Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability

<i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Samuel Simoni [verfasserIn] Clarissa Clemente [verfasserIn] Gabriele Usai [verfasserIn] Alberto Vangelisti [verfasserIn] Lucia Natali [verfasserIn] Silvia Tavarini [verfasserIn] Luciana G. Angelini [verfasserIn] Andrea Cavallini [verfasserIn] Flavia Mascagni [verfasserIn] Tommaso Giordani [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	Inter-Retrotransposon Amplified Polymorphism LTR-retrotransposons retrotransposon dynamics

Übergeordnetes Werk:	In: International Journal of Molecular Sciences - MDPI AG, 2003, 23(2022), 11, p 6220
Übergeordnetes Werk:	volume:23 ; year:2022 ; number:11, p 6220

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.3390/ijms23116220

Katalog-ID:	DOAJ041922131

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allfields	10.3390/ijms23116220 doi (DE-627)DOAJ041922131 (DE-599)DOAJ27911490b81d46238979b9958eedf3d3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Samuel Simoni verfasserin aut Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding. <i<Angela</i< retrotransposon Inter-Retrotransposon Amplified Polymorphism LTR-retrotransposons retrotransposon dynamics <i<Stevia rebaudiana</i< Biology (General) Chemistry Clarissa Clemente verfasserin aut Gabriele Usai verfasserin aut Alberto Vangelisti verfasserin aut Lucia Natali verfasserin aut Silvia Tavarini verfasserin aut Luciana G. Angelini verfasserin aut Andrea Cavallini verfasserin aut Flavia Mascagni verfasserin aut Tommaso Giordani verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 11, p 6220 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:11, p 6220 https://doi.org/10.3390/ijms23116220 kostenfrei https://doaj.org/article/27911490b81d46238979b9958eedf3d3 kostenfrei https://www.mdpi.com/1422-0067/23/11/6220 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 11, p 6220
spelling	10.3390/ijms23116220 doi (DE-627)DOAJ041922131 (DE-599)DOAJ27911490b81d46238979b9958eedf3d3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Samuel Simoni verfasserin aut Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding. <i<Angela</i< retrotransposon Inter-Retrotransposon Amplified Polymorphism LTR-retrotransposons retrotransposon dynamics <i<Stevia rebaudiana</i< Biology (General) Chemistry Clarissa Clemente verfasserin aut Gabriele Usai verfasserin aut Alberto Vangelisti verfasserin aut Lucia Natali verfasserin aut Silvia Tavarini verfasserin aut Luciana G. Angelini verfasserin aut Andrea Cavallini verfasserin aut Flavia Mascagni verfasserin aut Tommaso Giordani verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 11, p 6220 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:11, p 6220 https://doi.org/10.3390/ijms23116220 kostenfrei https://doaj.org/article/27911490b81d46238979b9958eedf3d3 kostenfrei https://www.mdpi.com/1422-0067/23/11/6220 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 11, p 6220
allfields_unstemmed	10.3390/ijms23116220 doi (DE-627)DOAJ041922131 (DE-599)DOAJ27911490b81d46238979b9958eedf3d3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Samuel Simoni verfasserin aut Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding. <i<Angela</i< retrotransposon Inter-Retrotransposon Amplified Polymorphism LTR-retrotransposons retrotransposon dynamics <i<Stevia rebaudiana</i< Biology (General) Chemistry Clarissa Clemente verfasserin aut Gabriele Usai verfasserin aut Alberto Vangelisti verfasserin aut Lucia Natali verfasserin aut Silvia Tavarini verfasserin aut Luciana G. Angelini verfasserin aut Andrea Cavallini verfasserin aut Flavia Mascagni verfasserin aut Tommaso Giordani verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 11, p 6220 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:11, p 6220 https://doi.org/10.3390/ijms23116220 kostenfrei https://doaj.org/article/27911490b81d46238979b9958eedf3d3 kostenfrei https://www.mdpi.com/1422-0067/23/11/6220 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 11, p 6220
allfieldsGer	10.3390/ijms23116220 doi (DE-627)DOAJ041922131 (DE-599)DOAJ27911490b81d46238979b9958eedf3d3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Samuel Simoni verfasserin aut Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding. <i<Angela</i< retrotransposon Inter-Retrotransposon Amplified Polymorphism LTR-retrotransposons retrotransposon dynamics <i<Stevia rebaudiana</i< Biology (General) Chemistry Clarissa Clemente verfasserin aut Gabriele Usai verfasserin aut Alberto Vangelisti verfasserin aut Lucia Natali verfasserin aut Silvia Tavarini verfasserin aut Luciana G. Angelini verfasserin aut Andrea Cavallini verfasserin aut Flavia Mascagni verfasserin aut Tommaso Giordani verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 11, p 6220 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:11, p 6220 https://doi.org/10.3390/ijms23116220 kostenfrei https://doaj.org/article/27911490b81d46238979b9958eedf3d3 kostenfrei https://www.mdpi.com/1422-0067/23/11/6220 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 11, p 6220
