Repetitive Sequences in Sesame Genome

Stingless bees of the genus Melipona are subdivided into 4 subgenera called Eomelipona, Melikerria, Melipona sensu stricto, and Michmelia according to species morphology. Cytogenetically, the species of the genus Melipona show variation in the amount and distribution of heterochromatin along their chromosomes and can be separated into 2 groups: the first with low content of heterochromatin and the second with high content of heterochromatin. These heterochromatin patterns and the number of chromosomes are characteristics exclusive to Melipona karyotypes that distinguish them from the other genera of the Meliponini. To better understand the karyotype organization in Melipona and the relationship among the subgenera, we mapped repetitive sequences and analyzed previously reported cytogenetic data with the aim to identify cytogenetic markers to be used for investigating the phylogenetic relationships and chromosome evolution in the genus. In general, Melipona species have 2n = 18 chromosomes, and the species of each subgenus share the same characteristics in relation to heterochromatin regions, DAPI/CMA3 fluorophores, and the number and distribution of 18S rDNA sites. Microsatellites were observed only in euchromatin regions, whereas the (TTAGG)6 repeats were found at telomeric sites in both groups. Our data indicate that in addition to the chromosome number, the karyotypes in Melipona could be separated into 2 groups that are characterized by conserved cytogenetic features and patterns that generally are shared by species within each subgenus, which may reflect evolutionary constraints. Our results agree with the morphological separation of the Melipona into 4 subgenera, suggesting that they must be independent evolutionary lineages.

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Non-repetitive sequences

Mathematical Proceedings of the Cambridge Philosophical Society ◽

10.1017/s0305004100046077 ◽

1970 ◽

Vol 68 (2) ◽

pp. 267-274 ◽

Cited By ~ 71

Author(s):

P. A. B. Pleasants

Keyword(s):

Repetitive Sequences ◽

Finite Set ◽

Infinite Sequences

This note is concerned with infinite sequences whose terms are chosen from a finite set of symbols. A segment of such a sequence is a set of one or more consecutive terms, and a repetition is a pair of finite segments that are adjacent and identical. A non-repetitive sequence is one that contains no repetitions.

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The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)

BMC Genomics ◽

10.1186/s12864-021-07558-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Huai-Jun Xue ◽

Yi-Wei Niu ◽

Kari A. Segraves ◽

Rui-E Nie ◽

Ya-Jing Hao ◽

...

Keyword(s):

Host Plant ◽

Plant Cell Wall ◽

Flea Beetle ◽

Repetitive Sequences ◽

Draft Genome ◽

Gene Families ◽

Ecological Speciation ◽

Secondary Chemistry ◽

Host Plant Specialization ◽

Insight Into

Abstract Background Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far. Results The genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation. Conclusions The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.

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Comparative study on the physical mapping of ribosomal genes and repetitive sequences in Friesella schrottkyi (Friese, 1900) (Hymenoptera: Apidae, Meliponini)

Zoologischer Anzeiger ◽

10.1016/j.jcz.2021.04.006 ◽

2021 ◽

Author(s):

Arthur Mayrink Elizeu ◽

Natalia Martins Travenzoli ◽

Riudo de Paiva Ferreira ◽

Denilce Meneses Lopes ◽

Mara Garcia Tavares

Keyword(s):

Comparative Study ◽

Physical Mapping ◽

Repetitive Sequences ◽

Ribosomal Genes ◽

Friesella Schrottkyi

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Assessment of the Telomere Length and Its Effect on the Symptomatology of Parkinson’s Disease

Antioxidants ◽

10.3390/antiox10010137 ◽

2021 ◽

Vol 10 (1) ◽

pp. 137

Author(s):

Tina Levstek ◽

Sara Redenšek ◽

Maja Trošt ◽

Vita Dolžan ◽

Katarina Trebušak Podkrajšek

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Telomere Length ◽

Repetitive Sequences ◽

Housekeeping Gene ◽

Cellular Aging ◽

Brain Diseases ◽

Motor Complications ◽

Telomere Attrition ◽

Significant Difference

Telomeres, which are repetitive sequences that cap the end of the chromosomes, shorten with each cell division. Besides cellular aging, there are several other factors that influence telomere length (TL), in particular, oxidative stress and inflammation, which play an important role in the pathogenesis of neurodegenerative brain diseases including Parkinson’s disease (PD). So far, the majority of studies have not demonstrated a significant difference in TL between PD patients and healthy individuals. However, studies investigating the effect of TL on the symptomatology and disease progression of PD are scarce, and thus, warranted. We analyzed TL of peripheral blood cells in a sample of 204 PD patients without concomitant autoimmune diseases and analyzed its association with several PD related phenotypes. Monochrome multiplex quantitative PCR (mmqPCR) was used to determine relative TL given as a ratio of the amount of DNA between the telomere and albumin as the housekeeping gene. We found a significant difference in the relative TL between PD patients with and without dementia, where shorter TL presented higher risk for dementia (p = 0.024). However, the correlation was not significant after adjustment for clinical factors (p = 0.509). We found no correlations between TLs and the dose of dopaminergic therapy when the analysis was adjusted for genetic variability in inflammatory or oxidative factors. In addition, TL influenced time to onset of motor complications after levodopa treatment initiation (p = 0.0134), but the association did not remain significant after adjustment for age at inclusion and disease duration (p = 0.0781). Based on the results of our study we conclude that TL contributes to certain PD-related phenotypes, although it may not have a major role in directing the course of the disease. Nevertheless, this expends currently limited knowledge regarding the association of the telomere attrition and the disease severity or motor complications in Parkinson’s disease.

