity level; 3) the amount of LTSA is more important than the repertoire of LTSA, i.e. the number of different activities; 4) all kinds of LTSA are equal in their effects, irrespective of spatial and organisational context conditions. Using data from the German SALLSA-Study (“Sport, Active Lifestyle and Life Satisfaction”), a large-scale CAWI-Survey (N = 1008) representing the population ≥ 14 years, the paper takes a closer look on these assumptions. Findings demonstrate that LTSA is associated with general life satisfaction and domain-specific satisfaction (concerning relationships, appearance, leisure, work and health), but that the relationship is most pronounced for leisure satisfaction. Associations of sport with life satisfaction, leisure satisfaction and subjective health are non-linear, approaching an injection point from which on additional LTSA is no longer beneficial. Moreover, findings lend support to the notion that diversity in LTSA matters, as individuals with higher variation in sports activities are more satisfied. Finally, results with regard to spatial and organizational context suggest that outdoor sports and club-organized sports have additional benefits.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

scholarly journals Meeting Highlights: Genome Sequencing and Biology 2001

2001 ◽  
Vol 2 (4) ◽  
pp. 243-251
Author(s):  
Jo Wixon
Keyword(s):  
Comparative Genomics ◽  
Functional Genomics ◽  
Genome Sequencing ◽  
Large Scale ◽  
Model Organism

We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.

A comparative analysis of “Hutsulka” in the performing interpretations by two violinists representing the tradition of the Kosmach-Brusturiv areal

Ethnomusic ◽  
2018 ◽  
Vol 14 (1) ◽  
pp. 142-177
Author(s):  
Jarema Pavliv ◽  
Keyword(s):  
Comparative Analysis ◽  
Large Scale ◽  
Mobile Elements ◽  
Strategic Performance ◽  
Distinctive Features ◽  
Eastern Carpathians ◽  
Linear Movement ◽  
Melodic Line ◽  
Individual Interpretation ◽  
Formal Features

In the offered article, a comparative analysis of two performing versions of the wedding ceremonial dance “Hutsulka”, dominant in the Eastern Carpathians region of Ukraine has been made, with outstanding violinists-capellists, which, based on traditions and their own virtuoso style, developed this dance genre due to the accumulation of stable and mobile elements of melo-, rhythm- and form-making, as well as the establishment of aesthetics of regional styles. The material for the study was the audio version of the “Hutsulka” recorded on the basis of the performance of two violinists representing the region of Kosmach- Brusturiv villages tradition – Kyrylo Lyndiuk (“Vityshyn”, 1929–2003) (recorded by prof. Bogdan Lukaniuk in 1991) and Ivan Sokoliuk (born in 1944; Musician's own recording of 2017) – and transcribed by the author of the article. The performance of “Hutsulka” by each violinist is characteristic of common and distinctive features concerning the formation of the variative composition, the thematic material (respectively, 29 and 43 themes of kolomyika, kozachok and voloshka bases), tonality and rhythmic structuring, individual interpretation of ornamentation, which is collectively connected with artistic orientation on certain artistic and performing directions, presented by iconic musicians-predecessors. The formal features of the Hutsulka composition depends on scenery where it is performed (1); the tonality outline determined by established regional tradition (2), and rhythmic outline, by the overall style, varyation technics, updating and ornamentation of rhythmic formulas, characteristic of the personal manner and style of the performer (3). Ornamentation, as the essence of the performing style of any Hutsul musician, in K. “Vityshyn” is characterized by intense interweaving of short melismatic legal groups and non-legal figurations within melodic line and texture. I. Sokoliuk 166 enriches the linear movement with prolonged melismatic groups and rhythm- intonational and figurational turns that decorate it and amplify the expression of dance overall sonority. In performing aesthetics of K. Lyndiuk prevails an acute articulation of melodic expressiveness with accented and often pointed rhythmic patterns that provides representative-temperamental virtuosity. For strategic performance aesthetics of I. Sokoliuk, rich in virtuosic expressiveness, is characterized by choral and transparent ringing articulation in the context of “stratum”-development creation of the whole large-scale virtuoso composition. Each version reveals individual compositional, improvised, techno-performing, emotional as well as aesthetic mind of their creators. All these qualities, formed by both musicians in a single tradition and expressed in related kolomyika and kozachok-voloshka tunes, present the decision of developmental, composite, rhythmic, intonational, articulation, tempo and many other aspects of style, characteristic of folk violinists – soloists and capellists, inherent to each of them, in their performing manner, evident in “Hutsulka” rendering.

