Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circul...
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Autor*in:	Chenxi Zhou [verfasserIn] Tania Duarte [verfasserIn] Rocio Silvestre [verfasserIn] Genoveva Rossel [verfasserIn] Robert O. M. Mwanga [verfasserIn] Awais Khan [verfasserIn] Andrew W. George [verfasserIn] Zhangjun Fei [verfasserIn] G. Craig Yencho [verfasserIn] David Ellis [verfasserIn] Lachlan J. M. Coin [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2020

Übergeordnetes Werk:	In: Gates Open Research - F1000 Research Ltd, 2018, 2(2020)
Übergeordnetes Werk:	volume:2 ; year:2020

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.12688/gatesopenres.12856.2

Katalog-ID:	DOAJ07033532X

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allfields	10.12688/gatesopenres.12856.2 doi (DE-627)DOAJ07033532X (DE-599)DOAJ7c2e31a351ba4593bd81d3bc0cc3ea88 DE-627 ger DE-627 rakwb eng Chenxi Zhou verfasserin aut Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations] 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato. Medicine R Tania Duarte verfasserin aut Rocio Silvestre verfasserin aut Genoveva Rossel verfasserin aut Robert O. M. Mwanga verfasserin aut Awais Khan verfasserin aut Andrew W. George verfasserin aut Zhangjun Fei verfasserin aut G. Craig Yencho verfasserin aut David Ellis verfasserin aut Lachlan J. M. Coin verfasserin aut In Gates Open Research F1000 Research Ltd, 2018 2(2020) (DE-627)1694655601 25724754 nnns volume:2 year:2020 https://doi.org/10.12688/gatesopenres.12856.2 kostenfrei https://doaj.org/article/7c2e31a351ba4593bd81d3bc0cc3ea88 kostenfrei https://gatesopenresearch.org/articles/2-41/v2 kostenfrei https://doaj.org/toc/2572-4754 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_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_2014 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 2 2020
spelling	10.12688/gatesopenres.12856.2 doi (DE-627)DOAJ07033532X (DE-599)DOAJ7c2e31a351ba4593bd81d3bc0cc3ea88 DE-627 ger DE-627 rakwb eng Chenxi Zhou verfasserin aut Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations] 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato. Medicine R Tania Duarte verfasserin aut Rocio Silvestre verfasserin aut Genoveva Rossel verfasserin aut Robert O. M. Mwanga verfasserin aut Awais Khan verfasserin aut Andrew W. George verfasserin aut Zhangjun Fei verfasserin aut G. Craig Yencho verfasserin aut David Ellis verfasserin aut Lachlan J. M. Coin verfasserin aut In Gates Open Research F1000 Research Ltd, 2018 2(2020) (DE-627)1694655601 25724754 nnns volume:2 year:2020 https://doi.org/10.12688/gatesopenres.12856.2 kostenfrei https://doaj.org/article/7c2e31a351ba4593bd81d3bc0cc3ea88 kostenfrei https://gatesopenresearch.org/articles/2-41/v2 kostenfrei https://doaj.org/toc/2572-4754 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_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_2014 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 2 2020
allfields_unstemmed	10.12688/gatesopenres.12856.2 doi (DE-627)DOAJ07033532X (DE-599)DOAJ7c2e31a351ba4593bd81d3bc0cc3ea88 DE-627 ger DE-627 rakwb eng Chenxi Zhou verfasserin aut Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations] 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato. Medicine R Tania Duarte verfasserin aut Rocio Silvestre verfasserin aut Genoveva Rossel verfasserin aut Robert O. M. Mwanga verfasserin aut Awais Khan verfasserin aut Andrew W. George verfasserin aut Zhangjun Fei verfasserin aut G. Craig Yencho verfasserin aut David Ellis verfasserin aut Lachlan J. M. Coin verfasserin aut In Gates Open Research F1000 Research Ltd, 2018 2(2020) (DE-627)1694655601 25724754 nnns volume:2 year:2020 https://doi.org/10.12688/gatesopenres.12856.2 kostenfrei https://doaj.org/article/7c2e31a351ba4593bd81d3bc0cc3ea88 kostenfrei https://gatesopenresearch.org/articles/2-41/v2 kostenfrei https://doaj.org/toc/2572-4754 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_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_2014 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 2 2020
