Genome editing in diatoms: achievements and goals

Kroth, Peter G.; Bones, Atle M.; Daboussi, Fayza; Ferrante, Maria I.; Jaubert, Marianne; Kolot, Misha; Nymark, Marianne; Río Bártulos, Carolina; Ritter, Andrés; Russo, Monia T.; Serif, Manuel; Winge, Per; Falciatore, Angela

doi:10.1007/s00299-018-2334-1

Review
Published: 23 August 2018

Genome editing in diatoms: achievements and goals

Peter G. Kroth ORCID: orcid.org/0000-0003-4734-8955¹,
Atle M. Bones²,
Fayza Daboussi³,
Maria I. Ferrante⁴,
Marianne Jaubert⁷,
Misha Kolot^5,6,
Marianne Nymark²,
Carolina Río Bártulos¹,
Andrés Ritter⁷,
Monia T. Russo⁴,
Manuel Serif³,
Per Winge² &
Angela Falciatore⁷

Plant Cell Reports volume 37, pages 1401–1408 (2018)Cite this article

2452 Accesses
32 Citations
15 Altmetric
Metrics details

Abstract

Diatoms are major components of phytoplankton and play a key role in the ecology of aquatic ecosystems. These algae are of great scientific importance for a wide variety of research areas, ranging from marine ecology and oceanography to biotechnology. During the last 20 years, the availability of genomic information on selected diatom species and a substantial progress in genetic manipulation, strongly contributed to establishing diatoms as molecular model organisms for marine biology research. Recently, tailored TALEN endonucleases and the CRISPR/Cas9 system were utilized in diatoms, allowing targeted genetic modifications and the generation of knockout strains. These approaches are extremely valuable for diatom research because breeding, forward genetic screens by random insertion, and chemical mutagenesis are not applicable to the available model species Phaeodactylum tricornutum and Thalassiosira pseudonana, which do not cross sexually in the lab. Here, we provide an overview of the genetic toolbox that is currently available for performing stable genetic modifications in diatoms. We also discuss novel challenges that need to be addressed to fully exploit the potential of these technologies for the characterization of diatom biology and for metabolic engineering.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

