GLORIA

GEOMAR Library Ocean Research Information Access

X

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • SAGE Publications  (7)
  • Biodiversity Research  (7)
Material
Publisher
  • SAGE Publications  (7)
Person/Organisation
Language
Years
FID
  • Biodiversity Research  (7)
  • 1
    Online Resource
    Online Resource
    Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences
    SAGE Publications ; 2020
    In:  Evolutionary Bioinformatics Vol. 16 ( 2020-01), p. 117693432090310-
    Details
    In: Evolutionary Bioinformatics, SAGE Publications, Vol. 16 ( 2020-01), p. 117693432090310-
    Abstract: Introns are well known for their high variation not only in length but also in base sequence. The evolution of intron sequences has aroused broad interest in the past decades. However, very little is known about the evolutionary pattern of introns due to the lack of efficient analytical method. In this study, we designed 2 evolutionary models, that is, mutation-and-deletion (MD) and mutation-and-insertion (MI), to simulate intron evolution using randomly generated and mutated bases by referencing to the phylogenetic tree constructed using 14 chordate introns from TF4 (transcription factor–like protein 4) gene. A comparison of attributes between model-generated sequences and chordate introns showed that the MD model with proper parameter settings could generate sequences that have attributes matchable to chordate introns, whereas the MI model with any parameter settings failed in doing so. These data suggest that the surveyed chordate introns have evolved from a long ancestral sequence through gradual reduction in length. The established methodology provides an effective measure to study the evolutionary pattern of intron sequences from organisms of various taxonomic groups. (C++ scripts of MD and MI models are available upon request.)
    Type of Medium: Online Resource
    ISSN: 1176-9343 , 1176-9343
    URL: Article
    DOI: 10.1177/1176934320903108
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2020
    detail.hit.zdb_id: 2227610-5
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 2
    Online Resource
    Online Resource
    Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion
    SAGE Publications ; 2012
    In:  Evolutionary Bioinformatics Vol. 8 ( 2012-01), p. EBO.S9758-
    Details
    In: Evolutionary Bioinformatics, SAGE Publications, Vol. 8 ( 2012-01), p. EBO.S9758-
    Abstract: Repetitive sequences (RSs) are redundant, complex at times, and often lineage-specific, representing significant “building” materials for genes and genomes. According to their origins, sequence characteristics, and ways of propagation, repetitive sequences are divided into transposable elements (TEs) and satellite sequences (SSs) as well as related subfamilies and subgroups hierarchically. The combined changes attributable to the repetitive sequences alter gene and genome architectures, such as the expansion of exonic, intronic, and intergenic sequences, and most of them propagate in a seemingly random fashion and contribute very significantly to the entire mutation spectrum of mammalian genomes. Principal findings Our analysis is focused on evolutional features of TEs and SSs in the intronic sequence of twelve selected mammalian genomes. We divided them into four groups–-primates, large mammals, rodents, and primary mammals–-and used four non-mammalian vertebrate species as the out-group. After classifying intron size variation in an intron-centric way based on RS-dominance (TE-dominant or SS-dominant intron expansions), we observed several distinct profiles in intron length and positioning in different vertebrate lineages, such as retrotransposon-dominance in mammals and DNA transposon-dominance in the lower vertebrates, amphibians and fishes. The RS patterns of mouse and rat genes are most striking, which are not only distinct from those of other mammals but also different from that of the third rodent species analyzed in this study–-guinea pig. Looking into the biological functions of relevant genes, we observed a two-dimensional divergence; in particular, genes that possess SS-dominant and/or RS-free introns are enriched in tissue-specific development and transcription regulation in all mammalian lineages. In addition, we found that the tendency of transposons in increasing intron size is much stronger than that of satellites, and the combined effect of both RSs is greater than either one of them alone in a simple arithmetic sum among the mammals and the opposite is found among the four non-mammalian vertebrates. Conclusions TE- and SS-derived RSs represent major mutational forces shaping the size and composition of vertebrate genes and genomes, and through natural selection they either fine-tune or facilitate changes in size expansion, position variation, and duplication, and thus in functions and evolutionary paths for better survival and fitness. When analyzed globally, not only are such changes significantly diversified but also comprehensible in lineages and biological implications.
