Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes

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.

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Asymmetrical canina meiosis is accompanied by the expansion of a pericentromeric satellite in non-recombining univalent chromosomes in the genus Rosa

Annals of Botany ◽

10.1093/aob/mcaa028 ◽

2020 ◽

Vol 125 (7) ◽

pp. 1025-1038 ◽

Cited By ~ 1

Author(s):

Jana Lunerová ◽

Veit Herklotz ◽

Melanie Laudien ◽

Radka Vozárová ◽

Marco Groth ◽

...

Keyword(s):

High Throughput Sequencing ◽

Diploid Species ◽

Mitotic Cell ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Satellite Repeat ◽

Meiotic Chromosomes ◽

High Throughput Sequencing Data ◽

Satellite Repeats ◽

And Cluster Analysis

Abstract Background and Aims Despite their abundant odd-ploidy (2n = 5x = 35), dogroses (Rosa sect. Caninae) are capable of sexual reproduction due to their unique meiosis. During canina meiosis, two sets of chromosomes form bivalents and are transmitted by male and female gametes, whereas the remaining chromosomes form univalents and are exclusively transmitted by the egg cells. Thus, the evolution of chromosomes is expected to be driven by their behaviour during meiosis. Methods To gain insight into differential chromosome evolution, fluorescence in situ hybridization was conducted for mitotic and meiotic chromosomes in four dogroses (two subsections) using satellite and ribosomal DNA probes. By exploiting high-throughput sequencing data, we determined the abundance and diversity of the satellite repeats in the genus Rosa by analysing 20 pentaploid, tetraploid and diploid species in total. Key Results A pericentromeric satellite repeat, CANR4, was found in all members of the genus Rosa, including the basal subgenera Hulthemia and Hesperhodos. The satellite was distributed across multiple chromosomes (5–20 sites per mitotic cell), and its genomic abundance was higher in pentaploid dogroses (2.3 %) than in non-dogrose species (1.3 %). In dogrose meiosis, univalent chromosomes were markedly enriched in CANR4 repeats based on both the number and the intensity of the signals compared to bivalent-forming chromosomes. Single-nucleotide polymorphisms and cluster analysis revealed high intragenomic homogeneity of the satellite in dogrose genomes. Conclusions The CANR4 satellite arose early in the evolution of the genus Rosa. Its high content and extraordinary homogeneity in dogrose genomes is explained by its recent amplification in non-recombining chromosomes. We hypothesize that satellite DNA expansion may contribute to the divergence of univalent chromosomes in Rosa species with non-symmetrical meiosis.

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Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

BMC Plant Biology ◽

10.1186/s12870-021-03194-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lianyu Lin ◽

Anupma Sharma ◽

Qingyi Yu

Keyword(s):

Transposable Elements ◽

Inverted Repeat ◽

Sequence Similarity ◽

Genome Structure ◽

Terminal Inverted Repeat ◽

Essential Information ◽

Dna Transposon ◽

Genome Wide ◽

Identification And Characterization

Abstract Background Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. Results We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. Conclusions Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.

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

10.1101/677575 ◽

2019 ◽

Cited By ~ 2

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.

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Cloning and characterization of serpin-like genes from the striped rice stem borer, Chilo suppressalis

Genome ◽

10.1139/gen-2013-0051 ◽

2013 ◽

Vol 56 (6) ◽

pp. 359-366 ◽

Cited By ~ 2

Author(s):

Zhao-Yu Ge ◽

Pin-Jun Wan ◽

Xiong-Feng Cheng ◽

Yang Zhang ◽

Guo-Qing Li ◽

...

Keyword(s):

Proteinase Inhibitors ◽

Sequence Similarity ◽

Serine Proteinase ◽

Stem Borer ◽

Chilo Suppressalis ◽

Specific Expression ◽

Rice Stem Borer ◽

Gut Physiology ◽

The Impact

Serpins, also called serine proteinase inhibitors, are widely distributed in eukaryotes. In insects, serpins play important roles in regulating immune responses, gut physiology, and other processes. Here, we report the cloning and characterization of 12 serpin-like cDNAs from the striped rice stem borer (Chilo suppressalis), a major rice pest. The putative proteins share significant sequence similarity with known insect serpins, especially those from lepidopterons. Analysis of functional domains revealed that nine of the cloned serpins are putative trypsin- or chymotrypsin-like inhibitors; two are mixed-type serpins that may act as inhibitors for trypsins, elastases, or thrombin; and the remaining one is truncate. The potential functions of these serpins in interacting with host plants were also investigated by analyzing tissue-specific expression and the impact of different host plant genotypes on gene expression. Our results provide a foundation for future studies on the role of serpins in gut physiology in the striped rice stem borer, and also useful information for comparative analyses of serpins from different insect species.

