A universal classification of eukaryotic transposable elements implemented in Repbase

Wicker, Thomas; Sabot, François; Hua-Van, Aurélie; Bennetzen, Jeffrey L.; Capy, Pierre; Chalhoub, Boulos; Flavell, Andrew J.; Leroy, Philippe; Morgante, Michèle; Panaud, Olivier; Paux, Etienne; SanMiguel, Phillip; Schulman, Alan H.

doi:10.1038/nrg2165-c1

Cited by 436 publications

(381 citation statements)

References 20 publications

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“…S5). A huge diversity of mobile elements has been described in the three domains of life (26)(27)(28), and the list is still growing (29). However, the PgV-16T repeats do not resemble any of them.…”

Section: Resultsmentioning

confidence: 99%

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Santini

Jeudy

Bartoli

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

176

213

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Large dsDNA viruses are involved in the population control of many globally distributed species of eukaryotic phytoplankton and have a prominent role in bloom termination. The genus Phaeocystis ( Haptophyta , Prymnesiophyceae ) includes several high-biomass-forming phytoplankton species, such as Phaeocystis globosa , the blooms of which occur mostly in the coastal zone of the North Atlantic and the North Sea. Here, we report the 459,984-bp-long genome sequence of P. globosa virus strain PgV-16T, encoding 434 proteins and eight tRNAs and, thus, the largest fully sequenced genome to date among viruses infecting algae. Surprisingly, PgV-16T exhibits no phylogenetic affinity with other viruses infecting microalgae (e.g., phycodnaviruses), including those infecting Emiliania huxleyi , another ubiquitous bloom-forming haptophyte. Rather, PgV-16T belongs to an emerging clade (the Megaviridae) clustering the viruses endowed with the largest known genomes, including Megavirus, Mimivirus (both infecting acanthamoeba), and a virus infecting the marine microflagellate grazer Cafeteria roenbergensis . Seventy-five percent of the best matches of PgV-16T–predicted proteins correspond to two viruses [Organic Lake phycodnavirus (OLPV)1 and OLPV2] from a hypersaline lake in Antarctica (Organic Lake), the hosts of which are unknown. As for OLPVs and other Megaviridae, the PgV-16T sequence data revealed the presence of a virophage-like genome. However, no virophage particle was detected in infected P. globosa cultures. The presence of many genes found only in Megaviridae in its genome and the presence of an associated virophage strongly suggest that PgV-16T shares a common ancestry with the largest known dsDNA viruses, the host range of which already encompasses the earliest diverging branches of domain Eukarya.

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Section: Resultsmentioning

confidence: 99%

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Santini

Jeudy

Bartoli

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

176

213

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“…Inter-specific variation in the occurrence of TEs Identified TEs were classified following the universal classification system of Kapitonov and Jurka (2008) implemented in Repbase. Information regarding TE transpositional mechanism (autonomous/non-autonomous) was obtained from Repbase and Web of Science reports.…”

Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

et al. 2010

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Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatelliteinducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

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“…At the DNA level, RepeatModeler (http://www.repeatmasker.org/RepeatModeler.html) and LTR_FINDER 44 software were used to build de novo repeat libraries. RepeatMasker (version 3.2.9) was run against de novo library and repbase 45 separately to identify homologous repeats, which were classified into known classes of repeats 46 . At the protein level, RM-BLASTX within RepeatProteinMask in RepeatMasker software package was used against the transposable elements protein database.…”

Section: Competing Financial Interestsmentioning

confidence: 99%

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

et al. 2012

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A universal classification of eukaryotic transposable elements implemented in Repbase

Cited by 436 publications

References 20 publications

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

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