Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration

Weber, B.; Heitkam, Tony; Holtgräwe, Daniela; Weißhaar, Bernd; Minoche, André E.; Dohm, Juliane C.; Himmelbauer, Heinz; Schmidt, Thomas

doi:10.1186/1759-8753-4-8

Cited by 38 publications

(59 citation statements)

References 79 publications

(100 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Not only were the most abundant quinoa copia - rt clones pCquty119/pCquty118 preferentially located in pericentromeric heterochromatin, but also the overall retrotransposon density was higher in pericentric regions (as evidenced from FISH with pooled rt regions, excluding pCquty119/pCquty118) than in subterminal chromosomal regions. Similar pericentromeric localization was reported for two Ty3- gypsy retrotransposons Beetle ( CRM/CR lineage) and Bingo1 ( Reina ) in B. vulgaris chromosomes (Weber et al 2013). However, other Ty3- gypsy elements showed different chromosomal organization in Beta .…”

Section: Discussionsupporting

confidence: 83%

“…Similarly, in the genomes of species of the genus Beta closely related to Chenopodium, several abundant Ty1- copia [Cotzilla1 ( Sire/Maximus ), SALIRE1 ( Tork/TAR ), Weber et al 2010] as well as Ty3- gypsy retroelements were reported [Bongo3 ( Del/Tekay ), Beetle7 ( CRM/CR ), Bingo1 ( Reina ), Weber et al 2013; Elbe3 ( Athila ), Wollrab et al 2012]. The copy number of individual LTR retroelement families in plant genomes can vary greatly from very few copies to thousands of copies (Du et al 2010).…”

Section: Discussionmentioning

confidence: 99%

“…However, other Ty3- gypsy elements showed different chromosomal organization in Beta . For example, Bongo3 ( Del/Tekay lineage) was clustered along all chromosomes with reduced hybridization signal intensity in some of centromeric regions (Weber et al 2013). SALIRE elements (Ty1- copia, Tork/TAR ) isolated from B. vulgaris revealed dispersed hybridization patterns with hybridization signals strongly reduced in the centromeric and pericentromeric regions (Weber et al 2010).…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae)

2013

View full text Add to dashboard Cite

Key messageHigh heterogeneity was observed among conserved domains of reverse transcriptase (rt)isolated from quinoa. Only one Ty1-copia rtwas highly amplified. Reverse transcriptase sequences were located predominantly in pericentromeric region of quinoa chromosomes.AbstractThe heterogeneity, genomic abundance, and chromosomal distribution of reverse transcriptase (rt)-coding fragments of Ty1-copia and Ty3-gypsy long terminal repeat retrotransposons were analyzed in the Chenopodium quinoa genome. Conserved domains of the rt gene were amplified and characterized using degenerate oligonucleotide primer pairs. Sequence analyses indicated that half of Ty1-copia rt (51 %) and 39 % of Ty3-gypsy rt fragments contained intact reading frames. High heterogeneity among rt sequences was observed for both Ty1-copia and Ty3-gypsy rt amplicons, with Ty1-copia more heterogeneous than Ty3-gypsy. Most of the isolated rt fragments were present in quinoa genome in low copy numbers, with only one highly amplified Ty1-copia rt sequence family. The gypsy-like RNase H fragments co-amplified with Ty1-copia-degenerate primers were shown to be highly amplified in the quinoa genome indicating either higher abundance of some gypsy families of which rt domains could not be amplified, or independent evolution of this gypsy-region in quinoa. Both Ty1-copia and Ty3-gypsy retrotransposons were preferentially located in pericentromeric heterochromatin of quinoa chromosomes. Phylogenetic analyses of newly amplified rt fragments together with well-characterized retrotransposon families from other organisms allowed identification of major lineages of retroelements in the genome of quinoa and provided preliminary insight into their evolutionary dynamics.

show abstract

Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae)

2013

View full text Add to dashboard Cite

show abstract

“…The main Gypsy lineages are OGRE/TAT, large LTR-REs with an open reading frame located upstream of the gag gene (Neumann et al 2003); Athila, first reported in Arabidopsis thaliana (Wright and Voytas 2002); and Chromovirus, a lineage of REs carrying a chromodomain at the 5′ end of the coding portion, which is especially abundant in centromeres (Gorinsek et al 2004;Llorens et al 2011). In certain species, chromoviruses were further subdivided into four sublineages (Galadriel, Tekay, CR, and Reina), based on the relative positions of the chromodomain and a polypurine tract (PPT), and on the LTRs length (Weber et al 2013). On the other hand, Copia REs can belong to many different lineages, the most frequent being AleI/Retrofit/Hopscotch, AleII, Angela, Bianca, Ivana/Oryco, TAR/Tork, and Maximus/SIRE (Wicker and Keller 2007).…”

