Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development

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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Autonomously Replicating Macronuclear DNA Pieces Are the Physical Basis of Genetic Coassortment Groups in Tetrahymena thermophila

Genetics ◽

10.1093/genetics/155.3.1119 ◽

2000 ◽

Vol 155 (3) ◽

pp. 1119-1125

Author(s):

Laura Wong ◽

Lana Klionsky ◽

Steve Wickert ◽

Virginia Merriam ◽

Eduardo Orias ◽

...

Keyword(s):

Random Distribution ◽

Tetrahymena Thermophila ◽

Physical Basis ◽

The Other ◽

Site Specific ◽

Phenotypic Assortment ◽

Somatic Genome

Abstract The macronucleus of the ciliate Tetrahymena thermophila contains a fragmented somatic genome consisting of several hundred identifiable chromosome pieces. These pieces are generated by site-specific fragmentation of the germline chromosomes and most of them are represented at an average of 45 copies per macronucleus. In the course of successive divisions of an initially heterozygous macronucleus, the random distribution of alleles of loci carried on these copies eventually generates macronuclei that are pure for one allele or the other. This phenomenon is called phenotypic assortment. We have previously reported the existence of loci that assort together (coassort) and hypothesized that these loci reside on the same macronuclear piece. The work reported here provides new, rigorous genetic support for the hypothesis that macronuclear autonomously replicating chromosome pieces are the physical basis of coassortment groups. Thus, coassortment allows the mapping of the somatic genome by purely genetic means. The data also strongly suggest that the random distribution of alleles in the Tetrahymena macronucleus is due to the random distribution of the MAC chromosome pieces that carry them.

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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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