Chromosomal Locations of a Non-LTR Retrotransposon, &lt;b&gt;&lt;i&gt;Menolird18&lt;/i&gt;&lt;/b&gt;, in &lt;b&gt;&lt;i&gt;Cucumis melo&lt;/i&gt;&lt;/b&gt; and &lt;b&gt;&lt;i&gt;Cucumis sativus&lt;/i&gt;&lt;/b&gt;, and Its Implication on Genome Evolution of &lt;b&gt;&lt;i&gt;Cucumis&lt;/i&gt;&lt;/b&gt; Species

Setiawan, Agus Budi; Teo, Chee How; Kikuchi, Shinichi; Sassa, Hidenori; Kato, Kenji; Koba, Takato

doi:10.1159/000511119

Cited by 9 publications

(9 citation statements)

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“…The Gag gene regulates the packaging of the RNA and the protein, while the other domains participate in the replication cycles ( Zhao et al 2016;Sanchez et al 2017). The transposable element, particularly the LTRretrotransposon contribute to the genetic variation in the plant because of the insertion and deletion events that are distributed extensively throughout the genome (Moghaddam et al 2014;Setiawan et al 2020a;Sormin et al 2021). Therefore, this repetitive sequence is pertinent for marker development, particularly in evaluating the segregated population created from the interspecific hybridization.…”

Section: Analysis Of Ltr-retrotransposon Sequences and Structures In ...mentioning

confidence: 99%

“…The retrotransposon is a mobile element that is prevalent in the plant genomes (Kalendar and Schulman 2014;Orozco-Arias et al 2019). Because of the insertion and deletion events that are widely dispersed throughout the genome, it is the primary driver of variation in plants (Moghaddam et al 2014;Setiawan et al 2020a;Sormin et al 2021), making it an excellent candidate to be utilized as a molecular marker to assess the genetic diversity in a segregated population. The retrotransposons are transposable elements (TEs) categorized into Long Terminal Repeat (LTR) and non-LTR retrotransposons (Elbarbary et al 2016;Schulman et al 2012).…”

Section: Introductionmentioning

confidence: 99%

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Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system

et al. 2021

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Abstract. Fatmawati Y, Setiawan AB, Purwantoro A, Respatie DW, Teo CH. 2021. Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system. Biodiversitas 22: 4880-4889. Mung bean (Vigna radiata L. Wilczek) categorized as one of the pivotal annual crops of Vigna genera is commonly cultivated in rotation with the cereal crops during the drought season. Conversely, to ameliorate its stunted productivity, the interspecific hybridization technique has been introduced between the mung bean and the common bean to promote genetic improvement with the breeding projects in Indonesia. However, since mung bean is a self-pollinated crop and has a narrow genetic base, the selection and improvement of a specific trait using marker-assisted selection is more challenging. Hence, a precautionary investigation is imperative to evaluate the progenies resulting from interspecific hybridization using an ideal marker. This study aimed to investigate the genetic variability of the F2 population of the interspecific mung bean hybrids using retrotransposon-based markers, particularly Inter-Retrotransposon Amplified Polymorphism (IRAP) markers. In this study, we identified retrotransposon from the mung bean genome and determined the Long Terminal Repeat (LTR) sequence using the LTR Finder. The IRAP primers were designed from a conserved region of the LTR sequence. One hundred of the F2 interspecific hybrids generated from the crossing between mung bean and common bean were successfully discriminated by IRAP markers. The IRAP marker showed high heterozygosity and moderate Polymorphic Information Content (PIC) values. The IRAP markers were able to detect genetic variability in the F2 progenies resulting from the interspecific hybridization. Cluster analysis showed that 100 of the F2 progenies were grouped into three clusters. This study demonstrated that retrotransposon-based markers can offer an effective approach for evaluating the segregation in the F2 population of intercross hybrids in the mung bean.