References

Alipanah L, Rohloff J, Winge P et al (2015) Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum. J Exp Bot 66:6281–6296. https://doi.org/10.1093/jxb/erv340
CAS Article PubMed PubMed Central Google Scholar
Allorent G, Guglielmino E, Giustini C, Courtois F (2018) Generation of mutants of nuclear-encoded plastid proteins using CRISPR/Cas9 in the diatom Phaeodactylum tricornutum. Methods Mol Biol 1829:367–378. https://doi.org/10.1007/978-1-4939-8654-5_24
Article Google Scholar
Apt KE, Kroth-Pancic PG, Grossman AR (1996) Stable nuclear transformation of the diatom Phaeodactylum tricornutum. Mol Gen Genet 252:572–579. https://doi.org/10.1007/BF02172403
CAS Article Google Scholar
Apt KE, Zaslavkaia L, Lippmeier JC et al (2002) In vivo characterization of diatom multipartite plastid targeting signals. J Cell Sci 115:4061–4069. https://doi.org/10.1242/jcs.00092
CAS Article Google Scholar
Archibald JM (2015) Endosymbiosis and eukaryotic cell evolution. Curr Biol 25:R911–R921. https://doi.org/10.1016/j.cub.2015.07.055
CAS Article Google Scholar
Armbrust EV (2009) The life of diatoms in the world’s oceans. Nature 459:185–192. https://doi.org/10.1038/nature08057
CAS Article Google Scholar
Azaro MA, Landy A (2002) λ Integrase and the Lambda int family. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM Press, Washington, DC, pp 118–148. https://doi.org/10.1128/9781555817954.ch7
Baek K, Kim DH, Jeong J et al (2016) DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins. Sci Rep 6:30620. https://doi.org/10.1038/srep30620
CAS Article PubMed PubMed Central Google Scholar
Basu S, Patil S, Mapleson D et al (2017) Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. New Phytol 215:140–156. https://doi.org/10.1111/nph.14557
CAS Article PubMed PubMed Central Google Scholar
Beurdeley M, Bietz F, Li J et al (2013) Compact designer TALENs for efficient genome engineering. Nature Commun 4:1762. https://doi.org/10.1038/ncomms2782
CAS Article Google Scholar
Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I (1998) FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci USA 95:10570–10575. https://doi.org/10.1073/pnas.95.18.10570
CAS Article Google Scholar
Buhmann MT, Poulsen N, Klemm J et al (2014) A tyrosine-rich cell surface protein in the diatom Amphora coffeaeformis identified through transcriptome analysis and genetic transformation. PLoS ONE 9:e110369. https://doi.org/10.1371/journal.pone.0110369
CAS Article PubMed PubMed Central Google Scholar
Buitrago-Flórez FJ, Restrepo S, Riaño-Pachón DM (2014) Identification of transcription factor genes and their correlation with the high diversity of stramenopiles. PLoS ONE 9:e111841. https://doi.org/10.1371/journal.pone.0111841
CAS Article PubMed PubMed Central Google Scholar
Chen X, Xu F, Zhu C et al (2014) Dual sgRNA-directed gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans. Sci Rep 4:7581. https://doi.org/10.1038/srep07581
CAS Article PubMed PubMed Central Google Scholar
Christian M, Cermak T, Doyle EL et al (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761. https://doi.org/10.1534/genetics.110.120717
CAS Article PubMed PubMed Central Google Scholar
Chu L, Ewe D, Río Bártulos C et al (2016) Rapid induction of GFP expression by the nitrate reductase promoter in the diatom Phaeodactylum tricornutum. Peer J 4:e2344. https://doi.org/10.7717/peerj.2344
CAS Article Google Scholar
Cong L, Ran FA, Cox D et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823. https://doi.org/10.1126/science.1231143
CAS Article PubMed PubMed Central Google Scholar
Daboussi F, Leduc S, Maréchal A et al (2014) Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology. Nature Commun 5:3831. https://doi.org/10.1038/ncomms4831
CAS Article Google Scholar
De Riso V, Raniello R, Maumus F et al (2009) Gene silencing in the marine diatom Phaeodactylum tricornutum. Nucleic Acids Res 37:e96–e96. https://doi.org/10.1093/nar/gkp448
CAS Article PubMed PubMed Central Google Scholar
Diner RE, Schwenck SM, McCrow JP et al (2016) Genetic manipulation of competition for nitrate between heterotrophic bacteria and diatoms. Front Microbiol 7:880. https://doi.org/10.3389/fmicb.2016.00880
Article PubMed PubMed Central Google Scholar
Diner RE, Noddings CM, Lian NC et al (2017) Diatom centromeres suggest a mechanism for nuclear DNA acquisition. Proc Natl Acad Sci USA 114:E6015–E6024. https://doi.org/10.1073/pnas.1700764114
CAS Article Google Scholar
Doudna JA, Charpentier E (2014) The new frontier of genome engineering with CRISPR-Cas9. Science 346:1258096–1258096. https://doi.org/10.1126/science.1258096
CAS Article PubMed PubMed Central Google Scholar
Doyle EL, Booher NJ, Standage DS et al (2012) TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res 40:W117–W122. https://doi.org/10.1093/nar/gks608
