Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny

Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Wang, Juan [verfasserIn] Li, Yuan Li, Chunjuan Yan, Caixia Zhao, Xiaobo Yuan, Cuiling Sun, Quanxi Shi, Chengren Shan, Shihua

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Peanut Chloroplast genome Phylogeny SNDs SSRs Genome type Genetic variation

Anmerkung:	© The Author(s). 2019

Übergeordnetes Werk:	Enthalten in: BMC plant biology - London : BioMed Central, 2001, 19(2019), 1 vom: 19. Nov.
Übergeordnetes Werk:	volume:19 ; year:2019 ; number:1 ; day:19 ; month:11

Links:	Volltext

DOI / URN:	10.1186/s12870-019-2121-3

Katalog-ID:	SPR02731393X

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520			\|a Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.
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allfields	10.1186/s12870-019-2121-3 doi (DE-627)SPR02731393X (SPR)s12870-019-2121-3-e DE-627 ger DE-627 rakwb eng Wang, Juan verfasserin aut Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. Peanut (dpeaa)DE-He213 Chloroplast genome (dpeaa)DE-He213 Phylogeny (dpeaa)DE-He213 SNDs (dpeaa)DE-He213 SSRs (dpeaa)DE-He213 Genome type (dpeaa)DE-He213 Genetic variation (dpeaa)DE-He213 Li, Yuan aut Li, Chunjuan aut Yan, Caixia aut Zhao, Xiaobo aut Yuan, Cuiling aut Sun, Quanxi aut Shi, Chengren aut Shan, Shihua aut Enthalten in BMC plant biology London : BioMed Central, 2001 19(2019), 1 vom: 19. Nov. (DE-627)335489060 (DE-600)2059868-3 1471-2229 nnns volume:19 year:2019 number:1 day:19 month:11 https://dx.doi.org/10.1186/s12870-019-2121-3 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_224 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 19 2019 1 19 11
spelling	10.1186/s12870-019-2121-3 doi (DE-627)SPR02731393X (SPR)s12870-019-2121-3-e DE-627 ger DE-627 rakwb eng Wang, Juan verfasserin aut Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. Peanut (dpeaa)DE-He213 Chloroplast genome (dpeaa)DE-He213 Phylogeny (dpeaa)DE-He213 SNDs (dpeaa)DE-He213 SSRs (dpeaa)DE-He213 Genome type (dpeaa)DE-He213 Genetic variation (dpeaa)DE-He213 Li, Yuan aut Li, Chunjuan aut Yan, Caixia aut Zhao, Xiaobo aut Yuan, Cuiling aut Sun, Quanxi aut Shi, Chengren aut Shan, Shihua aut Enthalten in BMC plant biology London : BioMed Central, 2001 19(2019), 1 vom: 19. Nov. (DE-627)335489060 (DE-600)2059868-3 1471-2229 nnns volume:19 year:2019 number:1 day:19 month:11 https://dx.doi.org/10.1186/s12870-019-2121-3 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_224 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 19 2019 1 19 11
allfields_unstemmed	10.1186/s12870-019-2121-3 doi (DE-627)SPR02731393X (SPR)s12870-019-2121-3-e DE-627 ger DE-627 rakwb eng Wang, Juan verfasserin aut Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. Peanut (dpeaa)DE-He213 Chloroplast genome (dpeaa)DE-He213 Phylogeny (dpeaa)DE-He213 SNDs (dpeaa)DE-He213 SSRs (dpeaa)DE-He213 Genome type (dpeaa)DE-He213 Genetic variation (dpeaa)DE-He213 Li, Yuan aut Li, Chunjuan aut Yan, Caixia aut Zhao, Xiaobo aut Yuan, Cuiling aut Sun, Quanxi aut Shi, Chengren aut Shan, Shihua aut Enthalten in BMC plant biology London : BioMed Central, 2001 19(2019), 1 vom: 19. Nov. (DE-627)335489060 (DE-600)2059868-3 1471-2229 nnns volume:19 year:2019 number:1 day:19 month:11 https://dx.doi.org/10.1186/s12870-019-2121-3 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_224 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 19 2019 1 19 11
allfieldsGer	10.1186/s12870-019-2121-3 doi (DE-627)SPR02731393X (SPR)s12870-019-2121-3-e DE-627 ger DE-627 rakwb eng Wang, Juan verfasserin aut Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. Peanut (dpeaa)DE-He213 Chloroplast genome (dpeaa)DE-He213 Phylogeny (dpeaa)DE-He213 SNDs (dpeaa)DE-He213 SSRs (dpeaa)DE-He213 Genome type (dpeaa)DE-He213 Genetic variation (dpeaa)DE-He213 Li, Yuan aut Li, Chunjuan aut Yan, Caixia aut Zhao, Xiaobo aut Yuan, Cuiling aut Sun, Quanxi aut Shi, Chengren aut Shan, Shihua aut Enthalten in BMC plant biology London : BioMed Central, 2001 19(2019), 1 vom: 19. Nov. (DE-627)335489060 (DE-600)2059868-3 1471-2229 nnns volume:19 year:2019 number:1 day:19 month:11 https://dx.doi.org/10.1186/s12870-019-2121-3 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_224 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 19 2019 1 19 11
allfieldsSound	10.1186/s12870-019-2121-3 doi (DE-627)SPR02731393X (SPR)s12870-019-2121-3-e DE-627 ger DE-627 rakwb eng Wang, Juan verfasserin aut Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s). 2019 Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. Peanut (dpeaa)DE-He213 Chloroplast genome (dpeaa)DE-He213 Phylogeny (dpeaa)DE-He213 SNDs (dpeaa)DE-He213 SSRs (dpeaa)DE-He213 Genome type (dpeaa)DE-He213 Genetic variation (dpeaa)DE-He213 Li, Yuan aut Li, Chunjuan aut Yan, Caixia aut Zhao, Xiaobo aut Yuan, Cuiling aut Sun, Quanxi aut Shi, Chengren aut Shan, Shihua aut Enthalten in BMC plant biology London : BioMed Central, 2001 19(2019), 1 vom: 19. Nov. (DE-627)335489060 (DE-600)2059868-3 1471-2229 nnns volume:19 year:2019 number:1 day:19 month:11 https://dx.doi.org/10.1186/s12870-019-2121-3 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_224 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 19 2019 1 19 11
