Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)
- Author
- Xiao Ma (UGent) , Jeanine L. Olsen, Thorsten B.H. Reusch, Gabriele Procaccini, Dave Kudrna, Melissa Williams, Jane Grimwood, Shanmugam Rajasekar, Jerry Jenkins, Jeremy Schmutz and Yves Van de Peer (UGent)
- Organization
- Abstract
- Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.
- Keywords
- Seagrass, Zostera marina, eelgrass, chromosome-scale genome assembly, annotation
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Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8704976
- MLA
- Ma, Xiao, et al. “Improved Chromosome-Level Genome Assembly and Annotation of the Seagrass, Zostera Marina (Eelgrass).” F1000RESEARCH, vol. 10, 2021, doi:10.12688/f1000research.38156.1.
- APA
- Ma, X., Olsen, J. L., Reusch, T. B. H., Procaccini, G., Kudrna, D., Williams, M., … Van de Peer, Y. (2021). Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass). F1000RESEARCH, 10. https://doi.org/10.12688/f1000research.38156.1
- Chicago author-date
- Ma, Xiao, Jeanine L. Olsen, Thorsten B.H. Reusch, Gabriele Procaccini, Dave Kudrna, Melissa Williams, Jane Grimwood, et al. 2021. “Improved Chromosome-Level Genome Assembly and Annotation of the Seagrass, Zostera Marina (Eelgrass).” F1000RESEARCH 10. https://doi.org/10.12688/f1000research.38156.1.
- Chicago author-date (all authors)
- Ma, Xiao, Jeanine L. Olsen, Thorsten B.H. Reusch, Gabriele Procaccini, Dave Kudrna, Melissa Williams, Jane Grimwood, Shanmugam Rajasekar, Jerry Jenkins, Jeremy Schmutz, and Yves Van de Peer. 2021. “Improved Chromosome-Level Genome Assembly and Annotation of the Seagrass, Zostera Marina (Eelgrass).” F1000RESEARCH 10. doi:10.12688/f1000research.38156.1.
- Vancouver
- 1.Ma X, Olsen JL, Reusch TBH, Procaccini G, Kudrna D, Williams M, et al. Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass). F1000RESEARCH. 2021;10.
- IEEE
- [1]X. Ma et al., “Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass),” F1000RESEARCH, vol. 10, 2021.
@article{8704976, abstract = {{Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.}}, articleno = {{289}}, author = {{Ma, Xiao and Olsen, Jeanine L. and Reusch, Thorsten B.H. and Procaccini, Gabriele and Kudrna, Dave and Williams, Melissa and Grimwood, Jane and Rajasekar, Shanmugam and Jenkins, Jerry and Schmutz, Jeremy and Van de Peer, Yves}}, issn = {{2046-1402}}, journal = {{F1000RESEARCH}}, keywords = {{Seagrass,Zostera marina,eelgrass,chromosome-scale genome assembly,annotation}}, language = {{eng}}, pages = {{10}}, title = {{Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)}}, url = {{http://doi.org/10.12688/f1000research.38156.1}}, volume = {{10}}, year = {{2021}}, }
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