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Diversification, evolution and methylation of short interspersed nuclear element families in sugar beet and related Amaranthaceae species

https://doi.org/10.1111/tpj.13103
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf01253964openalex-snapshot
Physical mapping of rRNA genes by fluorescent in-situ hybridization and structural analysis of 5S rRNA genes and intergenic spacer sequences in sugar beet (Beta vulgaris)
inferredcites →https://doi.org/10.1007/s00239-004-0259-5openalex-snapshot
BoS: A Large and Diverse Family of Short Interspersed Elements (SINEs) in Brassica oleracea
inferredcites →https://doi.org/10.1007/s00299-013-1468-4openalex-snapshot
Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae)
inferredcites →https://doi.org/10.1007/s11103-006-0026-7openalex-snapshot
A SINE Family Widely Distributed in the Plant Kingdom and its Evolutionary History
inferredcites →https://doi.org/10.1007/s11103-009-9542-6openalex-snapshot
An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris
inferredcites →https://doi.org/10.1016/0003-2697(90)90595-zopenalex-snapshot
Molecular cloning: A laboratory manual
inferredcites →https://doi.org/10.1016/0168-9525(89)90039-5openalex-snapshot
Eukaryotic transposable elements and genome evolution
inferredcites →https://doi.org/10.1016/j.cub.2007.01.009openalex-snapshot
The SRA Methyl-Cytosine-Binding Domain Links DNA and Histone Methylation
inferredcites →https://doi.org/10.1016/j.gene.2010.01.003openalex-snapshot
Jumping genes and epigenetics: Towards new species
inferredcites →https://doi.org/10.1016/j.gene.2011.01.020openalex-snapshot
Novel SINEs families in Medicago truncatula and Lotus japonicus: Bioinformatic analysis
inferredcites →https://doi.org/10.1016/s1360-1385(98)01232-1openalex-snapshot
Activation of plant retrotransposons under stress conditions
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/hdy.2010.52openalex-snapshot
Repeat elements and the Arabidopsis DNA methylation landscape
inferredcites →https://doi.org/10.1038/nature06745openalex-snapshot
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
inferredcites →https://doi.org/10.1038/nature12817openalex-snapshot
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)
inferredcites →https://doi.org/10.1038/nrg2072openalex-snapshot
Transposable elements and the epigenetic regulation of the genome
inferredcites →https://doi.org/10.1038/nrg2165openalex-snapshot
A unified classification system for eukaryotic transposable elements
inferredcites →https://doi.org/10.1038/nrg2719openalex-snapshot
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
inferredcites →https://doi.org/10.1038/nrg3374openalex-snapshot
How important are transposons for plant evolution?
inferredcites →https://doi.org/10.1073/pnas.81.24.8014openalex-snapshot
Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
inferredcites →https://doi.org/10.1080/10635150601047843openalex-snapshot
Short Interspersed Elements (SINEs) in Plants: Origin, Classification, and Use as Phylogenetic Markers
inferredcites →https://doi.org/10.1093/bioinformatics/btr167openalex-snapshot
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
inferredcites →https://doi.org/10.1093/bioinformatics/bts199openalex-snapshot
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
inferredcites →https://doi.org/10.1093/gbe/evt141openalex-snapshot
Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity
inferredcites →https://doi.org/10.1093/jhered/93.1.77openalex-snapshot
MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs
inferredcites →https://doi.org/10.1093/molbev/msi188openalex-snapshot
Evolutionary Diversity and Potential Recombinogenic Role of Integration Targets of Non-LTR Retrotransposons
inferredcites →https://doi.org/10.1093/molbev/msm092openalex-snapshot
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
inferredcites →https://doi.org/10.1093/nar/29.2.573openalex-snapshot
Target DNA chromatinization modulates nicking by L1 endonuclease
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkn772openalex-snapshot
tRNAdb 2009: compilation of tRNA sequences and tRNA genes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003778openalex-snapshot
The Evolutionary Origin and Genomic Organization of SINEs in Arabidopsis thaliana
inferredcites →https://doi.org/10.1101/gad.1667808openalex-snapshot
Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading
inferredcites →https://doi.org/10.1101/gr.091678.109openalex-snapshot
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
inferredcites →https://doi.org/10.1101/gr.146985.112openalex-snapshot
CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
inferredcites →https://doi.org/10.1101/gr.3421505openalex-snapshot
Analysis of 5′ junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5′-end attachment requiring microhomology-mediated end-joining
