Zeng D, Liu T, Tan J, Zhang Y, Zheng Z, Wang B, et al. PhieCBEs: plant high-efficiency cytidine base editors with expanded target range. Mol Plant. 2020;13(12):1666–9. https://doi.org/10.1016/j.molp.2020.11.001.
Article
CAS
PubMed
Google Scholar
Kim J-S. Precision genome engineering through adenine and cytosine base editing. Nat Plants. 2018;4(3):148–51. https://doi.org/10.1038/s41477-018-0115-z.
Article
CAS
PubMed
Google Scholar
Mao Y, Botella JR, Liu Y, Zhu J-K. Gene editing in plants: progress and challenges. Natl Sci Rev. 2019;6(3):421–37. https://doi.org/10.1093/nsr/nwz005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Gao C. Recent advances in DNA-free editing and precise base editing in plants. Emerg Top Life Sci. 2017;1(2):161–8. https://doi.org/10.1042/ETLS20170021.
Article
CAS
PubMed
Google Scholar
Manghwar H, Li B, Ding X, Hussain A, Lindsey K, Zhang X, et al. CRISPR/Cas systems in genome editing: methodologies and tools for sgRNA design, off-target evaluation, and strategies to mitigate off-target effects. Adv Sci. 2020;7(6):1902312–27. https://doi.org/10.1002/advs.201902312.
Article
CAS
Google Scholar
Manghwar H, Lindsey K, Zhang X, Jin S. CRISPR/Cas system: recent advances and future prospects for genome editing. Trends in Plant Science. 2019;24(12):1102–25. https://doi.org/10.1016/j.tplants.2019.09.006.
Article
CAS
PubMed
Google Scholar
Zong Y, Wang Y, Chao L, Zhang R, Chen K, Ran Y, et al. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat Biotechnol. 2017;35(5):438–40. https://doi.org/10.1038/nbt.3811.
Article
CAS
PubMed
Google Scholar
Henikoff S, Comai L. Single-nucleotide mutations for plant functional genomics. Ann Rev Plant Biol. 2003;54(1):375–401. https://doi.org/10.1146/annurev.arplant.54.031902.135009.
Article
CAS
Google Scholar
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420–4. https://doi.org/10.1038/nature17946.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017;551(7681):464–71. https://doi.org/10.1038/nature24644.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu J, Chen C, Xian G, Liu D, Lin L, Yin S, et al. Engineering herbicide-resistant oilseed rape by CRISPR/Cas9-mediated cytosine base-editing. Plant Biotechnol J. 2020;18(9):1857–9. https://doi.org/10.1111/pbi.13368.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qin L, Li J, Wang Q, Xu Z, Sun L, Alariqi M, et al. High-efficient and precise base editing of C•G to T•A in the allotetraploid cotton (Gossypium hirsutum) genome using a modified CRISPR/Cas9 system. Plant Biotechnol J. 2020;18(1):45–56. https://doi.org/10.1111/pbi.13168.
Article
CAS
PubMed
Google Scholar
Cai Y, Chen L, Zhang Y, Yuan S, Su Q, Sun S, et al. Target base editing in soybean using a modified CRISPR/Cas9 system. Plant Biotechnol J. 2020;18(10):1996–8. https://doi.org/10.1111/pbi.13386.
Article
PubMed Central
Google Scholar
Ren B, Yan F, Kuang Y, Li N, Zhang D, Zhou X, et al. Improved base editor for efficiently inducing genetic variations in rice with CRISPR/Cas9-guided hyperactive hAID mutant. Mol Plant. 2018;11(4):623–6. https://doi.org/10.1016/j.molp.2018.01.005.
Article
CAS
PubMed
Google Scholar
Li X, Wang Y, Liu Y, Yang B, Wang X, Wei J, et al. Base editing with a Cpf1–cytidine deaminase fusion. Nat Biotechnol. 2018;36(4):324–7. https://doi.org/10.1038/nbt.4102.
Article
CAS
PubMed
Google Scholar
Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science. 2016;353:aaf8729–8.
Article
PubMed
Google Scholar
Ma Y, Zhang J, Yin W, Zhang Z, Song Y, Chang X. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells. Nat Methods. 2016;13(12):1029–35. https://doi.org/10.1038/nmeth.4027.
Article
CAS
PubMed
Google Scholar
Hess GT, Frésard L, Han K, Lee CH, Li A, Cimprich KA, et al. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods. 2016;13(12):1036–42. https://doi.org/10.1038/nmeth.4038.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ren Q, Sretenovic S, Liu G, Zhong Z, Wang J, Huang L, et al. Improved plant cytosine base editors with high editing activity, purity, and specificity. Plant Biotechnol J. 2021;19(10):2052–68. https://doi.org/10.1111/pbi.13635.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jin S, Zong Y, Gao Q, Zhu Z, Wang Y, Qin P, et al. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science. 2019;364(6437):292–5. https://doi.org/10.1126/science.aaw7166.
