A single-cell genomics pipeline for environmental microbial eukaryotes

Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental...
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Autor*in:	Doina Ciobanu [verfasserIn] Alicia Clum [verfasserIn] Steven Ahrendt [verfasserIn] William B. Andreopoulos [verfasserIn] Asaf Salamov [verfasserIn] Sandy Chan [verfasserIn] C. Alisha Quandt [verfasserIn] Brian Foster [verfasserIn] Jan P. Meier-Kolthoff [verfasserIn] Yung Tsu Tang [verfasserIn] Patrick Schwientek [verfasserIn] Gerald L. Benny [verfasserIn] Matthew E. Smith [verfasserIn] Diane Bauer [verfasserIn] Shweta Deshpande [verfasserIn] Kerrie Barry [verfasserIn] Alex Copeland [verfasserIn] Steven W. Singer [verfasserIn] Tanja Woyke [verfasserIn] Igor V. Grigoriev [verfasserIn] Timothy Y. James [verfasserIn] Jan-Fang Cheng [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	Genomics Geomicrobiology Microbiology

Übergeordnetes Werk:	In: iScience - Elsevier, 2019, 24(2021), 4, Seite 102290-
Übergeordnetes Werk:	volume:24 ; year:2021 ; number:4 ; pages:102290-

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1016/j.isci.2021.102290

Katalog-ID:	DOAJ055202195

Internformat


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520			\|a Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
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allfields	10.1016/j.isci.2021.102290 doi (DE-627)DOAJ055202195 (DE-599)DOAJ506f8b6c69dd41728994c0947e3f3bf7 DE-627 ger DE-627 rakwb eng Doina Ciobanu verfasserin aut A single-cell genomics pipeline for environmental microbial eukaryotes 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes. Genomics Geomicrobiology Microbiology Science Q Alicia Clum verfasserin aut Steven Ahrendt verfasserin aut William B. Andreopoulos verfasserin aut Asaf Salamov verfasserin aut Sandy Chan verfasserin aut C. Alisha Quandt verfasserin aut Brian Foster verfasserin aut Jan P. Meier-Kolthoff verfasserin aut Yung Tsu Tang verfasserin aut Patrick Schwientek verfasserin aut Gerald L. Benny verfasserin aut Matthew E. Smith verfasserin aut Diane Bauer verfasserin aut Shweta Deshpande verfasserin aut Kerrie Barry verfasserin aut Alex Copeland verfasserin aut Steven W. Singer verfasserin aut Tanja Woyke verfasserin aut Igor V. Grigoriev verfasserin aut Timothy Y. James verfasserin aut Jan-Fang Cheng verfasserin aut In iScience Elsevier, 2019 24(2021), 4, Seite 102290- (DE-627)1019532106 25890042 nnns volume:24 year:2021 number:4 pages:102290- https://doi.org/10.1016/j.isci.2021.102290 kostenfrei https://doaj.org/article/506f8b6c69dd41728994c0947e3f3bf7 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221002583 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 24 2021 4 102290-
spelling	10.1016/j.isci.2021.102290 doi (DE-627)DOAJ055202195 (DE-599)DOAJ506f8b6c69dd41728994c0947e3f3bf7 DE-627 ger DE-627 rakwb eng Doina Ciobanu verfasserin aut A single-cell genomics pipeline for environmental microbial eukaryotes 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes. Genomics Geomicrobiology Microbiology Science Q Alicia Clum verfasserin aut Steven Ahrendt verfasserin aut William B. Andreopoulos verfasserin aut Asaf Salamov verfasserin aut Sandy Chan verfasserin aut C. Alisha Quandt verfasserin aut Brian Foster verfasserin aut Jan P. Meier-Kolthoff verfasserin aut Yung Tsu Tang verfasserin aut Patrick Schwientek verfasserin aut Gerald L. Benny verfasserin aut Matthew E. Smith verfasserin aut Diane Bauer verfasserin aut Shweta Deshpande verfasserin aut Kerrie Barry verfasserin aut Alex Copeland verfasserin aut Steven W. Singer verfasserin aut Tanja Woyke verfasserin aut Igor V. Grigoriev verfasserin aut Timothy Y. James verfasserin aut Jan-Fang Cheng verfasserin aut In iScience Elsevier, 2019 24(2021), 4, Seite 102290- (DE-627)1019532106 25890042 nnns volume:24 year:2021 number:4 pages:102290- https://doi.org/10.1016/j.isci.2021.102290 kostenfrei https://doaj.org/article/506f8b6c69dd41728994c0947e3f3bf7 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221002583 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 24 2021 4 102290-
