scholarly journals Correction to: low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Vanessa Carvalho Cayres Pamponét ◽  
Margarete Magalhães Souza ◽  
Gonçalo Santos Silva ◽  
Fabienne Micheli ◽  
Cláusio Antônio Ferreira de Melo ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Repetitive Dna ◽  
Satellite Dna ◽  
Dna Analysis ◽  
Passiflora Edulis ◽  
Passiflora Edulis Sims ◽  
Low Coverage

scholarly journals Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Vanessa Carvalho Cayres Pamponét ◽  
Margarete Magalhães Souza ◽  
Gonçalo Santos Silva ◽  
Fabienne Micheli ◽  
Cláusio Antônio Ferreira de Melo ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Repetitive Dna ◽  
Satellite Dna ◽  
Dna Analysis ◽  
Passiflora Edulis ◽  
Passiflora Edulis Sims ◽  
Low Coverage

scholarly journals Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Octavio M. Palacios-Gimenez ◽  
Julia Koelman ◽  
Marc Palmada-Flores ◽  
Tessa M. Bradford ◽  
Karl K. Jones ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Species Complex ◽  
Repetitive Dna Sequences ◽  
Dna Repeats ◽  
Large Genome ◽  
Chromosomal Races

Abstract Background Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution. Results We obtained linked-read genome assemblies of 2.73–3.27 Gb from estimated genome sizes of 4.26–5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314–463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. Conclusion This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.

Characterization of a repetitive element detected by NheI in the genomes of Salmo species

Genome ◽  
1994 ◽  
Vol 37 (4) ◽  
pp. 639-645 ◽  
Author(s):  
John L. Goodier ◽  
William S. Davidson
Keyword(s):  
Atlantic Salmon ◽  
Key Words ◽  
Repetitive Dna ◽  
Brown Trout ◽  
Restriction Enzyme ◽  
Satellite Dna ◽  
Repetitive Element ◽  
Recognition Sequence ◽  
Transposon Evolution

The genomes of the two species in the genus Salmo (Atlantic salmon, S. salar; brown trout, S. trutta) contain a 380-bp repetitive element that is flanked by the recognition sequence of the restriction enzyme NheI. These elements, which comprise approximately 1.2% of the salmon genome, do not exist in long tandem arrays as is typical of satellite DNA. A comparison of the sequences of 16 salmon and 7 trout elements revealed that members of this family of repetitive DNA are closely related to one another (over 95% identity). Subfamily structure exists and there is evidence that members of the same subfamilies are found in both Salmo species. A search of the GenBank database indicated that sequences homologous to the NheI repeat are located within a 1424-bp segment inserted immediately downstream of the 5′ end of a Tc1 transposon-like sequence isolated from Atlantic salmon (A.R. Radice, B. Bugaj, D.H. Fitch, and S.W. Emmons, unpublished data; GenBank accession No. L12206).Key words: satellite DNA, Atlantic salmon, brown trout, Tc1-like transposon, evolution.

scholarly journals Cytogenetic characterization of the Passiflora edulis Sims × Passiflora cincinnata Mast. interspecific hybrid and its parents

Euphytica ◽  
2016 ◽  
Vol 210 (1) ◽  
pp. 93-104 ◽  
Author(s):  
Maria do Socorro Evangelista Coelho ◽  
Kyria Cilene de Andrade Bortoleti ◽  
Francisco Pinheiro de Araújo ◽  
Natoniel Franklin de Melo
Keyword(s):  
Interspecific Hybrid ◽  
Passiflora Edulis ◽  
Cytogenetic Characterization ◽  
Passiflora Edulis Sims

Characterization of two unrelated satellite DNA families in the Colorado potato beetle Leptinotarsa decemlineata (Coleoptera, Chrysomelidae)

2013 ◽  
Vol 103 (5) ◽  
pp. 538-546 ◽  
Author(s):  
Pedro Lorite ◽  
M. Isabel Torres ◽  
Teresa Palomeque
Keyword(s):  
Repetitive Dna ◽  
Colorado Potato Beetle ◽  
Satellite Dna ◽  
Leptinotarsa Decemlineata ◽  
Cytogenetic Study ◽  
Consensus Sequences ◽  
Repeat Units ◽  
Potato Beetle