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Chromosomal Map of the Model LegumeLotus japonicus

Genetics ◽

10.1093/genetics/161.4.1661 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1661-1672 ◽

Cited By ~ 7

Author(s):

Andrea Pedrosa ◽

Niels Sandal ◽

Jens Stougaard ◽

Dieter Schweizer ◽

Andreas Bachmair

Keyword(s):

Repetitive Sequences ◽

Lotus Japonicus ◽

Chromosome Complement ◽

Linkage Groups ◽

Closely Related Species ◽

F1 Hybrid ◽

Bac Clones ◽

Genomic Regions ◽

Chromosomal Map

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

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Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

International Journal of Molecular Sciences ◽

10.3390/ijms22094707 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4707

Author(s):

Mariana Lopes ◽

Sandra Louzada ◽

Margarida Gama-Carvalho ◽

Raquel Chaves

Keyword(s):

Human Genome ◽

Satellite Dna ◽

Repetitive Sequences ◽

Nucleotide Composition ◽

Genomic Component ◽

Genomic Studies ◽

Human Genomic ◽

Definition Of ◽

High Degree

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.

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Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development

Horticulture Research ◽

10.1038/s41438-021-00487-1 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Anzhen Fu ◽

Qing Wang ◽

Jianlou Mu ◽

Lili Ma ◽

Changlong Wen ◽

...

Keyword(s):

Fruit Development ◽

Repetitive Sequences ◽

Genetic Research ◽

Future Research ◽

Agricultural Crop ◽

Protein Coding ◽

Third Generation Sequencing ◽

Sechium Edule ◽

Generation Sequencing ◽

Cucurbitaceae Family

AbstractChayote (Sechium edule) is an agricultural crop in the Cucurbitaceae family that is rich in bioactive components. To enhance genetic research on chayote, we used Nanopore third-generation sequencing combined with Hi–C data to assemble a draft chayote genome. A chromosome-level assembly anchored on 14 chromosomes (N50 contig and scaffold sizes of 8.40 and 46.56 Mb, respectively) estimated the genome size as 606.42 Mb, which is large for the Cucurbitaceae, with 65.94% (401.08 Mb) of the genome comprising repetitive sequences; 28,237 protein-coding genes were predicted. Comparative genome analysis indicated that chayote and snake gourd diverged from sponge gourd and that a whole-genome duplication (WGD) event occurred in chayote at 25 ± 4 Mya. Transcriptional and metabolic analysis revealed genes involved in fruit texture, pigment, flavor, flavonoids, antioxidants, and plant hormones during chayote fruit development. The analysis of the genome, transcriptome, and metabolome provides insights into chayote evolution and lays the groundwork for future research on fruit and tuber development and genetic improvements in chayote.

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In Vivo and In Vitro Assays Evaluating the Biological Activity of Taurine, Glucose and Energetic Beverages

Molecules ◽

10.3390/molecules26082198 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2198

Author(s):

Marcos Mateo-Fernández ◽

Fernando Valenzuela-Gómez ◽

Rafael Font ◽

Mercedes Del Río-Celestino ◽

Tania Merinas-Amo ◽

...

Keyword(s):

Dna Damage ◽

Drosophila Melanogaster ◽

Biological Activity ◽

Biological Effects ◽

Methylation Status ◽

Repetitive Sequences ◽

Energy Drinks ◽

Red Bull

Taurine is one of the main ingredients used in energy drinks which are highly consumed in adolescents for their sugary taste and stimulating effect. With energy drinks becoming a worldwide phenomenon, the biological effects of these beverages must be evaluated in order to fully comprehend the potential impact of these products on the health due to the fact nutrition is closely related to science since the population consumes food to prevent certain diseases. Therefore, the aim of this study was to evaluate the biological effects of taurine, glucose, classic Red Bull® and sugar-free Red Bull® in order to check the food safety and the nutraceutical potential of these compounds, characterising different endpoints: (i) Toxicology, antitoxicology, genotoxicology and life expectancy assays were performed in the Drosophila melanogaster model organism; (ii) The in vitro chemopreventive activity of testing compounds was determined by assessing their cytotoxicity, the proapoptotic DNA-damage capability to induce internucleosomal fragmentation, the strand breaks activity and the modulator role on the methylation status of genomic repetitive sequences of HL-60 promyelocytic cells. Whereas none tested compounds showed toxic or genotoxic effect, all tested compounds exerted antitoxic and antigenotoxic activity in Drosophila. Glucose, classic Red Bull® and sugar-free Red Bull® were cytotoxic in HL-60 cell line. Classic Red Bull® induced DNA internucleosomal fragmentation although none of them exhibited DNA damage on human leukaemia cells. In conclusion, the tested compounds are safe on Drosophila melanogaster and classic Red Bull® could overall possess nutraceutical potential in the in vivo and in vitro model used in this study. Besides, taurine could holistically be one of the bioactive compounds responsible for the biological activity of classic Red Bull®.

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