An improved genome assembly of the fluke Schistosoma japonicum.

<h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of th...
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Autor*in:	Fang Luo [verfasserIn] Mingbo Yin [verfasserIn] Xiaojin Mo [verfasserIn] Chengsong Sun [verfasserIn] Qunfeng Wu [verfasserIn] Bingkuan Zhu [verfasserIn] Manyu Xiang [verfasserIn] Jipeng Wang [verfasserIn] Yi Wang [verfasserIn] Jian Li [verfasserIn] Ting Zhang [verfasserIn] Bin Xu [verfasserIn] Huajun Zheng [verfasserIn] Zheng Feng [verfasserIn] Wei Hu [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Übergeordnetes Werk:	In: PLoS Neglected Tropical Diseases - Public Library of Science (PLoS), 2008, 13(2019), 8, p e0007612
Übergeordnetes Werk:	volume:13 ; year:2019 ; number:8, p e0007612

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

DOI / URN:	10.1371/journal.pntd.0007612

Katalog-ID:	DOAJ077354834

Internformat


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520			\|a <h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.
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allfields	10.1371/journal.pntd.0007612 doi (DE-627)DOAJ077354834 (DE-599)DOAJ3025bd9a10fb4bc0862301db366017a8 DE-627 ger DE-627 rakwb eng RC955-962 RA1-1270 Fang Luo verfasserin aut An improved genome assembly of the fluke Schistosoma japonicum. 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future. Arctic medicine. Tropical medicine Public aspects of medicine Mingbo Yin verfasserin aut Xiaojin Mo verfasserin aut Chengsong Sun verfasserin aut Qunfeng Wu verfasserin aut Bingkuan Zhu verfasserin aut Manyu Xiang verfasserin aut Jipeng Wang verfasserin aut Yi Wang verfasserin aut Jian Li verfasserin aut Ting Zhang verfasserin aut Bin Xu verfasserin aut Huajun Zheng verfasserin aut Zheng Feng verfasserin aut Wei Hu verfasserin aut In PLoS Neglected Tropical Diseases Public Library of Science (PLoS), 2008 13(2019), 8, p e0007612 (DE-627)568915356 (DE-600)2429704-5 19352735 nnns volume:13 year:2019 number:8, p e0007612 https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/article/3025bd9a10fb4bc0862301db366017a8 kostenfrei https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/toc/1935-2727 Journal toc kostenfrei https://doaj.org/toc/1935-2735 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 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_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_2522 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 13 2019 8, p e0007612
spelling	10.1371/journal.pntd.0007612 doi (DE-627)DOAJ077354834 (DE-599)DOAJ3025bd9a10fb4bc0862301db366017a8 DE-627 ger DE-627 rakwb eng RC955-962 RA1-1270 Fang Luo verfasserin aut An improved genome assembly of the fluke Schistosoma japonicum. 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future. Arctic medicine. Tropical medicine Public aspects of medicine Mingbo Yin verfasserin aut Xiaojin Mo verfasserin aut Chengsong Sun verfasserin aut Qunfeng Wu verfasserin aut Bingkuan Zhu verfasserin aut Manyu Xiang verfasserin aut Jipeng Wang verfasserin aut Yi Wang verfasserin aut Jian Li verfasserin aut Ting Zhang verfasserin aut Bin Xu verfasserin aut Huajun Zheng verfasserin aut Zheng Feng verfasserin aut Wei Hu verfasserin aut In PLoS Neglected Tropical Diseases Public Library of Science (PLoS), 2008 13(2019), 8, p e0007612 (DE-627)568915356 (DE-600)2429704-5 19352735 nnns volume:13 year:2019 number:8, p e0007612 https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/article/3025bd9a10fb4bc0862301db366017a8 kostenfrei https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/toc/1935-2727 Journal toc kostenfrei https://doaj.org/toc/1935-2735 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 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_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_2522 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 13 2019 8, p e0007612
allfields_unstemmed	10.1371/journal.pntd.0007612 doi (DE-627)DOAJ077354834 (DE-599)DOAJ3025bd9a10fb4bc0862301db366017a8 DE-627 ger DE-627 rakwb eng RC955-962 RA1-1270 Fang Luo verfasserin aut An improved genome assembly of the fluke Schistosoma japonicum. 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future. Arctic medicine. Tropical medicine Public aspects of medicine Mingbo Yin verfasserin aut Xiaojin Mo verfasserin aut Chengsong Sun verfasserin aut Qunfeng Wu verfasserin aut Bingkuan Zhu verfasserin aut Manyu Xiang verfasserin aut Jipeng Wang verfasserin aut Yi Wang verfasserin aut Jian Li verfasserin aut Ting Zhang verfasserin aut Bin Xu verfasserin aut Huajun Zheng verfasserin aut Zheng Feng verfasserin aut Wei Hu verfasserin aut In PLoS Neglected Tropical Diseases Public Library of Science (PLoS), 2008 13(2019), 8, p e0007612 (DE-627)568915356 (DE-600)2429704-5 19352735 nnns volume:13 year:2019 number:8, p e0007612 https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/article/3025bd9a10fb4bc0862301db366017a8 kostenfrei https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/toc/1935-2727 Journal toc kostenfrei https://doaj.org/toc/1935-2735 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 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_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_2522 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 13 2019 8, p e0007612
