A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One...
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Autor*in:	Jose Diesel [verfasserIn] Gary Molano [verfasserIn] Gabriel J. Montecinos [verfasserIn] Kelly DeWeese [verfasserIn] Sara Calhoun [verfasserIn] Alan Kuo [verfasserIn] Anna Lipzen [verfasserIn] Asaf Salamov [verfasserIn] Igor V. Grigoriev [verfasserIn] Daniel C. Reed [verfasserIn] Robert J. Miller [verfasserIn] Sergey V. Nuzhdin [verfasserIn] Filipe Alberto [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics

Übergeordnetes Werk:	In: BMC Genomics - BMC, 2003, 24(2023), 1, Seite 13
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:1 ; pages:13

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s12864-023-09658-x

Katalog-ID:	DOAJ093316054

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520			\|a Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
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allfields	10.1186/s12864-023-09658-x doi (DE-627)DOAJ093316054 (DE-599)DOAJ957b18a9522848a29951f51600f67901 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Jose Diesel verfasserin aut A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species. Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics Biotechnology Genetics Gary Molano verfasserin aut Gabriel J. Montecinos verfasserin aut Kelly DeWeese verfasserin aut Sara Calhoun verfasserin aut Alan Kuo verfasserin aut Anna Lipzen verfasserin aut Asaf Salamov verfasserin aut Igor V. Grigoriev verfasserin aut Daniel C. Reed verfasserin aut Robert J. Miller verfasserin aut Sergey V. Nuzhdin verfasserin aut Filipe Alberto verfasserin aut In BMC Genomics BMC, 2003 24(2023), 1, Seite 13 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:24 year:2023 number:1 pages:13 https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/article/957b18a9522848a29951f51600f67901 kostenfrei https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/toc/1471-2164 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 13
spelling	10.1186/s12864-023-09658-x doi (DE-627)DOAJ093316054 (DE-599)DOAJ957b18a9522848a29951f51600f67901 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Jose Diesel verfasserin aut A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species. Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics Biotechnology Genetics Gary Molano verfasserin aut Gabriel J. Montecinos verfasserin aut Kelly DeWeese verfasserin aut Sara Calhoun verfasserin aut Alan Kuo verfasserin aut Anna Lipzen verfasserin aut Asaf Salamov verfasserin aut Igor V. Grigoriev verfasserin aut Daniel C. Reed verfasserin aut Robert J. Miller verfasserin aut Sergey V. Nuzhdin verfasserin aut Filipe Alberto verfasserin aut In BMC Genomics BMC, 2003 24(2023), 1, Seite 13 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:24 year:2023 number:1 pages:13 https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/article/957b18a9522848a29951f51600f67901 kostenfrei https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/toc/1471-2164 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 13
allfields_unstemmed	10.1186/s12864-023-09658-x doi (DE-627)DOAJ093316054 (DE-599)DOAJ957b18a9522848a29951f51600f67901 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Jose Diesel verfasserin aut A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species. Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics Biotechnology Genetics Gary Molano verfasserin aut Gabriel J. Montecinos verfasserin aut Kelly DeWeese verfasserin aut Sara Calhoun verfasserin aut Alan Kuo verfasserin aut Anna Lipzen verfasserin aut Asaf Salamov verfasserin aut Igor V. Grigoriev verfasserin aut Daniel C. Reed verfasserin aut Robert J. Miller verfasserin aut Sergey V. Nuzhdin verfasserin aut Filipe Alberto verfasserin aut In BMC Genomics BMC, 2003 24(2023), 1, Seite 13 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:24 year:2023 number:1 pages:13 https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/article/957b18a9522848a29951f51600f67901 kostenfrei https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/toc/1471-2164 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 13