language	English
source	Enthalten in BMC plant biology 19(2019), 1 vom: 19. Nov. volume:19 year:2019 number:1 day:19 month:11
sourceStr	Enthalten in BMC plant biology 19(2019), 1 vom: 19. Nov. volume:19 year:2019 number:1 day:19 month:11
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Peanut Chloroplast genome Phylogeny SNDs SSRs Genome type Genetic variation
isfreeaccess_bool	true
container_title	BMC plant biology
authorswithroles_txt_mv	Wang, Juan @@aut@@ Li, Yuan @@aut@@ Li, Chunjuan @@aut@@ Yan, Caixia @@aut@@ Zhao, Xiaobo @@aut@@ Yuan, Cuiling @@aut@@ Sun, Quanxi @@aut@@ Shi, Chengren @@aut@@ Shan, Shihua @@aut@@
publishDateDaySort_date	2019-11-19T00:00:00Z
hierarchy_top_id	335489060
id	SPR02731393X
language_de	englisch
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The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. 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author	Wang, Juan
spellingShingle	Wang, Juan misc Peanut misc Chloroplast genome misc Phylogeny misc SNDs misc SSRs misc Genome type misc Genetic variation Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
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topic_title	Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny Peanut (dpeaa)DE-He213 Chloroplast genome (dpeaa)DE-He213 Phylogeny (dpeaa)DE-He213 SNDs (dpeaa)DE-He213 SSRs (dpeaa)DE-He213 Genome type (dpeaa)DE-He213 Genetic variation (dpeaa)DE-He213
topic	misc Peanut misc Chloroplast genome misc Phylogeny misc SNDs misc SSRs misc Genome type misc Genetic variation
topic_unstemmed	misc Peanut misc Chloroplast genome misc Phylogeny misc SNDs misc SSRs misc Genome type misc Genetic variation
topic_browse	misc Peanut misc Chloroplast genome misc Phylogeny misc SNDs misc SSRs misc Genome type misc Genetic variation
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title	Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
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title_full	Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
author_sort	Wang, Juan
journal	BMC plant biology
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author_browse	Wang, Juan Li, Yuan Li, Chunjuan Yan, Caixia Zhao, Xiaobo Yuan, Cuiling Sun, Quanxi Shi, Chengren Shan, Shihua
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title_sort	twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of arachis phylogeny
title_auth	Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
abstract	Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. © The Author(s). 2019
abstractGer	Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. © The Author(s). 2019
abstract_unstemmed	Background The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding. © The Author(s). 2019
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title_short	Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
url	https://dx.doi.org/10.1186/s12870-019-2121-3
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author2	Li, Yuan Li, Chunjuan Yan, Caixia Zhao, Xiaobo Yuan, Cuiling Sun, Quanxi Shi, Chengren Shan, Shihua
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The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. Results Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. Conclusion In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Peanut</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Chloroplast genome</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Phylogeny</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">SNDs</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">SSRs</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Genome type</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Genetic variation</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Li, Yuan</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Li, Chunjuan</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Yan, Caixia</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Zhao, Xiaobo</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Yuan, Cuiling</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Sun, Quanxi</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Shi, Chengren</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Shan, Shihua</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">Enthalten in</subfield><subfield code="t">BMC plant biology</subfield><subfield code="d">London : BioMed Central, 2001</subfield><subfield code="g">19(2019), 1 vom: 19. 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Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny

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