Article
CAS
PubMed
Google Scholar
Zuo E, Sun Y, Wei W, Yuan T, Ying W, Sun H, et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science. 2019;364(6437):289–92. https://doi.org/10.1126/science.aav9973.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zuo E, Sun Y, Yuan T, He B, Zhou C, Ying W, et al. A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects. Nat Methods. 2020;17(6):600–4. https://doi.org/10.1038/s41592-020-0832-x.
Article
CAS
PubMed
Google Scholar
Cheng T-L, Li S, Yuan B, Wang X, Zhou W, Qiu Z. Expanding C–T base editing toolkit with diversified cytidine deaminases. Nat Commun. 2019;10(1):3612–21. https://doi.org/10.1038/s41467-019-11562-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li G, Sretenovic S, Eisenstein E, Coleman G, Qi Y. Highly efficient C-to-T and A-to-G base editing in a Populus hybrid. Plant Biotechnol J. 2021;19(6):1086–8. https://doi.org/10.1111/pbi.13581.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li B, Rui H, Li Y, Wang Q, Alariqi M, Qin L, et al. Robust CRISPR/Cpf1 (Cas12a)-mediated genome editing in allotetraploid cotton (Gossypium hirsutum). Plant Biotechnol J. 2019;17(10):1862–4. https://doi.org/10.1111/pbi.13147.
Article
PubMed
PubMed Central
Google Scholar
Richter MF, Zhao KT, Eton E, Lapinaite A, Newby GA, Thuronyi BW, et al. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat Biotechnol. 2020;38(7):883–91. https://doi.org/10.1038/s41587-020-0453-z.
Article
CAS
PubMed
PubMed Central
Google Scholar
Braatz J, Harloff H-J, Mascher M, Stein N, Himmelbach A, Jung C. CRISPR-Cas9 targeted mutagenesis leads to simultaneous modification of different homoeologous gene copies in polyploid oilseed rape (Brassica napus). Plant Physiol. 2017;174(2):935–42. https://doi.org/10.1104/pp.17.00426.
Article
CAS
PubMed
PubMed Central
Google Scholar
Niu Q, Wu S, Xie H, Wu Q, Liu P, Xu Y, et al. Efficient A·T to G·C base conversions in dicots using adenine base editors expressed under the tomato EF1α promoter. Plant Biotechnol J. 2021. https://doi.org/10.1111/pbi.13736.
Wang P, Zhang J, Sun L, Ma Y, Xu J, Liang S, et al. High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system. Plant Biotechnol J. 2018;16(1):137–50. https://doi.org/10.1111/pbi.12755.
Article
CAS
PubMed
Google Scholar
Wang M, Tu L, Yuan D, Zhu D, Shen C, Li J, et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet. 2019;51(2):224–9. https://doi.org/10.1038/s41588-018-0282-x.
Article
CAS
PubMed
Google Scholar
Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, et al. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol. 2015;33(5):524–30. https://doi.org/10.1038/nbt.3208.
Article
CAS
PubMed
Google Scholar
Chen ZJ, Scheffler BE, Dennis E, Triplett BA, Zhang T, Guo W, et al. Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 2007;145(4):1303–10. https://doi.org/10.1104/pp.107.107672.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mao Y-B, Tao X-Y, Xue X-Y, Wang L-J, Chen X-Y. Cotton plants expressing CYP6AE14 double-stranded RNA show enhanced resistance to bollworms. Transgenic Research. 2011;20(3):665–73. https://doi.org/10.1007/s11248-010-9450-1.
Article
CAS
PubMed
Google Scholar
Yuan D, Tang Z, Wang M, Gao W, Tu L, Jin X, et al. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Sci Rep. 2015;5(1):17662–77. https://doi.org/10.1038/srep17662.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li J, Wang M, Li Y, Zhang Q, Lindsey K, Daniell H, et al. Multi-omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process. Plant Biotechnol J. 2019;17(2):435–50. https://doi.org/10.1111/pbi.12988.
Article
CAS
PubMed
Google Scholar
Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, et al. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet. 2017;49(4):579–87. https://doi.org/10.1038/ng.3807.
Article
CAS
PubMed
Google Scholar
Li B, Liang S, Alariqi M, Wang F, Wang G, Wang Q, et al. The application of temperature sensitivity CRISPR/LbCpf1 (LbCas12a) mediated genome editing in allotetraploid cotton (G. hirsutum) and creation of nontransgenic, gossypol-free cotton. Plant Biotechnol J. 2020;19(2):221–3. https://doi.org/10.1111/pbi.13470.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen Y, Fu M, Li H, Wang L, Liu R, Liu Z, et al. High-oleic acid content, nontransgenic allotetraploid cotton (Gossypium hirsutum L.) generated by knockout of GhFAD2 genes with CRISPR/Cas9 system. Plant Biotechnol J. 2021;19(3):424–6. https://doi.org/10.1111/pbi.13507.
Article
CAS
PubMed
Google Scholar
Gao W, Long L, Zhu L, Xu L, Gao W, Sun L, et al. Proteomic and virus-induced gene silencing (VIGS) analyses reveal that gossypol, brassinosteroids, and jasmonic acid contribute to the resistance of cotton to Verticillium dahliae. Mol Cell Proteomics MCP. 2013;12(12):3690–703. https://doi.org/10.1074/mcp.M113.031013.
