Fluorescent in situ hybridization and characterization of the SalI family of satellite repeats in the Haliotis L. species (abalone) of the Northeast Pacific

Genome ◽  
2008 ◽  
Vol 51 (8) ◽  
pp. 570-579 ◽  
Author(s):  
Norma Karina Hernández-Ibarra ◽  
Andrew R. Leitch ◽  
Pedro Cruz ◽  
Ana M. Ibarra
Keyword(s):  
Tandem Repeats ◽  
Sequence Divergence ◽  
Satellite Repeat ◽  
Northeast Pacific ◽  
Satellite Repeats ◽  
In The Wild ◽  
High Sequence Conservation ◽  
Heterochromatin Silencing

The SalI satellite repeat previously identified in Haliotis L. (abalone) was thought to be present in H. rufescens and absent in H. fulgens . However, we show here that SalI is also found in H. fulgens and is not useful for screening hybrid individuals bred in aquaculture or occurring naturally in the wild. SalI is a family of predominantly subtelomeric tandemly repeated sequences, and sequenced clones revealed clustering to species and little intraspecific variation. Analysis of SalI sequence divergence between Haliotis species of the Northeast Pacific revealed that evolutionary distances correlate well with bathymetric and latitudinal species distributions. Analysis of the structure of the tandem repeats revealed two regions of high sequence conservation that may contain conserved transcription factor binding sites, a surprise for an apparently “non-coding” tandem repeat. We speculate that these regions might be involved in heterochromatin silencing, perhaps mediated via transcriptional activity and RNA interference. The repeats show substantial differences in their chromosomal distributions, even between individuals of the same species, indicating a dynamic organization of repeats, perhaps mediated via sequence homogenization.

scholarly journals Genome-wide characterization of satellite DNA arrays in a complex plant genome using nanopore reads

2019 ◽  
Author(s):  
Tihana Vondrak ◽  
Laura Ávila Robledillo ◽  
Petr Novák ◽  
Andrea Koblížková ◽  
Pavel Neumann ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats ◽  
Length Distribution ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Satellite Repeat ◽  
Major Satellite ◽  
Satellite Repeats ◽  
Genome Wide

AbstractBackgroundAmplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities.ResultsWe have developed a computational workflow for similarity-based detection and downstream analysis of satellite repeats in individual nanopore reads that led to genome-wide characterization of their properties. Using the satellite DNA-rich legume plantLathyrus sativusas a model, we demonstrated this approach by analyzing eleven major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73x genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of theL. sativuschromosomes, which suggests that these genome regions are favorable for satellite DNA accumulation.ConclusionsThe presented approach proved to be efficient in revealing differences in long-range organization of satellite repeats that can be used to investigate their origin and evolution in the genome.

Characterization of wheat – Secale africanum introgression lines reveals evolutionary aspects of chromosome 1R in rye

Genome ◽  
2012 ◽  
Vol 55 (11) ◽  
pp. 765-774 ◽  
Author(s):  
Meng-Ping Lei ◽  
Guang-Rong Li ◽  
Cheng Liu ◽  
Zu-Jun Yang
Keyword(s):  
Sequence Divergence ◽  
Introgression Lines ◽  
Secale Africanum ◽  
Secale Cereale L ◽  
Disease Resistance Screening ◽  
High Conservation ◽  
Chromosome 1R ◽  
Evolutionary Aspects

Wild Secale species, Secale africanum Stapf., serve as a valuable source for increasing the diversity of cultivated rye (Secale cereale L.) and provide novel genes for wheat improvement. New wheat – S. africanum chromosome 1Rafr addition, 1Rafr(1D) substitution, 1BL.1RafrS and 1DS.1RafrL translocation, and 1RafrL monotelocentric addition lines were identified by chromosome banding and in situ hybridization. Disease resistance screening revealed that chromosome 1RafrS carries resistance gene(s) to new stripe rust races. Twenty-nine molecular markers were localized on S. africanum chromosome 1Rafr by the wheat – S. africanum introgression lines. Twenty markers can also identically amplify other reported wheat – S. cereale chromosome 1R derivative lines, indicating that there is high conservation between the wild and cultivated Secale chromosome 1R. Nine markers displayed polymorphic amplification between S. africanum and S. cereale chromosome 1Rafr derivatives. The comparison of the nucleotide sequences of these polymorphic markers suggested that gene duplication and sequence divergence may have occurred among Secale species during its evolution and domestication.

