LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice

Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Wang, Hao [verfasserIn] Xu, Zhao Yu, Hongjie

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2008

Schlagwörter:	Rice Genome Wild Rice Related Genome Syntenic Block Shared Element

Anmerkung:	© Wang et al; licensee BioMed Central Ltd. 2008

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 9(2008), 1 vom: 27. Nov.
Übergeordnetes Werk:	volume:9 ; year:2008 ; number:1 ; day:27 ; month:11

Links:	Volltext

DOI / URN:	10.1186/1471-2164-9-565

Katalog-ID:	SPR027039714

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245	1	0	\|a LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
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520			\|a Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome.
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Indexfelder

author_variant	h w hw z x zx h y hy
matchkey_str	article:14712164:2008----::trtornpsnrvarcnetnienesbpcenneircleob
hierarchy_sort_str	2008
publishDate	2008
allfields	10.1186/1471-2164-9-565 doi (DE-627)SPR027039714 (SPR)1471-2164-9-565-e DE-627 ger DE-627 rakwb eng Wang, Hao verfasserin aut LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al; licensee BioMed Central Ltd. 2008 Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome. Rice Genome (dpeaa)DE-He213 Wild Rice (dpeaa)DE-He213 Related Genome (dpeaa)DE-He213 Syntenic Block (dpeaa)DE-He213 Shared Element (dpeaa)DE-He213 Xu, Zhao aut Yu, Hongjie aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 27. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:27 month:11 https://dx.doi.org/10.1186/1471-2164-9-565 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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 9 2008 1 27 11
spelling	10.1186/1471-2164-9-565 doi (DE-627)SPR027039714 (SPR)1471-2164-9-565-e DE-627 ger DE-627 rakwb eng Wang, Hao verfasserin aut LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al; licensee BioMed Central Ltd. 2008 Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome. Rice Genome (dpeaa)DE-He213 Wild Rice (dpeaa)DE-He213 Related Genome (dpeaa)DE-He213 Syntenic Block (dpeaa)DE-He213 Shared Element (dpeaa)DE-He213 Xu, Zhao aut Yu, Hongjie aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 27. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:27 month:11 https://dx.doi.org/10.1186/1471-2164-9-565 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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 9 2008 1 27 11
allfields_unstemmed	10.1186/1471-2164-9-565 doi (DE-627)SPR027039714 (SPR)1471-2164-9-565-e DE-627 ger DE-627 rakwb eng Wang, Hao verfasserin aut LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al; licensee BioMed Central Ltd. 2008 Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome. Rice Genome (dpeaa)DE-He213 Wild Rice (dpeaa)DE-He213 Related Genome (dpeaa)DE-He213 Syntenic Block (dpeaa)DE-He213 Shared Element (dpeaa)DE-He213 Xu, Zhao aut Yu, Hongjie aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 27. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:27 month:11 https://dx.doi.org/10.1186/1471-2164-9-565 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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 9 2008 1 27 11
allfieldsGer	10.1186/1471-2164-9-565 doi (DE-627)SPR027039714 (SPR)1471-2164-9-565-e DE-627 ger DE-627 rakwb eng Wang, Hao verfasserin aut LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al; licensee BioMed Central Ltd. 2008 Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome. Rice Genome (dpeaa)DE-He213 Wild Rice (dpeaa)DE-He213 Related Genome (dpeaa)DE-He213 Syntenic Block (dpeaa)DE-He213 Shared Element (dpeaa)DE-He213 Xu, Zhao aut Yu, Hongjie aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 27. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:27 month:11 https://dx.doi.org/10.1186/1471-2164-9-565 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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 9 2008 1 27 11
allfieldsSound	10.1186/1471-2164-9-565 doi (DE-627)SPR027039714 (SPR)1471-2164-9-565-e DE-627 ger DE-627 rakwb eng Wang, Hao verfasserin aut LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al; licensee BioMed Central Ltd. 2008 Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome. Rice Genome (dpeaa)DE-He213 Wild Rice (dpeaa)DE-He213 Related Genome (dpeaa)DE-He213 Syntenic Block (dpeaa)DE-He213 Shared Element (dpeaa)DE-He213 Xu, Zhao aut Yu, Hongjie aut Enthalten in BMC genomics London : BioMed Central, 2000 9(2008), 1 vom: 27. Nov. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:9 year:2008 number:1 day:27 month:11 https://dx.doi.org/10.1186/1471-2164-9-565 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 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_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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 9 2008 1 27 11
language	English
source	Enthalten in BMC genomics 9(2008), 1 vom: 27. Nov. volume:9 year:2008 number:1 day:27 month:11
sourceStr	Enthalten in BMC genomics 9(2008), 1 vom: 27. Nov. volume:9 year:2008 number:1 day:27 month:11
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Rice Genome Wild Rice Related Genome Syntenic Block Shared Element
isfreeaccess_bool	true
container_title	BMC genomics
authorswithroles_txt_mv	Wang, Hao @@aut@@ Xu, Zhao @@aut@@ Yu, Hongjie @@aut@@
publishDateDaySort_date	2008-11-27T00:00:00Z
hierarchy_top_id	326644954
id	SPR027039714
language_de	englisch
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They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. 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author	Wang, Hao
spellingShingle	Wang, Hao misc Rice Genome misc Wild Rice misc Related Genome misc Syntenic Block misc Shared Element LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
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topic_title	LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice Rice Genome (dpeaa)DE-He213 Wild Rice (dpeaa)DE-He213 Related Genome (dpeaa)DE-He213 Syntenic Block (dpeaa)DE-He213 Shared Element (dpeaa)DE-He213
topic	misc Rice Genome misc Wild Rice misc Related Genome misc Syntenic Block misc Shared Element
topic_unstemmed	misc Rice Genome misc Wild Rice misc Related Genome misc Syntenic Block misc Shared Element
topic_browse	misc Rice Genome misc Wild Rice misc Related Genome misc Syntenic Block misc Shared Element
format_facet	Elektronische Aufsätze Aufsätze Elektronische Ressource
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title	LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
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title_full	LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
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author_browse	Wang, Hao Xu, Zhao Yu, Hongjie
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author-letter	Wang, Hao
doi_str_mv	10.1186/1471-2164-9-565
title_sort	ltr retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in asian cultivated rice
title_auth	LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
abstract	Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome. © Wang et al; licensee BioMed Central Ltd. 2008
abstractGer	Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome. © Wang et al; licensee BioMed Central Ltd. 2008
abstract_unstemmed	Background Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history. Results The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago. Conclusion A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome. © Wang et al; licensee BioMed Central Ltd. 2008
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title_short	LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
url	https://dx.doi.org/10.1186/1471-2164-9-565
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LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice

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