Article
CAS
PubMed
Google Scholar
Si Z, Liu H, Zhu J, Chen J, Wang Q, Fang L, et al. Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture. J Exp Botany. 2018;69(10):2543–53. https://doi.org/10.1093/jxb/ery093.
Article
CAS
Google Scholar
Chen W, Yao J, Li Y, Zhao L, Liu J, Guo Y, et al. Nulliplex-branch, a TERMINAL FLOWER 1 ortholog, controls plant growth habit in cotton. Theor Appl Genet. 2019;132(1):97–112. https://doi.org/10.1007/s00122-018-3197-0.
Article
CAS
PubMed
Google Scholar
Bae S, Park J, Kim J-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014;30(10):1473–5. https://doi.org/10.1093/bioinformatics/btu048.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou C, Sun Y, Yan R, Liu Y, Zuo E, Gu C, et al. Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature. 2019;571(7764):275–8. https://doi.org/10.1038/s41586-019-1314-0.
Article
CAS
PubMed
Google Scholar
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly. 2012;6(2):80–92. https://doi.org/10.4161/fly.19695.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576(7785):149–57. https://doi.org/10.1038/s41586-019-1711-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cuella-Martin R, Hayward SB, Fan X, Chen X, Huang J-W, Taglialatela A, et al. Functional interrogation of DNA damage response variants with base editing screens. Cell. 2021;184:1081–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hua K, Tao X, Zhu J-K. Expanding the base editing scope in rice by using Cas9 variants. Plant Biotechnol J. 2019;17(2):499–504. https://doi.org/10.1111/pbi.12993.
Article
PubMed
Google Scholar
Lassoued R, Phillips PWB, Macall DM, Hesseln H, Smyth SJ. Expert opinions on the regulation of plant genome editing. Plant Biotechnol J. 2021;19(6):1104–9. https://doi.org/10.1111/pbi.13597.
Article
PubMed
PubMed Central
Google Scholar
McGarry RC, Prewitt SF, Culpepper S, Eshed Y, Lifschitz E, Ayre BG. Monopodial and sympodial branching architecture in cotton is differentially regulated by the Gossypium hirsutum SINGLE FLOWER TRUSS and SELF-PRUNING orthologs. New Phytologist. 2016;212(1):244–58. https://doi.org/10.1111/nph.14037.
Article
CAS
PubMed
Google Scholar
Chatterjee P, Jakimo N, Lee J, Amrani N, Rodríguez T, Koseki SRT, et al. An engineered ScCas9 with broad PAM range and high specificity and activity. Nat Biotechnol. 2020;38(10):1154–8. https://doi.org/10.1038/s41587-020-0517-0.
Article
CAS
PubMed
Google Scholar
Chen Z, Sun J, Guan Y, Li M, Lou C, Wu B. Engineered DNase-inactive Cpf1 variants to improve targeting scope for base editing in E. coli. Synth Syst Biotechnol. 2021;6(4):326–34. https://doi.org/10.1016/j.synbio.2021.09.002.
Article
PubMed
PubMed Central
Google Scholar
Sun L, Jin S, Alariqi M, Zhu Y, Li J, Li Z, et al. Red fluorescent protein (DsRed2), an ideal reporter for cotton genetic transformation and molecular breeding. Crop J. 2018;6(4):366–76. https://doi.org/10.1016/j.cj.2018.05.002.
Article
Google Scholar
Porebski S, Bailey LG, Baum BR. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep. 1997;15(1):8–15. https://doi.org/10.1007/BF02772108.
Article
CAS
Google Scholar
Ståhlberg A, Krzyzanowski PM, Egyud M, Filges S, Stein L, Godfrey TE. Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing. Nat Protoc. 2017;12(4):664–82. https://doi.org/10.1038/nprot.2017.006.
Article
CAS
PubMed
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data; 2010.
Google Scholar
Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019;37(3):224–6. https://doi.org/10.1038/s41587-019-0032-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 2013;1303:3997.
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. Genome Project Data Processing S: The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.
Article
CAS
PubMed
PubMed Central
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303. https://doi.org/10.1101/gr.107524.110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wilm A, Aw PPK, Bertrand D, Yeo GHT, Ong SH, Wong CH, et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012;40:11189–201.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinforma. 2012;14(2):178–92. https://doi.org/10.1093/bib/bbs017.
Article
CAS
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6. https://doi.org/10.1038/nbt.1754.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. Variant review with the Integrative genomics viewer. Cancer Res. 2017;77(21):e31–4. https://doi.org/10.1158/0008-5472.CAN-17-0337.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu Z, Li J, Guo X, Jin S, Zhang X. Metabolic engineering of cottonseed oil biosynthesis pathway via RNA interference. Sci Rep. 2016;6(1):33342–55. https://doi.org/10.1038/srep33342.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bodenhofer U, Bonatesta E, Horejš-Kainrath C. Hochreiter S: msa: an R package for multiple sequence alignment. Bioinformatics. 2015;31(24):3997–9. https://doi.org/10.1093/bioinformatics/btv494.
Article
CAS
PubMed
Google Scholar