allfieldsGer	10.1371/journal.pntd.0007612 doi (DE-627)DOAJ077354834 (DE-599)DOAJ3025bd9a10fb4bc0862301db366017a8 DE-627 ger DE-627 rakwb eng RC955-962 RA1-1270 Fang Luo verfasserin aut An improved genome assembly of the fluke Schistosoma japonicum. 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future. Arctic medicine. Tropical medicine Public aspects of medicine Mingbo Yin verfasserin aut Xiaojin Mo verfasserin aut Chengsong Sun verfasserin aut Qunfeng Wu verfasserin aut Bingkuan Zhu verfasserin aut Manyu Xiang verfasserin aut Jipeng Wang verfasserin aut Yi Wang verfasserin aut Jian Li verfasserin aut Ting Zhang verfasserin aut Bin Xu verfasserin aut Huajun Zheng verfasserin aut Zheng Feng verfasserin aut Wei Hu verfasserin aut In PLoS Neglected Tropical Diseases Public Library of Science (PLoS), 2008 13(2019), 8, p e0007612 (DE-627)568915356 (DE-600)2429704-5 19352735 nnns volume:13 year:2019 number:8, p e0007612 https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/article/3025bd9a10fb4bc0862301db366017a8 kostenfrei https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/toc/1935-2727 Journal toc kostenfrei https://doaj.org/toc/1935-2735 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 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_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_2522 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 13 2019 8, p e0007612
allfieldsSound	10.1371/journal.pntd.0007612 doi (DE-627)DOAJ077354834 (DE-599)DOAJ3025bd9a10fb4bc0862301db366017a8 DE-627 ger DE-627 rakwb eng RC955-962 RA1-1270 Fang Luo verfasserin aut An improved genome assembly of the fluke Schistosoma japonicum. 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future. Arctic medicine. Tropical medicine Public aspects of medicine Mingbo Yin verfasserin aut Xiaojin Mo verfasserin aut Chengsong Sun verfasserin aut Qunfeng Wu verfasserin aut Bingkuan Zhu verfasserin aut Manyu Xiang verfasserin aut Jipeng Wang verfasserin aut Yi Wang verfasserin aut Jian Li verfasserin aut Ting Zhang verfasserin aut Bin Xu verfasserin aut Huajun Zheng verfasserin aut Zheng Feng verfasserin aut Wei Hu verfasserin aut In PLoS Neglected Tropical Diseases Public Library of Science (PLoS), 2008 13(2019), 8, p e0007612 (DE-627)568915356 (DE-600)2429704-5 19352735 nnns volume:13 year:2019 number:8, p e0007612 https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/article/3025bd9a10fb4bc0862301db366017a8 kostenfrei https://doi.org/10.1371/journal.pntd.0007612 kostenfrei https://doaj.org/toc/1935-2727 Journal toc kostenfrei https://doaj.org/toc/1935-2735 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 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_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_2522 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 13 2019 8, p e0007612
language	English
source	In PLoS Neglected Tropical Diseases 13(2019), 8, p e0007612 volume:13 year:2019 number:8, p e0007612
sourceStr	In PLoS Neglected Tropical Diseases 13(2019), 8, p e0007612 volume:13 year:2019 number:8, p e0007612
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Arctic medicine. Tropical medicine Public aspects of medicine
isfreeaccess_bool	true
container_title	PLoS Neglected Tropical Diseases
authorswithroles_txt_mv	Fang Luo @@aut@@ Mingbo Yin @@aut@@ Xiaojin Mo @@aut@@ Chengsong Sun @@aut@@ Qunfeng Wu @@aut@@ Bingkuan Zhu @@aut@@ Manyu Xiang @@aut@@ Jipeng Wang @@aut@@ Yi Wang @@aut@@ Jian Li @@aut@@ Ting Zhang @@aut@@ Bin Xu @@aut@@ Huajun Zheng @@aut@@ Zheng Feng @@aut@@ Wei Hu @@aut@@
publishDateDaySort_date	2019-01-01T00:00:00Z
hierarchy_top_id	568915356
id	DOAJ077354834
language_de	englisch
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callnumber-first	R - Medicine
author	Fang Luo
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topic_title	RC955-962 RA1-1270 An improved genome assembly of the fluke Schistosoma japonicum
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title	An improved genome assembly of the fluke Schistosoma japonicum.
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title_full	An improved genome assembly of the fluke Schistosoma japonicum
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author_browse	Fang Luo Mingbo Yin Xiaojin Mo Chengsong Sun Qunfeng Wu Bingkuan Zhu Manyu Xiang Jipeng Wang Yi Wang Jian Li Ting Zhang Bin Xu Huajun Zheng Zheng Feng Wei Hu
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title_sort	improved genome assembly of the fluke schistosoma japonicum
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title_auth	An improved genome assembly of the fluke Schistosoma japonicum.
abstract	<h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.
abstractGer	<h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.
abstract_unstemmed	<h4<Background</h4<Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.<h4<Conclusions</h4<Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.
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title_short	An improved genome assembly of the fluke Schistosoma japonicum.
url	https://doi.org/10.1371/journal.pntd.0007612 https://doaj.org/article/3025bd9a10fb4bc0862301db366017a8 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735
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A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.<h4<Findings</h4<In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. 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An improved genome assembly of the fluke Schistosoma japonicum.

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