allfieldsGer	10.1186/s12864-023-09658-x doi (DE-627)DOAJ093316054 (DE-599)DOAJ957b18a9522848a29951f51600f67901 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Jose Diesel verfasserin aut A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species. Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics Biotechnology Genetics Gary Molano verfasserin aut Gabriel J. Montecinos verfasserin aut Kelly DeWeese verfasserin aut Sara Calhoun verfasserin aut Alan Kuo verfasserin aut Anna Lipzen verfasserin aut Asaf Salamov verfasserin aut Igor V. Grigoriev verfasserin aut Daniel C. Reed verfasserin aut Robert J. Miller verfasserin aut Sergey V. Nuzhdin verfasserin aut Filipe Alberto verfasserin aut In BMC Genomics BMC, 2003 24(2023), 1, Seite 13 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:24 year:2023 number:1 pages:13 https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/article/957b18a9522848a29951f51600f67901 kostenfrei https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/toc/1471-2164 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 13
allfieldsSound	10.1186/s12864-023-09658-x doi (DE-627)DOAJ093316054 (DE-599)DOAJ957b18a9522848a29951f51600f67901 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Jose Diesel verfasserin aut A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species. Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics Biotechnology Genetics Gary Molano verfasserin aut Gabriel J. Montecinos verfasserin aut Kelly DeWeese verfasserin aut Sara Calhoun verfasserin aut Alan Kuo verfasserin aut Anna Lipzen verfasserin aut Asaf Salamov verfasserin aut Igor V. Grigoriev verfasserin aut Daniel C. Reed verfasserin aut Robert J. Miller verfasserin aut Sergey V. Nuzhdin verfasserin aut Filipe Alberto verfasserin aut In BMC Genomics BMC, 2003 24(2023), 1, Seite 13 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:24 year:2023 number:1 pages:13 https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/article/957b18a9522848a29951f51600f67901 kostenfrei https://doi.org/10.1186/s12864-023-09658-x kostenfrei https://doaj.org/toc/1471-2164 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 13
language	English
source	In BMC Genomics 24(2023), 1, Seite 13 volume:24 year:2023 number:1 pages:13
sourceStr	In BMC Genomics 24(2023), 1, Seite 13 volume:24 year:2023 number:1 pages:13
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics Biotechnology Genetics
isfreeaccess_bool	true
container_title	BMC Genomics
authorswithroles_txt_mv	Jose Diesel @@aut@@ Gary Molano @@aut@@ Gabriel J. Montecinos @@aut@@ Kelly DeWeese @@aut@@ Sara Calhoun @@aut@@ Alan Kuo @@aut@@ Anna Lipzen @@aut@@ Asaf Salamov @@aut@@ Igor V. Grigoriev @@aut@@ Daniel C. Reed @@aut@@ Robert J. Miller @@aut@@ Sergey V. Nuzhdin @@aut@@ Filipe Alberto @@aut@@
publishDateDaySort_date	2023-01-01T00:00:00Z
hierarchy_top_id	326644954
id	DOAJ093316054
language_de	englisch
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callnumber-first	T - Technology
author	Jose Diesel
spellingShingle	Jose Diesel misc TP248.13-248.65 misc QH426-470 misc Genome misc Giant kelp misc Macrocystis pyrifera misc Brown macroalga misc Population genetics misc Biotechnology misc Genetics A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)
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topic_title	TP248.13-248.65 QH426-470 A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics
topic	misc TP248.13-248.65 misc QH426-470 misc Genome misc Giant kelp misc Macrocystis pyrifera misc Brown macroalga misc Population genetics misc Biotechnology misc Genetics
topic_unstemmed	misc TP248.13-248.65 misc QH426-470 misc Genome misc Giant kelp misc Macrocystis pyrifera misc Brown macroalga misc Population genetics misc Biotechnology misc Genetics
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title	A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)
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title_full	A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)
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author_browse	Jose Diesel Gary Molano Gabriel J. Montecinos Kelly DeWeese Sara Calhoun Alan Kuo Anna Lipzen Asaf Salamov Igor V. Grigoriev Daniel C. Reed Robert J. Miller Sergey V. Nuzhdin Filipe Alberto
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title_sort	scaffolded and annotated reference genome of giant kelp (macrocystis pyrifera)
callnumber	TP248.13-248.65
title_auth	A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)
abstract	Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
abstractGer	Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
abstract_unstemmed	Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
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title_short	A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)
url	https://doi.org/10.1186/s12864-023-09658-x https://doaj.org/article/957b18a9522848a29951f51600f67901 https://doaj.org/toc/1471-2164
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A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

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