inferredcites →https://doi.org/10.1101/gr.384802openalex-snapshot
Active Alu Element “A-Tails”: Size Does Matter
inferredcites →https://doi.org/10.1105/tpc.111.088682openalex-snapshot
Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes
inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot
Matplotlib: A 2D Graphics Environment
inferredcites →https://doi.org/10.1111/j.1574-6941.2006.00060.xopenalex-snapshot
Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea
inferredcites →https://doi.org/10.1111/tpj.12285openalex-snapshot
Genome‐wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat
inferredcites →https://doi.org/10.1111/tpj.12519openalex-snapshot
The CHH motif in sugar beet satellite DNA : a modulator for cytosine methylation
inferredcites →https://doi.org/10.1111/tpj.12565openalex-snapshot
Profiling of extensively diversified plant LINE s reveals distinct plant‐specific subclades
inferredcites →https://doi.org/10.1139/g00-058openalex-snapshot
Retrotransposon activation followed by rapid repression in introgressed rice plants
inferredcites →https://doi.org/10.1146/annurev-arplant-050213-035811openalex-snapshot
The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes
inferredcites →https://doi.org/10.1146/annurev-genet-110711-155616openalex-snapshot
Active Transposition in Genomes
inferredcites →https://doi.org/10.1146/annurev.arplant.59.032607.092744openalex-snapshot
Epigenetic Regulation of Transposable Elements in Plants
inferredcites →https://doi.org/10.1159/000084981openalex-snapshot
SINEs and LINEs: symbionts of eukaryotic genomes with a common tail
inferredcites →https://doi.org/10.1266/ggs.76.169openalex-snapshot
Identification and structural analysis of SINE elements in the Arabidopsis thaliana genome.
inferredcites →https://doi.org/10.1371/journal.pgen.1000732openalex-snapshot
Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome
inferredcites →https://doi.org/10.2307/25065529openalex-snapshot
Understanding Mediterranean‐Californian disjunctions: molecular evidence from Chenopodiaceae‐Betoideae
inferredcites →https://doi.org/10.6026/97320630007276openalex-snapshot
Mapping and analysis of the LINE and SINE type of repetitive elements in rice

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4460655openalex-extracted
Antioxidant and Cytotoxic Effects of the Bioactive Compounds of Fodder Beet (Beta Vulgaris VAR. Crassa) Against Mcf-7 and Hela Cell Cultures
inferred← citeshttps://doi.org/10.1002/9781119521358.ch5openalex-snapshot
Sugar Beet Breeding
inferred← citeshttps://doi.org/10.1002/dvg.23399openalex-snapshot
The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations
inferred← citeshttps://doi.org/10.1007/978-1-0716-3226-0_8openalex-snapshot
Preparation of Mitotic Chromosomes with the Dropping Technique
inferred← citeshttps://doi.org/10.1007/978-3-030-28748-1_10openalex-snapshot
Application of Biotechnology
inferred← citeshttps://doi.org/10.1007/978-3-031-16061-5_2openalex-snapshot
Repeat DNA Sequences in Flax Genomes
inferred← citeshttps://doi.org/10.1007/s00438-016-1255-3openalex-snapshot
Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome
inferred← citeshttps://doi.org/10.1007/s12088-024-01269-8openalex-snapshot
Antimicrobial, Antioxidant and Cytotoxic Effects of Essential Oil, Fatty Acids and Bioactive Compounds of Beta vulgaris var. crassa (Fodder Beet)
inferred← citeshttps://doi.org/10.1007/s12355-021-01089-wopenalex-snapshot
Effects of Soil Covering on Growth and Physio-Biochemical Indices of Sugar Beet Seedlings Under Short-Term Low-Temperature Stress
inferred← citeshttps://doi.org/10.1016/j.fbr.2022.11.005openalex-snapshot
Advances in molecular interactions on the Rhizoctonia solani-sugar beet pathosystem
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2021.04.007openalex-snapshot
Assembly and characterization of the genome of chard (Beta vulgaris ssp. vulgaris var. cicla)
inferred← citeshttps://doi.org/10.1093/aob/mcaa176openalex-snapshot
The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty395openalex-snapshot
FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses
inferred← citeshttps://doi.org/10.1093/dnares/dsaa004openalex-snapshot
Genome-wide analysis of short interspersed nuclear elements provides insight into gene and genome evolution in citrus
inferred← citeshttps://doi.org/10.1093/gbe/evx145openalex-snapshot
Distribution, Diversity, and Long-Term Retention of Grass Short Interspersed Nuclear Elements (SINEs)
inferred← citeshttps://doi.org/10.1093/gbe/evy098openalex-snapshot
Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons
inferred← citeshttps://doi.org/10.1093/molbev/msw130openalex-snapshot
High Similarity between Distantly Related Species of a Plant SINE Family Is Consistent with a Scenario of Vertical Transmission without Horizontal Transfers