CAS Article PubMed PubMed Central Google Scholar
Dunahay TG, Jarvis EE, Roessler PG (1995) Genetic transformation of the diatoms Cyclotella cryptica and Navicula saprophila. J Phycol 31:1004–1012. https://doi.org/10.1111/j.0022-3646.1995.01004.x
CAS Article Google Scholar
Engler C, Kandzia R, Marillonnet S (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3:e3647. https://doi.org/10.1371/journal.pone.0003647
CAS Article PubMed PubMed Central Google Scholar
Falciatore A, Casotti R, Leblanc C et al (1999) Transformation of nonselectable reporter genes in marine diatoms. Mar Biotechnol 1:239–251. https://doi.org/10.1007/PL00011773
CAS Article Google Scholar
Ferenczi A, Pyott DE, Xipnitou A, Molnar A (2017) Efficient targeted DNA editing and replacement in Chlamydomonas reinhardtii using Cpf1 ribonucleoproteins and single-stranded DNA. Proc Natl Acad Sci USA 114:13567–13572. https://doi.org/10.1073/pnas.1710597114
CAS Article Google Scholar
Fischer H, Robl I, Sumper M, Kröger N (1999) Targeting and covalent modification of cell wall and membrane proteins heterologously expressed in the diatom Cylindrotheca fusformis. J Phycol 35:113–120. https://doi.org/10.1046/j.1529-8817.1999.3510113.x
CAS Article Google Scholar
Fortunato AE, Jaubert M, Enomoto G et al (2016) Diatom phytochromes reveal the existence of far-red-light-based sensing in the ocean. Plant Cell 28:616–628. https://doi.org/10.1105/tpc.15.00928
CAS Article PubMed PubMed Central Google Scholar
Gottfried P, Lotan O, Kolot M et al (2005) Site-specific recombination in Arabidopsis plants promoted by the Integrase protein of coliphage HK022. Plant Mol Biol 57:435–444. https://doi.org/10.1007/s11103-004-0076-7
CAS Article Google Scholar
Greiner A, Kelterborn S, Evers H et al (2017) Targeting of photoreceptor genes in Chlamydomonas reinhardtii via zinc-finger nucleases and CRISPR/Cas9. Plant Cell 29:2498–2518. https://doi.org/10.1105/tpc.17.00659
CAS Article PubMed PubMed Central Google Scholar
Haeussler M, Schönig K, Eckert H et al (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17:148. https://doi.org/10.1186/s13059-016-1012-2
CAS Article PubMed PubMed Central Google Scholar
Harel-Levi G, Goltsman J, Tuby CNJH et al (2008) Human genomic site-specific recombination catalyzed by coliphage HK022 integrase. J Biotechnol 134:46–54. https://doi.org/10.1016/j.jbiotec.2008.01.002
CAS Article Google Scholar
Hempel F, Bozarth AS, Lindenkamp N et al (2011) Microalgae as bioreactors for bioplastic production. Microb Cell Fact 10:81. https://doi.org/10.1186/1475-2859-10-81
CAS Article PubMed PubMed Central Google Scholar
Hopes A, Nekrasov V, Kamoun S, Mock T (2016) Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana. Plant Methods 12:49. https://doi.org/10.1186/s13007-016-0148-0
CAS Article PubMed PubMed Central Google Scholar
Huang W, Daboussi F (2017) Genetic and metabolic engineering in diatoms. Philos Trans R Soc Lond B Biol Sci 372:20160411. https://doi.org/10.1098/rstb.2016.0411
CAS Article PubMed PubMed Central Google Scholar
Ifuku K, Yan D, Miyahara M et al (2015) A stable and efficient nuclear transformation system for the diatom Chaetoceros gracilis. Photosynth Res 123:203–211. https://doi.org/10.1007/s11120-014-0048-y
CAS Article Google Scholar
Karas BJ, Diner RE, Lefebvre SC et al (2015) Designer diatom episomes delivered by bacterial conjugation. Nat Commun 6:6925. https://doi.org/10.1038/ncomms7925
CAS Article PubMed PubMed Central Google Scholar
Kirst H, Melis A (2014) The chloroplast signal recognition particle (CpSRP) pathway as a tool to minimize chlorophyll antenna size and maximize photosynthetic productivity. Biotechnol Adv 32:66–72. https://doi.org/10.1016/j.biotechadv.2013.08.018
CAS Article Google Scholar
Kolot M, Malchin N, Elias A et al (2015) Site promiscuity of coliphage HK022 integrase as a tool for gene therapy. Gene Ther 22:521–527. https://doi.org/10.1038/gt.2015.9
CAS Article Google Scholar
Kroth PG, Wilhelm C, Kottke T (2017) An update on aureochromes: Phylogeny—mechanism—function. J Plant Physiol 217:20–26. https://doi.org/10.1016/j.jplph.2017.06.010
CAS Article Google Scholar
Lau JB, Stork S, Moog D et al (2016) Protein-protein interactions indicate composition of a 480 kDa SELMA complex in the second outermost membrane of diatom complex plastids. Mol Microbiol 100:76–89. https://doi.org/10.1111/mmi.13302
CAS Article Google Scholar
Lepetit B, Sturm S, Rogato A et al (2013) High light acclimation in the secondary plastids containing diatom Phaeodactylum tricornutum is triggered by the redox state of the plastoquinone pool. Plant Physiol 161:853–865. https://doi.org/10.1104/pp.112.207811
CAS Article Google Scholar
Lieber MR (2010) The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79:181–211. https://doi.org/10.1146/annurev.biochem.052308.093131