allfieldsGer	10.12688/gatesopenres.12856.2 doi (DE-627)DOAJ07033532X (DE-599)DOAJ7c2e31a351ba4593bd81d3bc0cc3ea88 DE-627 ger DE-627 rakwb eng Chenxi Zhou verfasserin aut Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations] 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato. Medicine R Tania Duarte verfasserin aut Rocio Silvestre verfasserin aut Genoveva Rossel verfasserin aut Robert O. M. Mwanga verfasserin aut Awais Khan verfasserin aut Andrew W. George verfasserin aut Zhangjun Fei verfasserin aut G. Craig Yencho verfasserin aut David Ellis verfasserin aut Lachlan J. M. Coin verfasserin aut In Gates Open Research F1000 Research Ltd, 2018 2(2020) (DE-627)1694655601 25724754 nnns volume:2 year:2020 https://doi.org/10.12688/gatesopenres.12856.2 kostenfrei https://doaj.org/article/7c2e31a351ba4593bd81d3bc0cc3ea88 kostenfrei https://gatesopenresearch.org/articles/2-41/v2 kostenfrei https://doaj.org/toc/2572-4754 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_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_2014 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 2 2020
allfieldsSound	10.12688/gatesopenres.12856.2 doi (DE-627)DOAJ07033532X (DE-599)DOAJ7c2e31a351ba4593bd81d3bc0cc3ea88 DE-627 ger DE-627 rakwb eng Chenxi Zhou verfasserin aut Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations] 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato. Medicine R Tania Duarte verfasserin aut Rocio Silvestre verfasserin aut Genoveva Rossel verfasserin aut Robert O. M. Mwanga verfasserin aut Awais Khan verfasserin aut Andrew W. George verfasserin aut Zhangjun Fei verfasserin aut G. Craig Yencho verfasserin aut David Ellis verfasserin aut Lachlan J. M. Coin verfasserin aut In Gates Open Research F1000 Research Ltd, 2018 2(2020) (DE-627)1694655601 25724754 nnns volume:2 year:2020 https://doi.org/10.12688/gatesopenres.12856.2 kostenfrei https://doaj.org/article/7c2e31a351ba4593bd81d3bc0cc3ea88 kostenfrei https://gatesopenresearch.org/articles/2-41/v2 kostenfrei https://doaj.org/toc/2572-4754 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_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_2014 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 2 2020
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author	Chenxi Zhou
spellingShingle	Chenxi Zhou misc Medicine misc R Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]
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topic_title	Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]
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title	Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]
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title_full	Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]
author_sort	Chenxi Zhou
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author_browse	Chenxi Zhou Tania Duarte Rocio Silvestre Genoveva Rossel Robert O. M. Mwanga Awais Khan Andrew W. George Zhangjun Fei G. Craig Yencho David Ellis Lachlan J. M. Coin
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title_sort	insights into population structure of east african sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]
title_auth	Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]
abstract	Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.
abstractGer	Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.
abstract_unstemmed	Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.
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title_short	Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]
url	https://doi.org/10.12688/gatesopenres.12856.2 https://doaj.org/article/7c2e31a351ba4593bd81d3bc0cc3ea88 https://gatesopenresearch.org/articles/2-41/v2 https://doaj.org/toc/2572-4754
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author2	Tania Duarte Rocio Silvestre Genoveva Rossel Robert O. M. Mwanga Awais Khan Andrew W. George Zhangjun Fei G. Craig Yencho David Ellis Lachlan J. M. Coin
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Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 2; peer review: 2 approved, 3 approved with reservations]

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