    Type of Medium: Online Resource
    ISSN: 1176-9343 , 1176-9343
    URL: Article
    DOI: 10.4137/EBO.S9758
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2012
    detail.hit.zdb_id: 2227610-5
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 3
    Online Resource
    Online Resource
    An Intron of Invertebrate Microphthalmia Transcription Factor Gene Is Evolved from a Longer Ancestral Sequence
    SAGE Publications ; 2021
    In:  Evolutionary Bioinformatics Vol. 17 ( 2021-01), p. 117693432098855-
    Details
    In: Evolutionary Bioinformatics, SAGE Publications, Vol. 17 ( 2021-01), p. 117693432098855-
    Abstract: Introns are highly variable in number and size. Sequence simulation is an effective method to elucidate intron evolution patterns. Previously, we have reported that introns are more likely to evolve through mutation-and-deletion (MD) rather than through mutation-and-insertion (MI). In the present study, we further studied evolution models by allowing insertion in the MD model and by allowing deletion in the MI model at various frequencies. It was found that all deletion-biased models with proper parameter settings could generate sequences with attributes matchable to 16 invertebrate introns from the microphthalmia transcription factor gene, whereas all insertion-biased models with any parameter settings failed to generate such sequences. We conclude that the examined invertebrate introns may have evolved from a longer ancestral sequence in a deletion-biased pattern. The constructed models are useful for studying the evolution of introns from other genes and/or from other taxonomic groups. (C++ scripts of all deletion- and insertion-biased models are available upon request.)
    Type of Medium: Online Resource
    ISSN: 1176-9343 , 1176-9343
    URL: Article
    DOI: 10.1177/1176934320988558
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2021
    detail.hit.zdb_id: 2227610-5
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 4
    Online Resource
    Online Resource
    Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization
    SAGE Publications ; 2016
    In:  Evolutionary Bioinformatics Vol. 12 ( 2016-01), p. EBO.S40703-
    Details
    In: Evolutionary Bioinformatics, SAGE Publications, Vol. 12 ( 2016-01), p. EBO.S40703-
    Type of Medium: Online Resource
    ISSN: 1176-9343 , 1176-9343
    URL: Article
    DOI: 10.4137/EBO.S40703
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2016
    detail.hit.zdb_id: 2227610-5
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 5
    Online Resource
    Online Resource
    Identification of Transposable Elements in Conifer and Their Potential Application in Breeding
    SAGE Publications ; 2020
    In:  Evolutionary Bioinformatics Vol. 16 ( 2020-01), p. 117693432093026-
    Details
    In: Evolutionary Bioinformatics, SAGE Publications, Vol. 16 ( 2020-01), p. 117693432093026-
    Abstract: Transposable elements (TEs) are known to play a role in genome evolution, gene regulation, and epigenetics, representing potential tools for genetics research in and breeding of conifers. Recently, thanks to the development of high-throughput sequencing, more conifer genomes have been reported. Using bioinformatics tools, the TEs of 3 important conifers ( Picea abies, Picea glauce, and Pinus taeda) were identified in our previous study, which provided a foundation for accelerating the use of TEs in conifer breeding and genetic study. Here, we review recent studies on the functional biology of TEs and discuss the potential applications for TEs in conifers.