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

Genome ◽

10.1139/g08-041 ◽

2008 ◽

Vol 51 (8) ◽

pp. 570-579 ◽

Cited By ~ 7

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.

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The Analyses of Learning Strategies in English as a Second Language: Theoretical Classification and Measurement Test

Voices of English Language Education Society ◽

10.29408/veles.v4i2.2199 ◽

2020 ◽

Vol 4 (2) ◽

pp. 118-129

Author(s):

Asti Gumartifa ◽

◽

Indah Windra Dwie Agustiani

Keyword(s):

Language Learning ◽

Learning Outcomes ◽

Learning Strategies ◽

Learning Process ◽

English Learners ◽

English Language ◽

Point Of View ◽

Effective Learning ◽

The Impact

Gaining English language learning effectively has been discussed all years long. Similarly, Learners have various troubles outcomes in the learning process. Creating a joyful and comfortable situation must be considered by learners. Thus, the implementation of effective learning strategies is certainly necessary for English learners. This descriptive study has two purposes: first, to introduce the classification and characterization of learning strategies such as; memory, cognitive, metacognitive, compensation, social, and affective strategies that are used by learners in the classroom and second, it provides some questionnaires item based on Strategy of Inventory for Language Learning (SILL) version 5.0 that can be used to examine the frequency of students’ learning strategies in the learning process. The summary of this study explains and discusses the researchers’ point of view on the impact of learning outcomes by learning strategies used. Finally, utilizing appropriate learning strategies are certainly beneficial for both teachers and learners to achieve the learning target effectively.

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Modulation of Gut Microbiota and Oxidative Status by β-Carotene in Late Pregnant Sows

Frontiers in Nutrition ◽

10.3389/fnut.2020.612875 ◽

2020 ◽

Vol 7 ◽

Author(s):

Xupeng Yuan ◽

Jiahao Yan ◽

Ruizhi Hu ◽

Yanli Li ◽

Ying Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Dietary Supplementation ◽

Basal Diet ◽

Fecal Microbiota ◽

Control Group ◽

Metabolic Activities ◽

The Impact ◽

Positive Effect ◽

Β Carotene

Recent evidences suggest that gut microbiota plays an important role in regulating physiological and metabolic activities of pregnant sows, and β-carotene has a potentially positive effect on reproduction, but the impact of β-carotene on gut microbiota in pregnant sows remains unknown. This study aimed to explore the effect and mechanisms of β-carotene on the reproductive performance of sows from the aspect of gut microbiota. A total of 48 hybrid pregnant sows (Landrace × Yorkshire) with similar parity were randomly allocated into three groups (n = 16) and fed with a basal diet or a diet containing 30 or 90 mg/kg of β-carotene from day 90 of gestation until parturition. Dietary supplementation of 30 or 90 mg/kg β-carotene increased the number of live birth to 11.82 ± 1.54 and 12.29 ± 2.09, respectively, while the control group was 11.00 ± 1.41 (P = 0.201). Moreover, β-carotene increased significantly the serum nitric oxide (NO) level and glutathione peroxidase (GSH-Px) activity (P < 0.05). Characterization of fecal microbiota revealed that 90 mg/kg β-carotene increased the diversity of the gut flora (P < 0.05). In particular, β-carotene decreased the relative abundance of Firmicutes including Lachnospiraceae AC2044 group, Lachnospiraceae NK4B4 group and Ruminococcaceae UCG-008, but enriched Proteobacteria including Bilophila and Sutterella, and Actinobacteria including Corynebacterium and Corynebacterium 1 which are related to NO synthesis. These data demonstrated that dietary supplementation of β-carotene may increase antioxidant enzyme activity and NO, an important vasodilator to promote the neonatal blood circulation, through regulating gut microbiota in sows.