CAS Article PubMed PubMed Central Google Scholar
Lin Y, Fine EJ, Zheng Z et al (2014) SAPTA: a new design tool for improving TALE nuclease activity. Nucleic Acids Res 42:e47. https://doi.org/10.1093/nar/gkt1363
CAS Article PubMed PubMed Central Google Scholar
Malviya S, Scalco E, Audic S et al (2016) Insights into global diatom distribution and diversity in the world’s ocean. Proc Natl Acad Sci USA 113:E1516–E1525. https://doi.org/10.1073/pnas.1509523113
CAS Article Google Scholar
Malzahn A, Lowder L, Qi Y (2017) Plant genome editing with TALEN and CRISPR. Cell Biosci 7:21. https://doi.org/10.1186/s13578-017-0148-4
CAS Article PubMed PubMed Central Google Scholar
Matthijs M, Fabris M, Broos S et al (2016) Profiling of the early nitrogen stress response in the diatom Phaeodactylum tricornutum reveals a novel family of RING-domain transcription factors. Plant Physiol 170:489–498. https://doi.org/10.1104/pp.15.01300
CAS Article Google Scholar
Matthijs M, Fabris M, Obata T et al (2017) The transcription factor bZIP14 regulates the TCA cycle in the diatom Phaeodactylum tricornutum. EMBO J 36:1559–1576. https://doi.org/10.15252/embj.201696392
CAS Article PubMed PubMed Central Google Scholar
McCarthy JK, Smith SR, McCrow JP et al (2017) Nitrate reductase knockout uncouples nitrate transport from nitrate assimilation and drives repartitioning of carbon flux in a model pennate diatom. Plant Cell 29:2047–2070. https://doi.org/10.1105/tpc.16.00910
CAS Article PubMed PubMed Central Google Scholar
Meinke G, Bohm A, Hauber J et al (2016) Cre recombinase and other tyrosine recombinases. Chem Rev 116:12785–12820. https://doi.org/10.1021/acs.chemrev.6b00077
CAS Article Google Scholar
Melnikov O, Zaritsky A, Zarka A et al (2009) Site-specific recombination in the cyanobacterium anabaena sp. strain PCC 7120 catalyzed by the integrase of coliphage HK022. J Bacteriol 191:5879–5879. https://doi.org/10.1128/JB.00813-09
CAS Article PubMed PubMed Central Google Scholar
Miyagawa A, Okami T, Kira N et al (2009) Research note: high efficiency transformation of the diatom Phaeodactylum tricornutum with a promoter from the diatom Cylindrotheca fusiformis. Phycol Res 57:142–146. https://doi.org/10.1111/j.1440-1835.2009.00531.x
CAS Article Google Scholar
Miyahara M, Aoi M, Inoue-Kashino N et al (2013) Highly efficient transformation of the diatom Phaeodactylum tricornutum by multi-pulse electroporation. Biosci Biotechnol Biochem 77:874–876. https://doi.org/10.1271/bbb.120936
CAS Article Google Scholar
Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326:1501. https://doi.org/10.1126/science.1178817
CAS Article PubMed PubMed Central Google Scholar
Nafissi N, Slavcev R (2014) Bacteriophage recombination systems and biotechnical applications. Appl Microbiol Biotechnol 98:2841–2851. https://doi.org/10.1007/s00253-014-5512-2
CAS Article Google Scholar
Niu Y-F, Yang Z-K, Zhang M-H et al (2012) Transformation of diatom Phaeodactylum tricornutum by electroporation and establishment of inducible selection marker. Biotechniques 52:1–3. https://doi.org/10.2144/000113881
Article Google Scholar
Nymark M, Sharma AK, Sparstad T et al (2016) A CRISPR/Cas9 system adapted for gene editing in marine algae. Sci Rep 6:24951. https://doi.org/10.1038/srep24951
CAS Article PubMed PubMed Central Google Scholar
Nymark M, Sharma AK, Hafskjold MCG et al (2017) CRISPR/Cas9 gene editing in the marine diatom Phaeodactylum tricornutum. BioProtocols 7:15. https://doi.org/10.21769/BioProtoc.2442
Article Google Scholar
Ohno N, Inoue T, Yamashiki R et al (2012) CO2-cAMP-responsive cis-elements targeted by a transcription factor with CREB/ATF-like basic zipper domain in the marine diatom Phaeodactylum tricornutum. Plant Physiol 158:499–513. https://doi.org/10.1104/pp.111.190249
CAS Article Google Scholar
Poulsen N, Kröger N (2005) A new molecular tool for transgenic diatoms: control of mRNA and protein biosynthesis by an inducible promoter-terminator cassette. FEBS J 272:3413–3423. https://doi.org/10.1111/j.1742-4658.2005.04760.x
CAS Article Google Scholar
Poulsen N, Chesley PM, Kröger N (2006) Molecular genetic manipulation of the diatom Thalassiosira pseudonana (Bacillariophyceae). J Phycol 42:1059–1065. https://doi.org/10.1111/j.1529-8817.2006.00269.x
Article Google Scholar
Rastogi A, Murik O, Bowler C, Tirichine L (2016) PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing. BMC Bioinformatics 17:261. https://doi.org/10.1186/s12859-016-1143-1
Article PubMed PubMed Central Google Scholar
Rayko E, Maumus F, Maheswari U et al (2010) Transcription factor families inferred from genome sequences of photosynthetic stramenopiles. New Phytol 188:52–66. https://doi.org/10.1111/j.1469-8137.2010.03371.x
CAS Article Google Scholar