allfields_unstemmed	10.1016/j.isci.2021.102290 doi (DE-627)DOAJ055202195 (DE-599)DOAJ506f8b6c69dd41728994c0947e3f3bf7 DE-627 ger DE-627 rakwb eng Doina Ciobanu verfasserin aut A single-cell genomics pipeline for environmental microbial eukaryotes 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes. Genomics Geomicrobiology Microbiology Science Q Alicia Clum verfasserin aut Steven Ahrendt verfasserin aut William B. Andreopoulos verfasserin aut Asaf Salamov verfasserin aut Sandy Chan verfasserin aut C. Alisha Quandt verfasserin aut Brian Foster verfasserin aut Jan P. Meier-Kolthoff verfasserin aut Yung Tsu Tang verfasserin aut Patrick Schwientek verfasserin aut Gerald L. Benny verfasserin aut Matthew E. Smith verfasserin aut Diane Bauer verfasserin aut Shweta Deshpande verfasserin aut Kerrie Barry verfasserin aut Alex Copeland verfasserin aut Steven W. Singer verfasserin aut Tanja Woyke verfasserin aut Igor V. Grigoriev verfasserin aut Timothy Y. James verfasserin aut Jan-Fang Cheng verfasserin aut In iScience Elsevier, 2019 24(2021), 4, Seite 102290- (DE-627)1019532106 25890042 nnns volume:24 year:2021 number:4 pages:102290- https://doi.org/10.1016/j.isci.2021.102290 kostenfrei https://doaj.org/article/506f8b6c69dd41728994c0947e3f3bf7 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221002583 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 24 2021 4 102290-
allfieldsGer	10.1016/j.isci.2021.102290 doi (DE-627)DOAJ055202195 (DE-599)DOAJ506f8b6c69dd41728994c0947e3f3bf7 DE-627 ger DE-627 rakwb eng Doina Ciobanu verfasserin aut A single-cell genomics pipeline for environmental microbial eukaryotes 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes. Genomics Geomicrobiology Microbiology Science Q Alicia Clum verfasserin aut Steven Ahrendt verfasserin aut William B. Andreopoulos verfasserin aut Asaf Salamov verfasserin aut Sandy Chan verfasserin aut C. Alisha Quandt verfasserin aut Brian Foster verfasserin aut Jan P. Meier-Kolthoff verfasserin aut Yung Tsu Tang verfasserin aut Patrick Schwientek verfasserin aut Gerald L. Benny verfasserin aut Matthew E. Smith verfasserin aut Diane Bauer verfasserin aut Shweta Deshpande verfasserin aut Kerrie Barry verfasserin aut Alex Copeland verfasserin aut Steven W. Singer verfasserin aut Tanja Woyke verfasserin aut Igor V. Grigoriev verfasserin aut Timothy Y. James verfasserin aut Jan-Fang Cheng verfasserin aut In iScience Elsevier, 2019 24(2021), 4, Seite 102290- (DE-627)1019532106 25890042 nnns volume:24 year:2021 number:4 pages:102290- https://doi.org/10.1016/j.isci.2021.102290 kostenfrei https://doaj.org/article/506f8b6c69dd41728994c0947e3f3bf7 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221002583 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 24 2021 4 102290-
allfieldsSound	10.1016/j.isci.2021.102290 doi (DE-627)DOAJ055202195 (DE-599)DOAJ506f8b6c69dd41728994c0947e3f3bf7 DE-627 ger DE-627 rakwb eng Doina Ciobanu verfasserin aut A single-cell genomics pipeline for environmental microbial eukaryotes 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes. Genomics Geomicrobiology Microbiology Science Q Alicia Clum verfasserin aut Steven Ahrendt verfasserin aut William B. Andreopoulos verfasserin aut Asaf Salamov verfasserin aut Sandy Chan verfasserin aut C. Alisha Quandt verfasserin aut Brian Foster verfasserin aut Jan P. Meier-Kolthoff verfasserin aut Yung Tsu Tang verfasserin aut Patrick Schwientek verfasserin aut Gerald L. Benny verfasserin aut Matthew E. Smith verfasserin aut Diane Bauer verfasserin aut Shweta Deshpande verfasserin aut Kerrie Barry verfasserin aut Alex Copeland verfasserin aut Steven W. Singer verfasserin aut Tanja Woyke verfasserin aut Igor V. Grigoriev verfasserin aut Timothy Y. James verfasserin aut Jan-Fang Cheng verfasserin aut In iScience Elsevier, 2019 24(2021), 4, Seite 102290- (DE-627)1019532106 25890042 nnns volume:24 year:2021 number:4 pages:102290- https://doi.org/10.1016/j.isci.2021.102290 kostenfrei https://doaj.org/article/506f8b6c69dd41728994c0947e3f3bf7 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221002583 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 24 2021 4 102290-