    Type of Medium: Online Resource
    ISSN: 1176-9343 , 1176-9343
    URL: Article
    DOI: 10.1177/1176934320930263
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2020
    detail.hit.zdb_id: 2227610-5
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 6
    Online Resource
    Online Resource
    Bioinformatics Analysis Identifies Potential Related Genes in the Pathogenesis of Intrauterine Fetal Growth Retardation
    SAGE Publications ; 2022
    In:  Evolutionary Bioinformatics Vol. 18 ( 2022-01), p. 117693432211127-
    Details
    In: Evolutionary Bioinformatics, SAGE Publications, Vol. 18 ( 2022-01), p. 117693432211127-
    Abstract: Intrauterine growth retardation (IUGR) affects approximately 10% to 15% of all pregnancies worldwide. IUGR is not only associated with stillbirth and newborn death, but also the delay of cognition in childhood and the promotion of metabolic and vascular disorders in adulthood. Figuring out the mechanism of IUGR is rather meaningful and valuable. Methods: Datasets related to IUGR were searched in the Gene Expression Omnibus website. Principal component analysis (PCA) was used for normalization. Differential expressed genes (DEGs) were screened out using the ggpot2 tool. DEGs were used to conduct Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses, and protein-protein interaction (PPI) analysis. IUGR related genes were searched in the OMIM website to look for the intersection with the DEGs. The DEGs were analyzed for tissue-specific expression by the online resource BioGPS. The results were displayed through volcano map, Venn map, box plot, heat map, and GSEA enrichment plots drawn by R language packages. Results: Eleven DEGs were screened out of 2 datasets. One hundred ninety-five genes related to IUGR in OMIM were retrieved. EGR2 was the only intersection gene that was found in both groups. Genes associated with placental tissue expression include COL17A1, HSD11B1, and LGALS14. Molecular functions of the DEGs are related to the oxidoreductase activity. The following 4 signaling pathways, reactome signaling by interleukins, reactome collagen degradation, Naba secreted factors, and PID NFAT tfpathway, were enriched by GSEA. Two critical modules comprising 5 up-regulated genes (LEP, PRL, TAC3, MMP14, and ADAMTS4) and 4 down-regulated genes (TIMP4, FOS, CCK, and KISS1) were identified by PPI analysis. Finally, we identified 6 genes (PRL, LGALS14, EGR2, TAC3, LEP, and KISS1) that are potentially relevant to the pathophysiology of IUGR. Conclusion: The candidate down-regulated genes LGALS14 and KISS1, as well as the up-regulated genes PRL, EGR2, TAC3, and LEP, were found to be closely related to IUGR by bioinformatics analysis. These hub genes are related to hypoxia and oxidoreductase activities in placental development. We provide useful and novel information to explore the potential mechanism of IUGR and make efforts to the prevention of IUGR.
    Type of Medium: Online Resource
    ISSN: 1176-9343 , 1176-9343
    URL: Article
    DOI: 10.1177/11769343221112780
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2022
    detail.hit.zdb_id: 2227610-5
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 7
    Online Resource
    Online Resource
    Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family in Solanum pimpinellifolium and Arabidopsis thaliana
    SAGE Publications ; 2020
    In:  Evolutionary Bioinformatics Vol. 16 ( 2020-01), p. 117693432091105-
    Details
    In: Evolutionary Bioinformatics, SAGE Publications, Vol. 16 ( 2020-01), p. 117693432091105-
    Abstract: NBS-LRR (nucleotide-binding site and leucine-rich repeat) is one of the largest resistance gene families in plants. The completion of the genome sequencing of wild tomato Solanum pimpinellifolium provided an opportunity to conduct a comprehensive analysis of the NBS-LRR gene superfamily at the genome-wide level. In this study, gene identification, chromosome mapping, and phylogenetic analysis of the NBS-LRR gene family were analyzed using the bioinformatics methods. The results revealed 245 NBS-LRRs in total, similar to that in the cultivated tomato. These genes are unevenly distributed on 12 chromosomes, and ~59.6% of them form gene clusters, most of which are tandem duplications. Phylogenetic analysis divided the NBS-LRRs into 2 subfamilies (CNL-coiled-coil NBS-LRR and TNL-TIR NBS-LRR), and the expansion of the CNL subfamily was more extensive than the TNL subfamily. Novel conserved structures were identified through conserved motif analysis between the CNL and TNL subfamilies. Compared with the NBS-LRR sequences from the model plant Arabidopsis thaliana, wide genetic variation occurred after the divergence of S. pimpinellifolium and A thaliana. Species-specific expansion was also found in the CNL subfamily in S. pimpinellifolium. The results of this study provide the basis for the deeper analysis of NBS-LRR resistance genes and contribute to mapping and isolation of candidate resistance genes in S. pimpinellifolium.
    Type of Medium: Online Resource
    ISSN: 1176-9343 , 1176-9343
    URL: Article
    DOI: 10.1177/1176934320911055
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2020
    detail.hit.zdb_id: 2227610-5
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...