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

BMC Genomics

Research

Filipe Alberto¹  Gabriel J. Montecinos¹  Jose Diesel²  Sergey V. Nuzhdin²  Kelly DeWeese²  Gary Molano²  Daniel C. Reed³  Robert J. Miller³  Sara Calhoun⁴  Anna Lipzen⁴  Alan Kuo⁴  Asaf Salamov⁴  Igor V. Grigoriev⁵ 

[1]Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA

[2]Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA

[3]Marine Science Institute, University of California at Santa Barbara, 93106, Santa Barbara, CA, USA

[4]U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

[5]U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

[6]Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA

关键词: Genome;    Giant kelp;    Macrocystis pyrifera;    Brown macroalga;    Population genetics;   

DOI  :  10.1186/s12864-023-09658-x

 received in 2023-03-09, accepted in 2023-09-07,  发布年份 2023

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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