AbstractThe Colorado potato beetle (Leptinotarsa decemlineata, family Chrysomelidae), a phytophagous insect, which feeds preferably on potatoes, constitutes a serious pest of this crop and causes extensive damage to tomatoes and eggplants. It has a remarkable ability to develop resistance quickly against insecticides and shows a diversified and flexible life history. Consequently, the control of this pest has become difficult, requiring the development of new alternative biotechnology-based strategies. Such strategies require a thorough knowledge of the beetle's genome, including the repetitive DNA. Satellite DNA (stDNA), composed of long arrays of tandemly arranged repeat units, constitutes the major component of heterochromatin and is located mainly in centromeric and telomeric chromosomal regions. We have studied two different unrelated satellite-DNA families of which the consensus sequences were 295 and 109 bp in length, named LEDE-I and LEDE-II, respectively. Both were AT-rich (70.8% and 71.6%, respectively). Predictive models of sequence-dependent DNA bending and the study of electrophoretic mobility on non-denaturing polyacrylamide gels have shown that the DNA was curved in both satellite-DNA families. Among other features, the chromosome localization of both stDNAs has been studied. In situ hybridization performed on meiotic and mitotic nuclei showed chromosomes, including the X chromosome, with zero, one, or two stDNAs. In recent years, it has been proposed that the repetitive DNA may play a key role in biological diversification processes. This is the first molecular and cytogenetic study conducted on L. decemlineata repetitive DNA and specifically on stDNA, which is one of the important constituents of eukaryotic genomes.

scholarly journals Too much too many: comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

2020 ◽  
Author(s):  
Octavio M. Palacios-Gimenez ◽  
Julia Koelman ◽  
Marc Palmada Flores ◽  
Tessa M. Bradford ◽  
Karl K. Jones ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Species Complex ◽  
Rapid Evolution ◽  
Dna Repeats ◽  
Large Genome ◽  
Chromosomal Races

BackgroundThe repeatome, the collection of repetitive DNA sequences represented by transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), is found in high proportion in organisms across the tree of life. Grasshoppers have large genomes (average 9 Gb), containing large amounts of repetitive DNA which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of the repeatome and its contribution to genome evolution, in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex.ResultsWe obtained linked-read genome assemblies of 2.73-3.27 Gb from estimated genome sizes of 4.26-5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far (the largest being two locust grasshoppers). Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs constituting 66 to 75 % per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314-463 Mb per assembly), indicating that their large genome size is likely due to similar rates of TE accumulation across the four races. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a repertoire of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex.ConclusionIn-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Although the TE and satDNA repertoires were rather similar between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.

Cloning and characterization of a transposable-like repeat in the heterochromatin of the darkling beetle Misolampus goudoti

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 769-774 ◽  
Author(s):  
Joan Pons
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Satellite Dna ◽  
Molecular Mechanisms ◽  
Repeat Unit ◽  
Nucleotide Composition ◽  
Crossing Over ◽  
Unequal Crossing Over ◽  
Darkling Beetle

A long repeat unit of the PstI family in Misolampus goudoti (Coleoptera, Tenebrionodae) is characterized in this work. The 30 sequenced units have small differences in length (consensus 1169 bp), but very similar nucleotide composition (mean 61.1% A+T). PstI repeats contain a 36-bp-long inverted repeat at both the 5′ and 3′ ends, with a fully conserved 16-bp-long motif similar to those found in class II transposable elements. However, the transposable-like PstI repeats seems to be defective, since they do not encode for any protein related with transposition. Interestingly, energetically stable hairpins resembled the structure of a miniature interspersed transposable element, suggesting that the PstI satellite DNA family in M. goudoti may have originated from an ancestral active transposable element as also described in Drosophila guanche. The presence of transposable-like structure along with the non-detection of gene conversion or unequal crossing-over events suggest that transposition could be one of the putative molecular mechanisms involved in the strong amplification and (or) homogenization of these repeats. A putative transposition of PstI repeats allowing their genomic mobility also could explain why this satellite is widely distributed to all heterochromatic regions, telomeres, pericentromeric regions, and on the Y chromosome, whereas satellites of other tenebrionids lacking transposable-like structures are restricted only to pericentromeric regions.Key words: transposable elements, MITE, satellite DNA, heterochromatin, telomere, beetle, Tenebrionidae.

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