Abstract:Transposable elements (TEs) are mobile genetic elements with the ability to replicate themselves throughout the host genome. In some taxa TEs reach copy numbers in hundreds of thousands and can occupy more than half of the genome. The increasing number of reference genomes from nonmodel species has begun to outpace efforts to identify and annotate TE content and methods that are used vary significantly between projects. Here, we demonstrate variation that arises in TE annotations when less than optimal methods… Show more
“…In the case of the FOSC, we would not have detected any Helitrons using conventional approaches based on termini or DNA sequences of canonical Helitrons [5, 18, 20, 39]. Our analyses of predicted putative Helitrons in other fungi suggests that the same may hold true for many other species [38, 40]. …”
Section: Discussionmentioning
confidence: 86%
“…Most software designed to identify Helitrons are based on the DNA motifs of the Helitron1 variant and will overlook instances of Helitron2 because these have different termini [5, 18, 20, 38–40]. Moreover, DNA sequence similarity can be hard to recognize over long evolutionary distances and very few ascomycete Helitron sequences were available at the start of our studies.…”
Section: Resultsmentioning
confidence: 99%
“…Genome assemblies based on second generation sequencing data are unlikely to include recently transposed elements of more than 5 kb [44, 45, 54]. Hence the repeat content of genomes that are assembled to different levels of completeness cannot be directly compared [40, 54]. Similarly, non-autonomous elements are often more abundant than their autonomous counterparts [1, 3], which can be explained by the intuitive assumption that shorter sequences are more efficiently transposed.…”
BackgroundHelitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi.ResultsHere, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics.ConclusionsFOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0083-7) contains supplementary material, which is available to authorized users.
“…In the case of the FOSC, we would not have detected any Helitrons using conventional approaches based on termini or DNA sequences of canonical Helitrons [5, 18, 20, 39]. Our analyses of predicted putative Helitrons in other fungi suggests that the same may hold true for many other species [38, 40]. …”
Section: Discussionmentioning
confidence: 86%
“…Most software designed to identify Helitrons are based on the DNA motifs of the Helitron1 variant and will overlook instances of Helitron2 because these have different termini [5, 18, 20, 38–40]. Moreover, DNA sequence similarity can be hard to recognize over long evolutionary distances and very few ascomycete Helitron sequences were available at the start of our studies.…”
Section: Resultsmentioning
confidence: 99%
“…Genome assemblies based on second generation sequencing data are unlikely to include recently transposed elements of more than 5 kb [44, 45, 54]. Hence the repeat content of genomes that are assembled to different levels of completeness cannot be directly compared [40, 54]. Similarly, non-autonomous elements are often more abundant than their autonomous counterparts [1, 3], which can be explained by the intuitive assumption that shorter sequences are more efficiently transposed.…”
BackgroundHelitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi.ResultsHere, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics.ConclusionsFOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0083-7) contains supplementary material, which is available to authorized users.
“…This implies that the minimal transposable elements accumulation has occurred in the recent past, or that newly inserted transposable elements are being actively removed from the genome [135]. However, with high divergences between potentially novel transposable elements in P. regina and transposable elements in RepBase is possible that lineage-specific SINEs are present but unidentifiable using homology based searches [136] and a full TE curation of the genome is necessary.Fig. 4Transposable element accumulation in the female ( a ) and male ( b ) Phormia regina genome assemblies.…”
BackgroundBlow flies (Diptera: Calliphoridae) are important medical, veterinary and forensic insects encompassing 8 % of the species diversity observed in the calyptrate insects. Few genomic resources exist to understand the diversity and evolution of this group.ResultsWe present the hybrid (short and long reads) draft assemblies of the male and female genomes of the common North American blow fly, Phormia regina (Diptera: Calliphoridae). The 550 and 534 Mb draft assemblies contained 8312 and 9490 predicted genes in the female and male genomes, respectively; including > 93 % conserved eukaryotic genes. Putative X and Y chromosomes (21 and 14 Mb, respectively) were assembled and annotated. The P. regina genomes appear to contain few mobile genetic elements, an almost complete absence of SINEs, and most of the repetitive landscape consists of simple repetitive sequences. Candidate gene approaches were undertaken to annotate insecticide resistance, sex-determining, chemoreceptors, and antimicrobial peptides.ConclusionsThis work yielded a robust, reliable reference calliphorid genome from a species located in the middle of a calliphorid phylogeny. By adding an additional blow fly genome, the ability to tease apart what might be true of general calliphorids vs. what is specific of two distinct lineages now exists. This resource will provide a strong foundation for future studies into the evolution, population structure, behavior, and physiology of all blow flies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3187-z) contains supplementary material, which is available to authorized users.
“…Parsing out the repetitive content of genomes is difficult and a number of computational methods have been developed (Janicki et al 2011). This wealth of options can be a curse though, as different methodologies across and between different genomes will often give different answers as to whether all TEs are detected or properly grouped together (Platt et al 2016). TEs have a system of classification which mirrors the hierarchical taxonomic system employed by biologists for organisms, based upon the character of nucleic acid intermediates during replication (Finnegan 1989;Wicker et al 2007).…”
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