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...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09658-x |
| _version_ | 1827724420654825472 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Jose Diesel |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T22:15:33Z |
| format | Article |
| id | doaj.art-957b18a9522848a29951f51600f67901 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:33Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-957b18a9522848a29951f51600f679012023-11-19T12:28:11ZengBMCBMC Genomics1471-21642023-09-0124111310.1186/s12864-023-09658-xA scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)Jose Diesel0Gary Molano1Gabriel J. Montecinos2Kelly DeWeese3Sara Calhoun4Alan Kuo5Anna Lipzen6Asaf Salamov7Igor V. Grigoriev8Daniel C. Reed9Robert J. Miller10Sergey V. Nuzhdin11Filipe Alberto12Department of Molecular and Computational Biology, University of Southern CaliforniaDepartment of Molecular and Computational Biology, University of Southern CaliforniaDepartment of Biological Sciences, University of Wisconsin-MilwaukeeDepartment of Molecular and Computational Biology, University of Southern CaliforniaU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National LaboratoryU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National LaboratoryU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National LaboratoryU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National LaboratoryU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National LaboratoryMarine Science Institute, University of California at Santa BarbaraMarine Science Institute, University of California at Santa BarbaraDepartment of Molecular and Computational Biology, University of Southern CaliforniaDepartment of Biological Sciences, University of Wisconsin-MilwaukeeAbstract 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.https://doi.org/10.1186/s12864-023-09658-xGenomeGiant kelpMacrocystis pyriferaBrown macroalgaPopulation genetics |
| spellingShingle | 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 A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) BMC Genomics Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics |
| title | A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) |
| title_full | A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) |
| title_fullStr | A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) |
| title_full_unstemmed | A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) |
| title_short | A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera) |
| title_sort | scaffolded and annotated reference genome of giant kelp macrocystis pyrifera |
| topic | Genome Giant kelp Macrocystis pyrifera Brown macroalga Population genetics |
| url | https://doi.org/10.1186/s12864-023-09658-x |
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