allfieldsSound	10.3390/ijms23116220 doi (DE-627)DOAJ041922131 (DE-599)DOAJ27911490b81d46238979b9958eedf3d3 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Samuel Simoni verfasserin aut Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding. <i<Angela</i< retrotransposon Inter-Retrotransposon Amplified Polymorphism LTR-retrotransposons retrotransposon dynamics <i<Stevia rebaudiana</i< Biology (General) Chemistry Clarissa Clemente verfasserin aut Gabriele Usai verfasserin aut Alberto Vangelisti verfasserin aut Lucia Natali verfasserin aut Silvia Tavarini verfasserin aut Luciana G. Angelini verfasserin aut Andrea Cavallini verfasserin aut Flavia Mascagni verfasserin aut Tommaso Giordani verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 11, p 6220 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:11, p 6220 https://doi.org/10.3390/ijms23116220 kostenfrei https://doaj.org/article/27911490b81d46238979b9958eedf3d3 kostenfrei https://www.mdpi.com/1422-0067/23/11/6220 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 11, p 6220
language	English
source	In International Journal of Molecular Sciences 23(2022), 11, p 6220 volume:23 year:2022 number:11, p 6220
sourceStr	In International Journal of Molecular Sciences 23(2022), 11, p 6220 volume:23 year:2022 number:11, p 6220
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	<i<Angela</i< retrotransposon Inter-Retrotransposon Amplified Polymorphism LTR-retrotransposons retrotransposon dynamics <i<Stevia rebaudiana</i< Biology (General) Chemistry
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authorswithroles_txt_mv	Samuel Simoni @@aut@@ Clarissa Clemente @@aut@@ Gabriele Usai @@aut@@ Alberto Vangelisti @@aut@@ Lucia Natali @@aut@@ Silvia Tavarini @@aut@@ Luciana G. Angelini @@aut@@ Andrea Cavallini @@aut@@ Flavia Mascagni @@aut@@ Tommaso Giordani @@aut@@
publishDateDaySort_date	2022-01-01T00:00:00Z
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language_de	englisch
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callnumber-first	Q - Science
author	Samuel Simoni
spellingShingle	Samuel Simoni misc QH301-705.5 misc QD1-999 misc <i<Angela</i< retrotransposon misc Inter-Retrotransposon Amplified Polymorphism misc LTR-retrotransposons misc retrotransposon dynamics misc <i<Stevia rebaudiana</i< misc Biology (General) misc Chemistry Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability
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topic_title	QH301-705.5 QD1-999 Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability <i<Angela</i< retrotransposon Inter-Retrotransposon Amplified Polymorphism LTR-retrotransposons retrotransposon dynamics <i<Stevia rebaudiana</i<
topic	misc QH301-705.5 misc QD1-999 misc <i<Angela</i< retrotransposon misc Inter-Retrotransposon Amplified Polymorphism misc LTR-retrotransposons misc retrotransposon dynamics misc <i<Stevia rebaudiana</i< misc Biology (General) misc Chemistry
topic_unstemmed	misc QH301-705.5 misc QD1-999 misc <i<Angela</i< retrotransposon misc Inter-Retrotransposon Amplified Polymorphism misc LTR-retrotransposons misc retrotransposon dynamics misc <i<Stevia rebaudiana</i< misc Biology (General) misc Chemistry
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title	Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability
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title_full	Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability
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author_browse	Samuel Simoni Clarissa Clemente Gabriele Usai Alberto Vangelisti Lucia Natali Silvia Tavarini Luciana G. Angelini Andrea Cavallini Flavia Mascagni Tommaso Giordani
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title_sort	characterisation of ltr-retrotransposons of <i<stevia rebaudiana</i< and their use for the analysis of genetic variability
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title_auth	Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability
abstract	<i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding.
abstractGer	<i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding.
abstract_unstemmed	<i<Stevia rebaudiana</i< is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i<Gypsy</i< retrotransposons were twice as abundant as the <i<Copia</i< ones. A disproportionate abundance of elements belonging to the <i<Chromovirus/Tekay</i< lineage was observed among the <i<Gypsy</i< elements. Only the <i<SIRE</i< and <i<Angela</i< lineages represented significant portions of the genome among the <i<Copia</i< elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i<Angela</i< was used to analyse the genetic variability in 25 accessions of <i<S. rebaudiana</i< using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding.
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Characterisation of LTR-Retrotransposons of <i<Stevia rebaudiana</i< and Their Use for the Analysis of Genetic Variability

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