scholarly journals High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-Read Technologies

2019 ◽  
Vol 36 (11) ◽  
pp. 2415-2431 ◽  
Author(s):  
Monika Cechova ◽  
Robert S Harris ◽  
Marta Tomaszkiewicz ◽  
Barbara Arbeithuber ◽  
Francesca Chiaromonte ◽  
...  
Keyword(s):  
Great Apes ◽  
Great Ape ◽  
Satellite Repeat ◽  
Satellite Sequences ◽  
Satellite Repeats ◽  
Repetitive Nature ◽  
Oxford Nanopore ◽  
Long Read ◽  
Genome Assemblies

AbstractSatellite repeats are a structural component of centromeres and telomeres, and in some instances, their divergence is known to drive speciation. Due to their highly repetitive nature, satellite sequences have been understudied and underrepresented in genome assemblies. To investigate their turnover in great apes, we studied satellite repeats of unit sizes up to 50 bp in human, chimpanzee, bonobo, gorilla, and Sumatran and Bornean orangutans, using unassembled short and long sequencing reads. The density of satellite repeats, as identified from accurate short reads (Illumina), varied greatly among great ape genomes. These were dominated by a handful of abundant repeated motifs, frequently shared among species, which formed two groups: 1) the (AATGG)n repeat (critical for heat shock response) and its derivatives; and 2) subtelomeric 32-mers involved in telomeric metabolism. Using the densities of abundant repeats, individuals could be classified into species. However, clustering did not reproduce the accepted species phylogeny, suggesting rapid repeat evolution. Several abundant repeats were enriched in males versus females; using Y chromosome assemblies or Fluorescent In Situ Hybridization, we validated their location on the Y. Finally, applying a novel computational tool, we identified many satellite repeats completely embedded within long Oxford Nanopore and Pacific Biosciences reads. Such repeats were up to 59 kb in length and consisted of perfect repeats interspersed with other similar sequences. Our results based on sequencing reads generated with three different technologies provide the first detailed characterization of great ape satellite repeats, and open new avenues for exploring their functions.

scholarly journals Identification and characterization of satellite DNAs in two-toed sloths of the genus Choloepus (Megalonychidae, Xenarthra)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Radarane Santos Sena ◽  
Pedro Heringer ◽  
Mirela Pelizaro Valeri ◽  
Valéria Socorro Pereira ◽  
Gustavo C. S. Kuhn ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Satellite Dnas ◽  
Phylogenetic Studies ◽  
Tandem Repeat Sequences ◽  
Mammalian Genomes ◽  
Living Species ◽  
Bradypus Variegatus ◽  
Identification And Characterization

Abstract Choloepus, the only extant genus of the Megalonychidae family, is composed of two living species of two-toed sloths: Choloepus didactylus and C. hoffmanni. In this work, we identified and characterized the main satellite DNAs (satDNAs) in the sequenced genomes of these two species. SATCHO1, the most abundant satDNA in both species, is composed of 117 bp tandem repeat sequences. The second most abundant satDNA, SATCHO2, is composed of ~ 2292 bp tandem repeats. Fluorescence in situ hybridization in C. hoffmanni revealed that both satDNAs are located in the centromeric regions of all chromosomes, except the X. In fact, these satDNAs present some centromeric characteristics in their sequences, such as dyad symmetries predicted to form secondary structures. PCR experiments indicated the presence of SATCHO1 sequences in two other Xenarthra species: the tree-toed sloth Bradypus variegatus and the anteater Myrmecophaga tridactyla. Nevertheless, SATCHO1 is present as large tandem arrays only in Choloepus species, thus likely representing a satDNA exclusively in this genus. Our results reveal interesting features of the satDNA landscape in Choloepus species with the potential to aid future phylogenetic studies in Xenarthra and mammalian genomes in general.

