Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics

Makałowski, Wojciech; Gotea, Valer; Pande, Amit; Makałowska, Izabela

doi:10.1007/978-1-4939-9074-0_6

Cited by 87 publications

(65 citation statements)

References 148 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Hence, this may be a novel event distinct from standard DNA rearrangement events such as transposition and recombination. This is also evident from the fact that it is a 38-amino acids small predicted protein coded by 117 nucleotides in the 2019-nCoV genome, while transposons and insertion sequences are much longer sequences, characterized by sizes ranging from 700 bp to several thousands bp (1). Even there is no possibility of occurence of long terminal repeat sequences, since the ORF10 protein or nucleotide sequence is not a repetitive sequence as observed from GenBank sequence accession number MT106054.1/RefSeq sequence NC_045512.2 harbouring sequences from two different human sources, and there are no flanking repeated sequences, either.…”

Section: Open Reading Frame 10 (Orf10) May Be the Reason For Contagiomentioning

confidence: 98%

ORF10: Molecular Insights into the Contagious Nature of Pandemic Novel Coronavirus 2019-nCoV

Mishra

2020

Preprint

View full text Add to dashboard Cite

2019-novel coronavirus (nCoV), the virus causing Covid19 disease, is a highly contagious virus and has created a pandemic. In efforts to combat this virus, subunit vaccine designing using immunoinformatics tools was undertaken. During these studies, new hypotheses began to emerge, the prominent among these was that the newly acquired ORF10 protein may be the key protein responsible for its highly contagious nature. ORF10 is a hitherto unknown protein with no homology to any known protein in organisms present till date. Through immunoinformatics studies, it has been observed that among all ten 2019-nCoV proteins, ORF10 presents amongst the highest number of immunogenic, promiscuous CTL epitopes. These epitopes are part of a cluster with HTL epitopes, suggesting that there is a high degree of epitope conservation in ORF10. Conservation of protein sequence across organisms is not seen, and there is no known structural template on which to model and derive a

show abstract

Section: Open Reading Frame 10 (Orf10) May Be the Reason For Contagiomentioning

confidence: 98%

ORF10: Molecular Insights into the Contagious Nature of Pandemic Novel Coronavirus 2019-nCoV

Mishra

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Reverse transcription is followed by reintegration into the host genome. Through the copy and paste mechanism of transposition, Class I elements are the main source of increased repetitive fractions, thereby having a major impact in large genomes [ 153 , 154 , 155 ]. Class I mobile elements are composed of long terminal repeat (LTR) and non-LTR subclasses.…”

Section: Mobile Elementsmentioning

confidence: 99%

“… Mobile genetic element classification based on transposition mechanisms (according to Wicker et al [ 153 ]). The main structural components of the elements are reported on the right (modified from Makalowsky et al [ 155 ]). …”

Section: Figurementioning

confidence: 99%

Mobile Elements in Ray-Finned Fish Genomes

Carducci

Barucca

Canapa

et al. 2020

Life

View full text Add to dashboard Cite

Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.

show abstract

“…Consequently, they would provide a valuable and complementary set of genetic markers to analyze neutral and adaptive population structure in both basic and applied studies. However, with the exception of targeted candidate genes studies, CNV genotyping remained expensive for a long time as it required whole genome sequencing data with deep coverage (Pirooznia et al 2015, Makałowski et al 2019, precluding the use of these markers in population genomic studies that involve thousands of samples from dozens of populations. This situation has recently changed through the development of a novel methodological approach allowing the identification of CNVs in a cost-effective way using RAD-seq data (McKinney et al 2017, Dorant et al 2020.…”

Section: Introductionmentioning

confidence: 99%

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

Cayuela

Dorant

Mérot

et al. 2020

Preprint

View full text Add to dashboard Cite

Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic region and transposable elements (TEs) may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be important drivers of population genetic structure, whose study is generally restricted to the use of SNPs. Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local thermal conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene amplification. We also identified 175 CNVs associated with the divergence of three parapatric glacial lineages, of which 24% were located within protein-coding genes, which might contribute to genetic incompatibilities and ultimately, reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, that was very different from that inferred based on SNPs in a previous study. Our findings underscore the complementarity of those two types of markers in population genomics studies.

show abstract

Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics

Cited by 87 publications

References 148 publications

ORF10: Molecular Insights into the Contagious Nature of Pandemic Novel Coronavirus 2019-nCoV

ORF10: Molecular Insights into the Contagious Nature of Pandemic Novel Coronavirus 2019-nCoV

Mobile Elements in Ray-Finned Fish Genomes

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

Contact Info

Product

Resources

About