Russo MT, Annunziata R, Sanges R et al (2015) The upstream regulatory sequence of the light harvesting complex Lhcf2 gene of the marine diatom Phaeodactylum tricornutum enhances transcription in an orientation- and distance-independent fashion. Mar Genom 24(Pt 1):69–79. https://doi.org/10.1016/j.margen.2015.06.010
Article Google Scholar
Sanjana NE, Cong L, Zhou Y et al (2012) A transcription activator-like effector toolbox for genome engineering. Nat Protoc 7:171–192. https://doi.org/10.1038/nprot.2011.431
CAS Article PubMed PubMed Central Google Scholar
Santurtún A, Riancho JA, Arozamena J et al (2017) Indel analysis by droplet digital PCR: a sensitive method for DNA mixture detection and chimerism analysis. Int J Legal Med 131:67–72. https://doi.org/10.1007/s00414-016-1422-4
Article Google Scholar
Serif M, Lepetit B, Weißert K et al (2017) A fast and reliable strategy to generate TALEN-mediated gene knockouts in the diatom Phaeodactylum tricornutum. Algal Res 23:186–195. https://doi.org/10.1016/j.algal.2017.02.005
Article Google Scholar
Shalem O, Sanjana NE, Hartenian E et al (2014) Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343:84–87. https://doi.org/10.1126/science.1247005
CAS Article Google Scholar
Shin S-E, Lim J-M, Koh HG et al (2016) CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii. Sci Rep 6:27810. https://doi.org/10.1038/srep27810
CAS Article PubMed PubMed Central Google Scholar
Shrestha RP, Hildebrand M (2017) Development of a silicon limitation inducible expression system for recombinant protein production in the centric diatoms Thalassiosira pseudonana and Cyclotella cryptica. Microb Cell Fact. https://doi.org/10.1186/s12934-017-0760-3
Article PubMed PubMed Central Google Scholar
Siaut M, Heijde M, Mangogna M et al (2007) Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene 406:23–35. https://doi.org/10.1016/j.gene.2007.05.022
CAS Article Google Scholar
Slattery SS, Diamond A, Wang H et al (2018) An expanded plasmid-based genetic toolbox enables Cas9 genome editing and stable maintenance of synthetic pathways in Phaeodactylum tricornutum. ACS Synth Biol 7:328–338. https://doi.org/10.1021/acssynbio.7b00191
CAS Article Google Scholar
Smith J, Grizot S, Arnould S et al (2006) A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res 34:e149–e149. https://doi.org/10.1093/nar/gkl720
CAS Article PubMed PubMed Central Google Scholar
Steinert J, Schiml S, Puchta H (2016) Homology-based double-strand break-induced genome engineering in plants. Plant Cell Rep 35:1429–1438. https://doi.org/10.1007/s00299-016-1981-3
CAS Article Google Scholar
Stukenberg D, Zauner S, Dell’Aquila G, Maier UG (2018) Optimizing CRISPR/Cas9 for the diatom Phaeodactylum tricornutum. Front Plant Sci 9:740. https://doi.org/10.3389/fpls.2018.00740
Article PubMed PubMed Central Google Scholar
Valenzuela J, Mazurie A, Carlson RP et al (2012) Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum. Biotechnol Biofuels 5:40. https://doi.org/10.1186/1754-6834-5-40
CAS Article PubMed PubMed Central Google Scholar
Weber E, Engler C, Gruetzner R et al (2011) A modular cloning system for standardized assembly of multigene constructs. PLoS One 6:e16765. https://doi.org/10.1371/journal.pone.0016765
CAS Article PubMed PubMed Central Google Scholar
Weyman PD, Beeri K, Lefebvre SC et al (2015) Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis. Plant Biotechnol J 13:460–470. https://doi.org/10.1111/pbi.12254
CAS Article Google Scholar
Wirth D, Gama-Norton L, Riemer P et al (2007) Road to precision: recombinase-based targeting technologies for genome engineering. Curr Opin Biotechnol 18:411–419. https://doi.org/10.1016/j.copbio.2007.07.013
CAS Article Google Scholar
Wu Y, Gao T, Wang X et al (2014) TALE nickase mediates high efficient targeted transgene integration at the human multi-copy ribosomal DNA locus. Biochem Biophys Res Commun 446:261–266. https://doi.org/10.1016/j.bbrc.2014.02.099
CAS Article Google Scholar
Yoshinaga R, Niwa-Kubota M, Matsui H, Matsuda Y (2014) Characterization of iron-responsive promoters in the marine diatom Phaeodactylum tricornutum. Mar Genom 16:55–62. https://doi.org/10.1016/j.margen.2014.01.005
Article Google Scholar
Zhang C, Hu H (2014) High-efficiency nuclear transformation of the diatom Phaeodactylum tricornutum by electroporation. Mar Genom 16:63–66. https://doi.org/10.1016/j.margen.2013.10.003
CAS Article Google Scholar
Zischewski J, Fischer R, Bortesi L (2017) Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases. Biotechnol Adv 35:95–104. https://doi.org/10.1016/j.biotechadv.2016.12.003
CAS Article Google Scholar
Zu Y, Tong X, Wang Z et al (2013) TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat Methods 10:329–331. https://doi.org/10.1038/nmeth.2374
CAS Article Google Scholar