scholarly journals Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 527
Author(s):  
Nusrat Sultana ◽  
Gerhard Menzel ◽  
Tony Heitkam ◽  
Kenji K. Kojima ◽  
Weidong Bao ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Sequence Similarity ◽  
Diploid Species ◽  
Vaccinium Corymbosum ◽  
Satellite Repeat ◽  
Comprehensive Overview ◽  
Vaccinium Uliginosum ◽  
Satellite Repeats ◽  
The Impact

Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well as the tetraploid species Vaccinium corymbosum and Vaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid V. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in Vaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.

scholarly journals Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species

Agronomy ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 60 ◽  
Author(s):  
Tao Lang ◽  
Guangrong Li ◽  
Zhihui Yu ◽  
Jiwei Ma ◽  
Qiheng Chen ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats ◽  
Chromosomal Rearrangements ◽  
Wide Distribution ◽  
Fish Analysis ◽  
Satellite Repeats ◽  
Genome Wide ◽  
Rapid Sequence ◽  
Group 5

A large proportion of the genomes of grasses is comprised of tandem repeats (TRs), which include satellite DNA. A mini-satellite DNA sequence with a length of 44 bp, named Ta-3A1, was found to be highly accumulated in wheat genome, as revealed by a comprehensive sequence analysis. The physical distribution of Ta-3A1 in chromosomes 3A, 5A, 5B, 5D, and 7A of wheat was confirmed by nondenaturing fluorescence in situ hybridization (ND-FISH) after labeling the oligonucleotide probe. The analysis of monomer variants indicated that rapid sequence amplification of Ta-3A1 occurred first on chromosomes of linkage group 5, then groups 3 and 7. Comparative ND-FISH analysis suggested that rapid changes occurred in copy number and chromosomal locations of Ta-3A1 among the different species in the tribe Triticeae, which may have been associated with chromosomal rearrangements during speciation and polyploidization. The labeling and subsequent use of Ta-3A1 by ND-FISH may assist in the precise identification and documentation of novel wheat germplasm engineered by chromosome manipulation.

scholarly journals Identification and characterization of abundant repetitive sequences in Allium cepa

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jiaping Fu ◽  
Hao Zhang ◽  
Fengling Guo ◽  
Lu Ma ◽  
Jinping Wu ◽  
...  
Keyword(s):  
Allium Cepa ◽  
Repetitive Sequences ◽  
Economic Significance ◽  
Satellite Repeats ◽  
Production Value ◽  
Next Generation Sequencing Ngs ◽  
Low Coverage ◽  
Identification And Characterization

AbstractSpecies of the genus Allium are well known for their large genomes. Allium cepa is of great economic significance. Among vegetables, it ranks second after tomato in terms of the global production value. However, there is limited genomics information available on A. cepa. In this study, we sequenced the A. cepa genome at low-coverage and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. Nearly 92% of 16 Gb haploid onion genome were defined as repetitive sequences, organized in 162 clusters of at least 0.01 percent of the genome. Of these, a proportion representing 40.5% of the genome were further analyzed in detail to obtain an overview of representative repetitive elements present in the A. cepa genome. Few representative satellite repeats were studied by fluorescence in situ hybridization (FISH) and southern blotting. These results provided a basis for evolutionary cytogenomics within the Allium genus.

Characterization of two families of tandem repeated DNA sequences in Potamogeton pectinatus L.

Genome ◽  
2008 ◽  
Vol 51 (11) ◽  
pp. 871-877 ◽  
Author(s):  
Marilena Ceccarelli ◽  
Vania Sarri ◽  
Stefania Minelli ◽  
Maria Teresa Gelati
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Potamogeton Pectinatus ◽  
Target Sequence ◽  
Entire Genome ◽  
Diploid Parent

DNA sequences belonging to two families of tandem repeats, PpeRsa1 (362–364 bp in length, 62% A+T residues) and PpeRsa2 (355–359 bp in length, 59% A+T residues), have been isolated from the Potamogeton pectinatus L. genome. The two sequence families do not share significant nucleotide sequence similarity, even if an evolutionary relationship between them could be assumed. The comparison of the cleaving activity of isoschizomeres that are either sensitive or insensitive to methylation of cytosine residues in the target sequence revealed high methylation in both sequence families. The copy number per 1C DNA of PpeRsa1- and PpeRsa2-related sequences is estimated to be 4.92 × 104 and 7.96 × 104, respectively. Taken together, these sequences account for about 7.5% of the entire genome of P. pectinatus. The chromosomal organization of these sequences was investigated by fluorescent in situ hybridization. PpeRsa1 and PpeRsa2 repeats found related sequences in 52 chromosomes of the P. pectinatus complement (2n = 78). The related sequences were localized around the centromeres and at the chromosome ends in three pairs of chromosomes, while they were found only at the chromosome ends in the remaining pairs. Twenty-six chromosomes did not show any hybridization signal. The hypothesis that the species is a hybrid between a diploid parent and an allotetraploid parent is put forward.