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Section: Analysis Of Ltr-retrotransposon Sequences and Structures In ...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system

et al. 2021

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“…Non-LTR retrotransposons have been less studied in plants ( Schmidt, 1999 ) despite their known role in genomic evolutionary processes ( Noma et al, 1999 ; Setiawan et al, 2020 ). In mammalian systems, these elements are considered silent because of DNA methylation and tend to be inserted in gene-rich regions ( Carnell, 2003 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) D.A. Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond × Peach Hybrid Population

et al. 2022

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Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important nut crop susceptible to the genetic disorder, Non-infectious Bud Failure (NBF). Despite the severity of exhibition in several prominent almond cultivars, no causal mechanism has been identified underlying NBF development. The disorder is hypothesized to be associated with differential DNA methylation patterns based on patterns of inheritance (i.e., via sexual reproduction and clonal propagation) and previous work profiling methylation in affected trees. Peach (Prunus persica L. Batsch) is a closely related species that readily hybridizes with almond; however, peach is not known to exhibit NBF. A cross between an NBF-exhibiting ‘Carmel’ cultivar and early flowering peach (‘40A17’) produced an F1 where ∼50% of progeny showed signs of NBF, including canopy die-back, erratic branching patterns (known as “crazy-top”), and rough bark. In this study, whole-genome DNA methylation profiles were generated for three F1 progenies exhibiting NBF and three progenies considered NBF-free. Subsequent alignment to both the almond and peach reference genomes showed an increase in genome-wide methylation levels in NBF hybrids in CG and CHG contexts compared to no-NBF hybrids when aligned to the almond genome but no difference in methylation levels when aligned to the peach genome. Significantly differentially methylated regions (DMRs) were identified by comparing methylation levels across the genome between NBF- and no-NBF hybrids in each methylation context. In total, 115,635 DMRs were identified based on alignment to the almond reference genome, and 126,800 DMRs were identified based on alignment to the peach reference genome. Nearby genes were identified as associated with the 39 most significant DMRs occurring either in the almond or peach alignments alone or occurring in both the almond and peach alignments. These DMR-associated genes include several uncharacterized proteins and transposable elements. Quantitative PCR was also performed to analyze the gene expression patterns of these identified gene targets to determine patterns of differential expression associated with differential DNA methylation. These DMR-associated genes, particularly those showing corresponding patterns of differential gene expression, represent key targets for almond breeding for future cultivars and mitigating the effects of NBF-exhibition in currently affected cultivars.

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“…As for plants, integration of TEs in the IGS has been described for Allium cernuum , where a Ty1/copia retrotransposon, which occurs in and outside of the rDNA arrays ( Chester et al 2010 ). Also, in species from the genus Cucumis , LINEs were detected in the internal transcribed spacers (ITS) and ETS rDNA regions ( Setiawan et al 2020 ). As the mentioned examples encompass animals, fungi, and plants, we conclude that TE integration in the IGS is a widespread phenomenon.…”

Section: Tes In Ribosomal Dnamentioning

confidence: 99%

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

Garcia,

Kovarik,

Maiwald

et al. 2024

Molecular Biology and Evolution

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Although both are salient features of genomes, at first glance ribosomal DNAs (rDNAs) and transposable elements (TEs) are genetic elements with not much in common: whereas rDNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, TEs are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (rDNAs) versus organization in a dispersed manner (TEs); evolution in a concerted manner (rDNAs) versus evolution by diversification (TEs); and activity that prolongs genomic stability (rDNAs) versus activity that shortens it (TEs). Re-visiting relevant instances in which rDNA-TE interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales; (2) they exchange structural motifs and can enter co-evolution processes; (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging; and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional and evolutionary characteristics of both rDNAs and TEs, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding rDNA-TE associations.

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Chromosomal Locations of a Non-LTR Retrotransposon, <b><i>Menolird18</i></b>, in <b><i>Cucumis melo</i></b> and <b><i>Cucumis sativus</i></b>, and Its Implication on Genome Evolution of <b><i>Cucumis</i></b> Species

Cited by 9 publications

References 61 publications

Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system

Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system

Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) D.A. Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond × Peach Hybrid Population

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

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