language	English
source	In iScience 24(2021), 4, Seite 102290- volume:24 year:2021 number:4 pages:102290-
sourceStr	In iScience 24(2021), 4, Seite 102290- volume:24 year:2021 number:4 pages:102290-
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Genomics Geomicrobiology Microbiology Science Q
isfreeaccess_bool	true
container_title	iScience
authorswithroles_txt_mv	Doina Ciobanu @@aut@@ Alicia Clum @@aut@@ Steven Ahrendt @@aut@@ William B. Andreopoulos @@aut@@ Asaf Salamov @@aut@@ Sandy Chan @@aut@@ C. Alisha Quandt @@aut@@ Brian Foster @@aut@@ Jan P. Meier-Kolthoff @@aut@@ Yung Tsu Tang @@aut@@ Patrick Schwientek @@aut@@ Gerald L. Benny @@aut@@ Matthew E. Smith @@aut@@ Diane Bauer @@aut@@ Shweta Deshpande @@aut@@ Kerrie Barry @@aut@@ Alex Copeland @@aut@@ Steven W. Singer @@aut@@ Tanja Woyke @@aut@@ Igor V. Grigoriev @@aut@@ Timothy Y. James @@aut@@ Jan-Fang Cheng @@aut@@
publishDateDaySort_date	2021-01-01T00:00:00Z
hierarchy_top_id	1019532106
id	DOAJ055202195
language_de	englisch
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author	Doina Ciobanu
spellingShingle	Doina Ciobanu misc Genomics misc Geomicrobiology misc Microbiology misc Science misc Q A single-cell genomics pipeline for environmental microbial eukaryotes
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topic_title	A single-cell genomics pipeline for environmental microbial eukaryotes Genomics Geomicrobiology Microbiology
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title	A single-cell genomics pipeline for environmental microbial eukaryotes
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title_full	A single-cell genomics pipeline for environmental microbial eukaryotes
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author_browse	Doina Ciobanu Alicia Clum Steven Ahrendt William B. Andreopoulos Asaf Salamov Sandy Chan C. Alisha Quandt Brian Foster Jan P. Meier-Kolthoff Yung Tsu Tang Patrick Schwientek Gerald L. Benny Matthew E. Smith Diane Bauer Shweta Deshpande Kerrie Barry Alex Copeland Steven W. Singer Tanja Woyke Igor V. Grigoriev Timothy Y. James Jan-Fang Cheng
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title_sort	single-cell genomics pipeline for environmental microbial eukaryotes
title_auth	A single-cell genomics pipeline for environmental microbial eukaryotes
abstract	Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
abstractGer	Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
abstract_unstemmed	Summary: Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
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title_short	A single-cell genomics pipeline for environmental microbial eukaryotes
url	https://doi.org/10.1016/j.isci.2021.102290 https://doaj.org/article/506f8b6c69dd41728994c0947e3f3bf7 http://www.sciencedirect.com/science/article/pii/S2589004221002583 https://doaj.org/toc/2589-0042
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author2Str	Alicia Clum Steven Ahrendt William B. Andreopoulos Asaf Salamov Sandy Chan C. Alisha Quandt Brian Foster Jan P. Meier-Kolthoff Yung Tsu Tang Patrick Schwientek Gerald L. Benny Matthew E. Smith Diane Bauer Shweta Deshpande Kerrie Barry Alex Copeland Steven W. Singer Tanja Woyke Igor V. Grigoriev Timothy Y. James Jan-Fang Cheng
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up_date	2024-07-03T13:35:33.586Z
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However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. 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A single-cell genomics pipeline for environmental microbial eukaryotes

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