mentioning

confidence: 99%

A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome

Natali

Cossu

Mascagni

et al. 2015

Tree Genetics & Genomes

View full text Add to dashboard Cite

In this work, we report a comprehensive study of\ud long terminal repeat retrotransposons of Populus trichocarpa.\ud Our research group studied the retrotransposon component of\ud the poplar genome in 2012, isolating 1479 putative full-length\ud elements. However, in that study, it was not possible to identify\ud the superfamily to which the majority of isolated full-length\ud elements belonged. Moreover, during recent years, the genome\ud sequence of P. trichocarpa has been updated, deciphering thek\ud sequences of a number of previously unresolved loci. In this\ud work, we performed a complete scan of the updated version of\ud the genome sequence to isolate full-length retrotransposons\ud based on sequence and structural features. The new dataset\ud showed a reduced number of elements (958), and 21 fulllength\ud elements were discovered for the first time. The majority\ud of retroelements belonged to the Gypsy superfamily (57%),\ud while Copia elements amounted to 41.1% of the dataset. Fulllength\ud elements were dispersed throughout the chromosomes.\ud However, Gypsy and, to a lesser extent, Copia elements accumulated\ud preferentially at putative centromeres. Gypsy elements\ud were more active in retrotransposition than Copia elements,\ud with the exception of during the past million years, in which\ud Copia elements were the most active. Improved annotation\ud procedures also allowed us to determine the specific lineages\ud to which isolated elements belonged. The three Gypsy lineages,\ud Athila, OGRE, and Chromovirus (in the decreasing order),\ud were by far the most abundant. On the other hand, each\ud identified Copia lineage represented less than 1 % of the genome.\ud Significant differences in the insertion age were found\ud among lineages, suggesting specific activation mechanisms.\ud Moreover, different chromosomal regions were affected by\ud retrotransposition in different ages. In all chromosomes, putative\ud pericentromeric regions were filled with elements older\ud than themean insertion age. Overall, results demonstrate structural\ud and functional differences among plant retrotransposon\ud lineages and further support the view of retrotransposons as a\ud community of different organisms in the genome

show abstract

“…One widespread group of Gypsy retrotransposons, the so-called chromoviruses or CRM clade, is interesting for the presence of chromodomains at the C-terminus of the IN (Gorinsek et al 2005). The chromodomain is similar to domains of heterochromatin protein 1 (HP1), which may confer particular integration patterns to some chromoviruses (Weber et al 2013). Phylogenetic and sequence analysis of members of the CRM clade in plants (Neumann et al 2011), defined one particular group that contains a CR motif similar that found in the chromodomain-bearing MAGGY retrotransposons of fungi (Gao et al 2008) and is concentrated in centromeric regions.…”

Section: Ltr Retrotransposon Replication and Growth In Genome Sizementioning

confidence: 99%

Genome Size and the Role of Transposable Elements

Schulman

2015

Genetics and Genomics of Brachypodium

View full text Add to dashboard Cite

The lack of correlation between genome size and organismal complexity was early on dubbed the "C-value Paradox;" it holds even when gene number is considered instead of overall organismal complexity. The sequencing of large eukaryotic genomes has now conclusively solved this conundrum with the demonstration that most nuclear DNA comprises various classes of repeats, primarily transposable elements (TEs). The inherent and variable capacity of the TEs for mobility and replication explains how genome size can vary so greatly on their account. The Class I TEs or retrotransposons have a replication cycle involving the copying of a transcribed, genomic RNA into dsDNA by reverse transcriptase. As a result of their replicative life cycle, the retrotransposons comprise most of large genomes among plants; differences in their prevalence explain most of the variation in genome size on the monoploid level. However, retrotransposons are not only gained through the propagative life cycle described above, but they also can be lost through a combination of progressive small deletions and truncations. The genome of Brachypodium distachyon, at~372 Mb, is at the lower end of the distribution for flowering plants. The compactness of the B. distachyon genome is correlated with a relatively low number of retrotransposons, although it contains many recently inserted transposable elements. The B. distachyon genome appears to stay trim through recombinational shedding of retrotransposons, despite their continuing propagation. Nevertheless, the chromosomes show remarkable differences among them regarding the gain and loss of retrotransposons over time and the relative accumulation of the two superfamilies, Copia and Gypsy.

show abstract

Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration

Cited by 38 publications

References 79 publications

Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae)

Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae)

A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome

Genome Size and the Role of Transposable Elements

Contact Info

Product

Resources

About