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Clonal approaches to understanding the impact of mutations on hematologic disease development

Blood ◽

10.1182/blood-2018-11-835405 ◽

2019 ◽

Vol 133 (13) ◽

pp. 1436-1445 ◽

Cited By ~ 6

Author(s):

Jyoti Nangalia ◽

Emily Mitchell ◽

Anthony R. Green

Keyword(s):

Somatic Mutations ◽

Clonal Selection ◽

Single Cells ◽

Driver Mutations ◽

Great Promise ◽

Tumor Evolution ◽

Disease Development ◽

Hematopoietic Tissue ◽

The Impact

Abstract Interrogation of hematopoietic tissue at the clonal level has a rich history spanning over 50 years, and has provided critical insights into both normal and malignant hematopoiesis. Characterization of chromosomes identified some of the first genetic links to cancer with the discovery of chromosomal translocations in association with many hematological neoplasms. The unique accessibility of hematopoietic tissue and the ability to clonally expand hematopoietic progenitors in vitro has provided fundamental insights into the cellular hierarchy of normal hematopoiesis, as well as the functional impact of driver mutations in disease. Transplantation assays in murine models have enabled cellular assessment of the functional consequences of somatic mutations in vivo. Most recently, next-generation sequencing–based assays have shown great promise in allowing multi-“omic” characterization of single cells. Here, we review how clonal approaches have advanced our understanding of disease development, focusing on the acquisition of somatic mutations, clonal selection, driver mutation cooperation, and tumor evolution.

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Comprehensive Overview of Sleep Disorders in Patients with Chronic Liver Disease

Brain Sciences ◽

10.3390/brainsci11020142 ◽

2021 ◽

Vol 11 (2) ◽

pp. 142

Author(s):

Oana-Mihaela Plotogea ◽

Madalina Ilie ◽

Simona Bungau ◽

Alexandru Laurentiu Chiotoroiu ◽

Ana Maria Alexandra Stanescu ◽

...

Keyword(s):

Sleep Disorders ◽

Daily Practice ◽

Chronic Liver ◽

Asian Countries ◽

Chronic Liver Diseases ◽

Comprehensive Overview ◽

The Usa ◽

The Impact ◽

Reliable Methods

The impact of sleep disorders (SDs) on patients with chronic liver diseases (CLD) is tremendous. SDs are frequently encountered among these patients and interfere with their quality of life. This review aims to present the data available so far about the prevalence, phenotypes, and proposed pathophysiological mechanisms of SDs in CLD. Moreover, we proposed to search the literature regarding the most reliable methods to assess SDs and the possible therapeutic options in patients with CLD. The main results of this review show that when it comes to prevalence, the percentages reported vary widely between studies performed among populations from the USA or Europe and those coming from Asian countries. Furthermore, it has been proven that SDs may also be present in the absence of neurocognitive disorders attributable to hepatic encephalopathy (HE), which contradicts traditional suppositions where SDs were considered part of the clinical scenario of HE. Currently, there are no specific recommendations or protocols to assess SDs in CLD patients and data about the therapeutic management are limited. Taking into consideration their impact, a protocol for diagnosing and managing SDs should be developed and included in the daily practice of hepatologists.

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Exploring the Characteristics and Influencing Factors of Leisure Walking Based on the Demand of Behavior

Sustainability ◽

10.3390/su13084105 ◽

2021 ◽

Vol 13 (8) ◽

pp. 4105

Author(s):

Yupei Jiang ◽

Honghu Sun

Keyword(s):

Health Benefits ◽

Health Benefit ◽

Public Health Research ◽

Space Time ◽

Time Behavior ◽

Walking Behavior ◽

Face To Face ◽

Residential Neighborhood ◽

The Impact

Leisure walking has been an important topic in space-time behavior and public health research. However, prior studies pay little attention to the integration and the characterization of diverse and multilevel demands of leisure walking. This study constructs a theoretical framework of leisure walking behavior demands from three different dimensions and levels of activity participation, space-time opportunity, and health benefit. On this basis, through a face-to-face survey in Nanjing, China (N = 1168, 2017–2018 data), this study quantitatively analyzes the characteristics of leisure walking demands, as well as the impact of the built environment and individual factors on it. The results show that residents have a high demand for participation and health benefits of leisure walking. The residential neighborhood provides more space opportunities for leisure walking, but there is a certain constraint on the choice of walking time. Residential neighborhood with medium or large parks is more likely to satisfy residents’ demands for engaging in leisure walking and obtaining high health benefits, while neighborhood with a high density of walking paths tends to limit the satisfaction of demands for space opportunity and health benefit. For residents aged 36 and above, married, or retired, their diverse demands for leisure walking are more likely to be fulfilled, while those with high education, medium-high individual income, general and above health status, or children (<18 years) are less likely to be fulfilled. These finding that can have important implications for the healthy neighborhood by fully considering diverse and multilevel demands of leisure walking behavior.

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