Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Paço, Ana; Freitas, Renata; Vieira-da-Silva, A.

doi:10.3390/genes10121014

Cited by 35 publications

(31 citation statements)

References 136 publications

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“…In ferns, the PBS is located 8 nt from the 5S rDNA sequence whereas in Brassica species it is up to 173 bp away. Therefore, we used following linked-sequences query in FASTA format to search both fern and seed plant genomes for Cassandra sequences: >Cassandra RGTTAAGYRHGY [15][16][17][18][19][20][21][22][23][24][25]RRRATRGGTRACY TGGTATCAGAGC.…”

Section: In Silico Query For Cassandra In Plant Genomesmentioning

confidence: 99%

“…In addition, we performed the "Linked (Associated) search" tool to identify long tandem arrays for Cassandra within all studied plant species. The search for long tandem arrays of Cassandra were specified as: (RGTTAAGYRHGY [15][16][17][18][19][20][21][22][23][24][25]RRRATRGGTRACY(5-200)TGGTATCAGAGC)n, where n is the amount of tandem arrays, n = 1 for a single copy of Cassandra and >1 for a tandem array: >Cassandra_tandem RGTTAAGYRHGY [15][16][17][18][19][20][21][22][23][24][25]…”

Section: In Silico Query For Cassandra In Plant Genomesmentioning

confidence: 99%

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Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

Kalendar

Raskina

Belyayev

et al. 2020

IJMS

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Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.

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Section: In Silico Query For Cassandra In Plant Genomesmentioning

confidence: 99%

Section: In Silico Query For Cassandra In Plant Genomesmentioning

confidence: 99%

Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

Kalendar

Raskina

Belyayev

et al. 2020

IJMS

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“…Many of the found sequences (54,434 out of 76,174) belong to transposons or previously known repeats ( Table 5 ), which may indicate an organic relationship between TRs and transposonomy as suggested by Paço et al [ 44 ], who also discussed a possibility of TR conversion into genes. The latter hypothesis is supported by our results, which revealed that many regions with triplet periodicity were located within the genes.…”

Section: Discussionmentioning

confidence: 77%

Detection of Highly Divergent Tandem Repeats in the Rice Genome

Korotkov

Kamionskya

Korotkova

2021

Genes

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Currently, there is a lack of bioinformatics approaches to identify highly divergent tandem repeats (TRs) in eukaryotic genomes. Here, we developed a new mathematical method to search for TRs, which uses a novel algorithm for constructing multiple alignments based on the generation of random position weight matrices (RPWMs), and applied it to detect TRs of 2 to 50 nucleotides long in the rice genome. The RPWM method could find highly divergent TRs in the presence of insertions or deletions. Comparison of the RPWM algorithm with the other methods of TR identification showed that RPWM could detect TRs in which the average number of base substitutions per nucleotide (x) was between 1.5 and 3.2, whereas T-REKS and TRF methods could not detect divergent TRs with x > 1.5. Applied to the search of TRs in the rice genome, the RPWM method revealed that TRs occupied 5% of the genome and that most of them were 2 and 3 bases long. Using RPWM, we also revealed the correlation of TRs with dispersed repeats and transposons, suggesting that some transposons originated from TRs. Thus, the novel RPWM algorithm is an effective tool to search for highly divergent TRs in the genomes.

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“…The close relationship of tandem repeats and TEs has been recently well documented, with several micro, mini and satellite DNAs found embedded within TEs [ 65 – 70 ]. The existence of tandem repeats in multiple families and copies of Merlin indicates this TE could help to spread tandem repeats by transposition as proto-satellites that could be next amplified and homogenized such as the model suggested by Paço and colleagues [ 67 ].…”

Section: Resultsmentioning

confidence: 99%

Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists

et al. 2021

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DNA transposons are defined as repeated DNA sequences that can move within the host genome through the action of transposases. The transposon superfamily Merlin was originally found mainly in animal genomes. Here, we describe a global distribution of the Merlin in animals, fungi, plants and protists, reporting for the first time their presence in Rhodophyceae, Metamonada, Discoba and Alveolata. We identified a great variety of potentially active Merlin families, some containing highly imperfect terminal inverted repeats and internal tandem repeats. Merlin-related sequences with no evidence of mobilization capacity were also observed and may be products of domestication. The evolutionary trees support that Merlin is likely an ancient superfamily, with early events of diversification and secondary losses, although repeated re-invasions probably occurred in some groups, which would explain its diversity and discontinuous distribution. We cannot rule out the possibility that the Merlin superfamily is the product of multiple horizontal transfers of related prokaryotic insertion sequences. Moreover, this is the first account of a DNA transposon in kinetoplastid flagellates, with conserved Merlin transposase identified in Bodo saltans and Perkinsela sp., whereas it is absent in trypanosomatids. Based on the level of conservation of the transposase and overlaps of putative open reading frames with Merlin, we propose that in protists it may serve as a raw material for gene emergence.

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Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

Cited by 35 publications

References 136 publications

Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

Detection of Highly Divergent Tandem Repeats in the Rice Genome

Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists

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