scholarly journals From STRs to SNPs via ddRAD-seq: geographic assignment of confiscated tortoises at reduced costs

2021 ◽  
Author(s):  
Roberto Biello ◽  
Mauro Zampiglia ◽  
Silvia Fuselli ◽  
Giulia Fabbri ◽  
Roberta Bisconti ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Low Cost ◽  
Geographic Origin ◽  
Unknown Origin ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
In The Wild ◽  
Testudo Hermanni ◽  
Source Populations

Assigning individuals to their source populations is crucial for conservation research, especially for endangered species threatened by illegal trade and translocations. Genetic assignment can be achieved with different types of molecular markers, but technical advantages and cost saving are recently promoting the shift from short tandem repeats (STRs) to single nucleotide polymorphisms (SNPs). Here, we designed, developed, and tested a small panel of SNPs for cost-effective geographic assignment of individuals with unknown origin of the endangered Mediterranean tortoise Testudo hermanni. We started by performing a ddRAD-seq experiment on 70 wild individuals of T. hermanni from 38 locations. Results obtained using 3,182 SNPs are comparable to those previously obtained using STR markers in terms of genetic structure and power to identify the macro-area of origin. However, our SNPs revealed further insights into the substructure in Western populations, especially in Southern Italy. A small panel of highly informative SNPs was then selected and tested by genotyping 190 individuals using the KASP genotyping chemistry. All the samples from wild populations of known geographic origin were genetically re-assigned with high accuracy to the original population. This reduced SNPs panel represents an efficient molecular tool that enables individuals to be genotyped at low cost (less than €15 per sample) for geographical assignment and identification of hybrids. This information is crucial for the management in-situ of confiscated animals and their possible re-allocation in the wild. Our methodological pipeline can easily be extended to other species.

scholarly journals Molecular Characterization of a Family of Tandemly Repeated DNA Sequences, TR-1, in Heterochromatic Knobs of Maize and Its Relatives

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1087-1097 ◽  
Author(s):  
F C Hsu ◽  
C J Wang ◽  
C M Chen ◽  
H Y Hu ◽  
C C Chen
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
B Chromosome ◽  
Repeated Dna ◽  
Sequence Comparisons ◽  
Repeat Units ◽  
Entire Sequence ◽  
Single Sequence

Abstract Two families of tandem repeats, 180-bp and TR-1, have been found in the knobs of maize. In this study, we isolated 59 clones belonging to the TR-1 family from maize and teosinte. Southern hybridization and sequence analysis revealed that members of this family are composed of three basic sequences, A (67 bp); B (184 bp) or its variants B′ (184 bp), 2/3B (115 bp), 2/3B′ (115 bp); and C (108 bp), which are arranged in various combinations to produce repeat units that are multiples of ∼180 bp. The molecular structure of TR-1 elements suggests that: (1) the B component may evolve from the 180-bp knob repeat as a result of mutations during evolution; (2) B′ may originate from B through lateral amplification accompanied by base-pair changes; (3) C plus A may be a single sequence that is added to B and B′, probably via nonhomologous recombination; and (4) 69 bp at the 3′ end of B or B′, and the entire sequence of C can be removed from the elements by an unknown mechanism. Sequence comparisons showed partial homologies between TR-1 elements and two centromeric sequences (B repeats) of the supernumerary B chromosome. This result, together with the finding of other investigators that the B repeat is also fragmentarily homologous to the 180-bp repeat, suggests that the B repeat is derived from knob repeats in A chromosomes, which subsequently become structurally modified. Fluorescence in situ hybridization localized the B repeat to the B centromere and the 180-bp and TR-1 repeats to the proximal heterochromatin knob on the B chromosome.

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