Computational modeling of Weibo user influence based on information interactive network

2016 ◽  
Vol 40 (7) ◽  
pp. 867-881 ◽  
Author(s):  
Dingguo Yu ◽  
Nan Chen ◽  
Xu Ran
Keyword(s):  
Social Networks ◽  
Computational Model ◽  
Large Scale ◽  
Mobile Internet ◽  
Activity Level ◽  
Message Content ◽  
Data Set ◽  
Sina Weibo ◽  
Content Type ◽  
User Influence

Purpose With the development and application of mobile internet access, social media represented by Weibo, WeChat, etc. has become the main channel for information release and sharing. High-impact users in social networks are key factors stimulating the large-scale propagation of information within social networks. User influence is usually related to the user’s attention rate, activity level, and message content. The paper aims to discuss these issues. Design/methodology/approach In this paper, the authors focused on Sina Weibo users, centered on users’ behavior and interactive information, and formulated a weighted interactive information network model, then present a novel computational model for Weibo user influence, which combined multiple indexes such as the user’s attention rate, activity level, and message content influence, etc., the model incorporated the time dimension, through the calculation of users’ attribute influence and interactive influence, to comprehensively measure the user influence of Sina Weibo users. Findings Compared with other models, the model reflected the dynamics and timeliness of the user influence in a more accurate way. Extensive experiments are conducted on the real-world data set, and the results validate the performance of the approach, and demonstrate the effectiveness of the dynamics and timeliness. Due to the similarity in platform architecture and user behavior between Sina Weibo and Twitter, the calculation model is also applicable to Twitter. Originality/value This paper presents a novel computational model for Weibo user influence, which combined multiple indexes such as the user’s attention rate, activity level, and message content influence, etc.

scholarly journals New Insights into the Evolutionary and Genomic Landscape of Molluscum Contagiosum Virus (MCV) based on Nine MCV1 and Six MCV2 Complete Genome Sequences

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 586 ◽  
Author(s):  
Tomaž Zorec ◽  
Denis Kutnjak ◽  
Lea Hošnjak ◽  
Blanka Kušar ◽  
Katarina Trčko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Nk Cell ◽  
Molluscum Contagiosum ◽  
Molluscum Contagiosum Virus ◽  
Genome Sequences ◽  
Viral Interference ◽  
Genomic Landscape ◽  
Genetic Landscape ◽  
Common Skin

Molluscum contagiosum virus (MCV) is the sole member of the Molluscipoxvirus genus and the causative agent of molluscum contagiosum (MC), a common skin disease. Although it is an important and frequent human pathogen, its genetic landscape and evolutionary history remain largely unknown. In this study, ten novel complete MCV genome sequences of the two most common MCV genotypes were determined (five MCV1 and five MCV2 sequences) and analyzed together with all MCV complete genomes previously deposited in freely accessible sequence repositories (four MCV1 and a single MCV2). In comparison to MCV1, a higher degree of nucleotide sequence conservation was observed among MCV2 genomes. Large-scale recombination events were identified in two newly assembled MCV1 genomes and one MCV2 genome. One recombination event was located in a newly identified recombinant region of the viral genome, and all previously described recombinant regions were re-identified in at least one novel MCV genome. MCV genes comprising the identified recombinant segments have been previously associated with viral interference with host T-cell and NK-cell immune responses. In conclusion, the two most common MCV genotypes emerged along divergent evolutionary pathways from a common ancestor, and the differences in the heterogeneity of MCV1 and MCV2 populations may be attributed to the strictness of the constraints imposed by the host immune response.

scholarly journals Poly(ADP-ribose) polymerase 1 in genome-wide expression control in Drosophila

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guillaume Bordet ◽  
Niraj Lodhi ◽  
Danping Guo ◽  
Andrew Kossenkov ◽  
Alexei V. Tulin
Keyword(s):  
Cytochrome P450 ◽  
Transcription Factors ◽  
Transcription Regulation ◽  
Large Scale ◽  
Mobile Elements ◽  
Expression Control ◽  
Genome Wide ◽  
Cytochrome P450 Family ◽  
Parp 1

AbstractPoly(ADP-ribose) polymerase 1 (PARP-1) is a nuclear enzyme involved in DNA repair and transcription regulation, among other processes. Malignant transformations, tumor progression, the onset of some neuropathies and other disorders have been linked to misregulation of PARP-1 activity. Despite intensive studies during the last few decades, the role of PARP-1 in transcription regulation is still not well understood. In this study, a transcriptomic analysis in Drosophila melanogaster third instar larvae was carried out. A total of 602 genes were identified, showing large-scale changes in their expression levels in the absence of PARP-1 in vivo. Among these genes, several functional gene groups were present, including transcription factors and cytochrome family members. The transcription levels of genes from the same functional group were affected by the absence of PARP-1 in a similar manner. In the absence of PARP-1, all misregulated genes coding for transcription factors were downregulated, whereas all genes coding for members of the cytochrome P450 family were upregulated. The cytochrome P450 proteins contain heme as a cofactor and are involved in oxidoreduction. Significant changes were also observed in the expression of several mobile elements in the absence of PARP-1, suggesting that PARP-1 may be involved in regulating the expression of mobile elements.

scholarly journals Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

2020 ◽  
Author(s):  
Agata Motyka-Pomagruk ◽  
Sabina Zoledowska ◽  
Agnieszka Emilia Misztak ◽  
Wojciech Sledz ◽  
Alessio Mengoni ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
De Novo ◽  
Genetic Material ◽  
Soft Rot ◽  
Potato Production ◽  
Core Gene ◽  
Ecological Niches ◽  
Dickeya Solani ◽  
High Level

Abstract Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

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