Download references

Acknowledgements

The authors would like to thank the Gordon and Betty Moore Foundation for generously supporting the project GBMF 4966 “DiaEdit—Development of genetic tools for the establishment of routine genome editing in the marine diatom Phaeodactylum tricornutum”. Research on genome editing in AF and MF labs is also supported by the European Assemble plus (Association of European Marine Biological Research Laboratories Expanded, H2020-INFRAIA-1-2016-2017) consortium. Several vectors for P. tricornutum genome editing generated in the framework of the DiaEdit consortium are available through Addgene: the CRISPR-Cas9 pKS_diaCas9_sgRNA (Addgene ID: 74923, https://www.addgene.org/74923/), the pPtPuc3m_diaCas9_sgRNA for episome-based genome editing (Addgene ID: 109219, https://www.addgene.org/109219/) (Winge et al. unpublished), and 8 TALEN Vectors (Addgene ID: 90415–90423; https://www.addgene.org/Peter_Kroth/).

Author information

Affiliations

Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
Peter G. Kroth & Carolina Río Bártulos
Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
Atle M. Bones, Marianne Nymark & Per Winge
LISBP, Université de Toulouse, CNRS, INSA, 135 Avenue de Rangueil, 31077, Toulouse, France
Fayza Daboussi & Manuel Serif
Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
Maria I. Ferrante & Monia T. Russo
Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
Misha Kolot
Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv, 69978, Israel
Misha Kolot
Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France
Marianne Jaubert, Andrés Ritter & Angela Falciatore

Authors

Peter G. Kroth
View author publications
You can also search for this author in PubMed Google Scholar
Atle M. Bones
View author publications
You can also search for this author in PubMed Google Scholar
Fayza Daboussi
View author publications
You can also search for this author in PubMed Google Scholar
Maria I. Ferrante
View author publications
You can also search for this author in PubMed Google Scholar
Marianne Jaubert
View author publications
You can also search for this author in PubMed Google Scholar
Misha Kolot
View author publications
You can also search for this author in PubMed Google Scholar
Marianne Nymark
View author publications
You can also search for this author in PubMed Google Scholar
Carolina Río Bártulos
View author publications
You can also search for this author in PubMed Google Scholar
Andrés Ritter
View author publications
You can also search for this author in PubMed Google Scholar
Monia T. Russo
View author publications
You can also search for this author in PubMed Google Scholar
Manuel Serif
View author publications
You can also search for this author in PubMed Google Scholar
Per Winge
View author publications
You can also search for this author in PubMed Google Scholar
Angela Falciatore
View author publications
You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Peter G. Kroth or Angela Falciatore.

Additional information

Communicated by Neal Stewart.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kroth, P.G., Bones, A.M., Daboussi, F. et al. Genome editing in diatoms: achievements and goals. Plant Cell Rep 37, 1401–1408 (2018). https://doi.org/10.1007/s00299-018-2334-1

Download citation

Received: 28 March 2018
Accepted: 07 August 2018
Published: 23 August 2018
Issue Date: October 2018
DOI: https://doi.org/10.1007/s00299-018-2334-1

Keywords

Diatom
Genome editing
TALEN
CRISPR
Conjugation
Promoter
Mutant screening