inferred← citeshttps://doi.org/10.1093/nargab/lqaf142openalex-snapshot
Sugar beet long-read reference assembly of genotype KWS2320
inferred← citeshttps://doi.org/10.1111/tpj.13170openalex-snapshot
Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family‐specific impact on gene structure and genome organization
inferred← citeshttps://doi.org/10.1111/tpj.13526openalex-snapshot
DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)
inferred← citeshttps://doi.org/10.1111/tpj.13676openalex-snapshot
Evolutionary modes of emergence of short interspersed nuclear element ( SINE ) families in grasses
inferred← citeshttps://doi.org/10.1111/tpj.14567openalex-snapshot
The conserved 3′ Angio‐domain defines a superfamily of short interspersed nuclear elements (SINEs) in higher plants
inferred← citeshttps://doi.org/10.1111/tpj.14721openalex-snapshot
Divergence of 3′ ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae
inferred← citeshttps://doi.org/10.1111/tpj.16599openalex-snapshot
Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets
inferred← citeshttps://doi.org/10.1139/cjfr-2020-0209openalex-snapshot
Application of retrotransposon-based Inter-SINE Amplified Polymorphism (ISAP) markers for the differentiation of common poplar genotypes
inferred← citeshttps://doi.org/10.1186/s12864-021-07543-zopenalex-snapshot
Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.1186/s12864-023-09522-yopenalex-snapshot
Genetic diversity and genome-wide association study of 13 agronomic traits in 977 Beta vulgaris L. germplasms
inferred← citeshttps://doi.org/10.1186/s12870-016-0805-5openalex-snapshot
Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris)
inferred← citeshttps://doi.org/10.1186/s13100-021-00246-yopenalex-snapshot
SINE jumping contributes to large-scale polymorphisms in the pig genomes
inferred← citeshttps://doi.org/10.1186/s13100-026-00416-wopenalex-snapshot
Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons
inferred← citeshttps://doi.org/10.1186/s13104-024-06993-4openalex-snapshot
BeetRepeats: reference sequences for genome and polymorphism annotation in sugar beet and wild relatives
inferred← citeshttps://doi.org/10.21608/eajbsh.2023.293954openalex-snapshot
Response of Sugar Beet Growth to Soil Application of Humic Acid and Foliar Application of Some Biostimulators under Saline Soil Conditions
inferred← citeshttps://doi.org/10.26479/2019.0503.25openalex-snapshot
Phenetic Analysis of Seedling Morphology of Some Members of Amaranthaceae
inferred← citeshttps://doi.org/10.30901/2227-8834-2025-4-168-181openalex-snapshot
In silico analysis of the genomes within the Rosaceae Juss. family to develop ISAP markers
inferred← citeshttps://doi.org/10.3389/fpls.2020.575462openalex-snapshot
Genome-Wide Analysis of Transposable Elements and Satellite DNAs in Spinacia Species to Shed Light on Their Roles in Sex Chromosome Evolution
inferred← citeshttps://doi.org/10.3390/plants13212954openalex-snapshot
Assessment of Genetic Diversity and Population Structure of Exotic Sugar Beet (Beta vulgaris L.) Varieties Using Three Molecular Markers
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355280openalex-snapshot
Additional file 10 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355283openalex-snapshot
Additional file 11 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355286openalex-snapshot
Additional file 12 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355289openalex-snapshot
Additional file 1 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355292openalex-snapshot
Additional file 2 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355295openalex-snapshot
Additional file 3 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355298openalex-snapshot
Additional file 4 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355301openalex-snapshot
Additional file 5 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355304openalex-snapshot
Additional file 6 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355307openalex-snapshot
Additional file 7 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355310openalex-snapshot
Additional file 8 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.14355313openalex-snapshot
Additional file 9 of Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts
inferred← citeshttps://doi.org/10.6084/m9.figshare.26606140openalex-snapshot
Additional file 1 of Genetic diversity and genome-wide association study of 13 agronomic traits in 977 Beta vulgaris L. germplasms
inferred← citeshttps://doi.org/10.6084/m9.figshare.26606143openalex-snapshot
Additional file 2 of Genetic diversity and genome-wide association study of 13 agronomic traits in 977 Beta vulgaris L. germplasms
inferred← citeshttps://doi.org/10.64898/2026.03.01.708851openalex-snapshot
Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons
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