【文献】Ruby基因相关文献

一、首发文献

He, Y., Zhang, T., Sun, H. et al. A reporter for noninvasively monitoring gene expression and plant transformation. Hortic Res 7, 152 (2020). https://doi.org/10.1038/s41438-020-00390-1

二、Ruby基因序列 

烟草和拟南芥的2A肽序列不太一样，如何设计2A肽？

We took advantage of the P2A peptide, which has the sequence of (GSGATNFSLLKQAGDVEENPGP), to link the CYP76AD1, DODA, and glucosyltransferase (GT) coding regions. The entire sequence of RUBY and terminator was shown in Supplemental Fig. 1.

The three genes were linked by sequences (red) that encode 2A peptides. Note that the two 2A sequences differed in DNA sequences, but both encoded the same peptide, which had a sequence of GSGATNFSLLKQAGDVEENPGP. The RUBY ORF was followed by the Arabidopsis HSP18.2 terminator.

For rice plasmids, we used F2A peptide (QLLNFDLLKLAGDVESNPGP). The corresponding DNA sequence is: CAATTGTTGAATTTTGATTTGTTGAAGTTGGCTGGAGATGTTGAATCTAATCCTGGAC CT

杨树的连接肽可以用这个：

Cho JS, Jeon HW, Kim MH, Vo TK, Kim J, Park EJ, Choi YI, Lee H, Han KH, Ko JH. Wood forming tissue-specific bicistronic expression of PdGA20ox1 and PtrMYB221 improves both the quality and quantity of woody biomass production in a hybrid poplar. Plant Biotechnol J. 2019 Jun;17(6):1048-1057. doi: 10.1111/pbi.13036. Epub 2018 Dec 5. PMID: 30515982; PMCID: PMC6523601.

烟草相关连接肽文献：

Zhang B, Rapolu M, Kumar S, Gupta M, Liang Z, Han Z, Williams P, Su WW. Coordinated protein co-expression in plants by harnessing the synergy between an intein and a viral 2A peptide. Plant Biotechnol J. 2017 Jun;15(6):718-728. doi: 10.1111/pbi.12670. Epub 2017 Mar 30. PMID: 27879048; PMCID: PMC5425387.

密码子优化的相关网站

当前主流的密码子优化网站基本主要以优化CAI作为指标，主要有：

• https://www.vectorbuilder.cn/tool/codon-optimization.html
• http://genomes.urv.es/OPTIMIZER/
• https://climsprod.genewiz.com.cn/Toolbox/CodonOptimization
• https://www.genscript.com/tools/gensmart-codon-optimization
• http://www.jcat.de/

• http://www.detaibio.com/tools/（功能强大）
• 1、thermo的在线工具：https://www.thermofisher.cn/order/geneartgenes

• 2、benchling的在线工具：https://www.benchling.com/

  3、IDT的在线工具：https://sg.idtdna.com/pages/too

2021年10月，张贺等人发表文章LinearDesign: Efficient Algorithms for Optimized mRNA Sequence Design，开发了一种新的算法来更加有效地优化mRNA序列，网站http://rna.baidu.com/

三、载体构建

1、拟南芥：plasmid pHDE：Various promoters can be cloned into the PmeI site of pHDE-RUBY to drive RUBY expression.Transgenic plants for YUC4:RUBY were selected on MS medium containing hygromycin (16.7 μg/ml).

2、水稻：pDX2181.To construct the pDR5:RUBY plasmid, we linked the three betalain biosynthetic genes through 2A peptides. Here, we used the F2A peptide, which has the following peptide sequence: QLLNFDLLKLAGDVESNPGP. 

四、2Apeptide设计

五、其他文献

（一）Wang D, Zhong Y, Feng B, et al. The RUBY reporter enables efficient haploid identification in maize and tomato[J]. Plant Biotechnology Journal, 2023.

1、载体：pICH41308， pISCL4723