Analysis of genetic diversity and evolutionary relationships among hexaploid wheats Triticum L. using LTR-retrotransposon-based molecular markers

Novoselskaya-Dragovich, Alexandra Yu.; Фисенко, А. В.; Коновалов, Ф. А.; Митрофанова, О. П.; Шишкіна, А. А.; Kudryavtsev, A. M.

doi:10.1007/s10722-017-0520-6

Cited by 7 publications

(3 citation statements)

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“…In most plants, LTR-RTs contribute to genome size expansion via their rapid proliferation (8,9). For example, LTR-RTs account for more than 70% of the maize (Zea mays) and wheat (Triticum aestivum) genomes (8,10). Intact LTR-RTs contain two similar or identical LTRs that ank an internal region containing a functional domain, target site duplications (TSDs), a polypurine tract (PPT), and a primer-binding site (PBS) (6).…”

Section: Introductionmentioning

confidence: 99%

Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin

Koo

Kim

Park

et al. 2022

Preprint

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BackgroundLong terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants.ResultsTo identify active LTR-RTs in rice (Oryza sativa), we characterized 1,783 intact LTR-RTs in the rice reference genome. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, we amplified LTRs of eclDNA (ALE)-seq to uncover the current transpositional potential of the LTR-RTs in callus of the Korean rice variety Dongjin. Tos17 was discovered in callus of the reference rice variety Nipponbare, and we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in Dongjin callus. Each Oryco family member has paired LTRs with identical sequences and internal domain regions. Comparison of the two LTR-RTs revealed 97% sequence identity in their internal domains and 65% sequence identity in their LTRs. ConclusionsWe identified two active LTR-RTs in the callus of Korean rice variety Dongjin using ALE-seq. These two putatively active Oryco LTR-RT family members could be used to expand our knowledge of retrotransposition mechanisms and the effects of LTR-RTs on the rice genome.

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Section: Introductionmentioning

confidence: 99%

Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin

Koo

Kim

Park

et al. 2022

Preprint

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show abstract

“…In most plants, LTR-RTs contribute to genome size expansion via their rapid proliferation [ 8 , 9 ]. For example, LTR-RTs account for more than 70% of the maize ( Zea mays ) and wheat ( Triticum aestivum ) genomes [ 8 , 10 ]. Intact LTR-RTs contain two similar or identical LTRs that flank an internal region containing a functional domain, target site duplications (TSDs), a polypurine tract (PPT), and a primer-binding site (PBS) [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin

et al. 2022

View full text Add to dashboard Cite

Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, amplification LTRs of eclDNAs followed by sequencing (ALE-seq) uncover the current transpositional potential of the LTR-RTs. The ALE-seq protocol was validated by identification of Tos17 in callus of Nipponbare cultivar. Here, we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in rice cultivar Dongjin callus based on the ALE-seq technology. Each Oryco family member has paired LTRs with identical sequences and internal domain regions. Comparison of the two LTR-RTs revealed 97% sequence identity in their internal domains and 65% sequence identity in their LTRs. These two putatively active Oryco LTR-RT family members could be used to expand our knowledge of retrotransposition mechanisms and the effects of LTR-RTs on the rice genome.

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“…Научные интересы Ольги Павловны сосредоточены на исследовании генетических ресурсов пшеницы (Mitrofanova, 2012;Mitrofanova et al, 2016), направленном на выявление особенностеи� эволюции рода Triticum L. (Dragovich et al, 2009;Riaz et al, 2016;Novoselskaya-Dragovich et al, 2018;Badaeva et al, 2018;Temirbekova et al, 2019), на оценку генетического разнообразия пшеницы (Fadeeva et al, 2020;Fadeeva et al, 2022), на выявление особенно-стеи� наследования селекционно значимых признаков (Plotnikova et al, 2018;Riaz et al, 2018;Lysenko et al, 2019;Zverev et al, 2020;Shcherban et al, 2021;Gultyaeva et al, 2022), на маркирование ценных генов и разработку тех-нологии� маркер-контролируемого отбора (совместно с лабораториеи� молекулярнои� селекции и ДНК-паспортизации) (Porotnikov et al, 2020;Porotnikov et al, 2022a;Porotnikov et al, 2022b), на изучение линии� , созданных от скрещивания мягкои� озимои� пшеницы с рожью (Pyukkenen et al, 2019), и линии� синтетическои� гексаплоиднои� пшеницы (Khakimova et al, 2019;Khakimova et al, 2021).…”

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Olga P. Mitrofanova (celebrating the 75<sup>th</sup> birthday)

Зуев

Lyapunova

Хлесткина

2023

Trudy po prikladnoy botanike, genetike i selektsii

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Analysis of genetic diversity and evolutionary relationships among hexaploid wheats Triticum L. using LTR-retrotransposon-based molecular markers

Cited by 7 publications

References 24 publications

Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin

Amplification of LTRs of Extrachromosomal Linear DNAs (ALE-seq) Identifies Two Active Oryco LTR Retrotransposons in the Rice Cultivar Dongjin

Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin

Olga P. Mitrofanova (celebrating the 75<sup>th</sup> birthday)

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