Chorus2

Design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization (FISH)

Documentation

Citation

Zhang T†*, Liu GQ†, Zhao HN, Braz G.T, Jiang JM*. Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization. Plant Biotechnology Journal 2021, 19(10):1967-1978

Video tutorials

YouTube (EN)

bilibili (中文)

Oligo design with Chorus/Chorus2

• Wheat:

  • Li GR†, Zhang T†, Yu ZH, Wang HJ, Yang EN, Yang ZJ*. An efficient Oligo‐FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae. The Plant Journal 2021, 105(4):978-993
  • Shi PY, Sun HJ, Liu GQ, Zhang X, Zhou JW, Song RR, Xiao J, Yuan CX, Sun L, Wang ZK, Lou QF, Jiang JM, Wang XE*, Wang HY*. Chromosome painting reveals inter-chromosomal rearrangements and evolution of subgenome D of wheat. The Plant Journal 2022, 112(1):55-67

• Rice:

  • Liu XY†, Sun S†, Wu Y, Zhou Y, Gu S.W, Yu H.X, Yi CD, Gu MH, Jiang JM, Liu B, Zhang T*, Gong ZY*. Dual‐color oligo‐FISH can reveal chromosomal variations and evolution in Oryza species. The Plant Journal 2020, 101:112-121
  • Xue C†, Liu GQ†, Sun S, Liu XY, Guo R, Cheng ZK, Yu HX, Gu MH, Liu K, Zhou Y*, Zhang T*, Gong ZY*. De Novo Centromere Formation in Pericentromeric Region of Rice Chromosome 8. The Plant Journal 2022, 111(3):859-871
  • You HL, Tang D, Liu HX, Zhou Y, Li YF, Shen Y, Gong ZY, Yu HX, Gu MH, Jinag JM, Zhang T*, Cheng ZK*. Chromosome ends initiate homologous chromosome pairing during rice meiosis. Plant Physiology 2024, 195(4):2617–2634

• Maize:

  • Albert P.S†, Zhang T†, Semrau K, Rouillard JM, Kao YH, Wang CJ, Danilova T.V, Jiang JM, and Birchler J*. Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships Proceedings of the National Academy of Sciences of the United States of America 2019, 16(5):1679-1685
  • Martins LV†, Yu F†, Zhao HN†, Dennison T, Lauter N, Wang HY, Deng ZH, Thompson A, Semrau K, Rouilard JM, Bichler J, Jiang JM*. Meiotic crossovers characterized by haplotype-specific chromosome painting in maize. Nature Communications 2019, 10:4604

• Populus:

  • Xin HY†, Zhang T†, Wu YF, Zhang WL, Zhang PD, Xi ML*, Jiang JM. An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. The Plant Journal 2020, 101:253-264
  • Wang ZY, Lei YJ, Liu GQ, Ning Y, Ning YR, Zhang T*, Xi M*. Male-Specific Sequence in Populus simonii Provides Insights into Gender Determination of Poplar. Forests 2023, 14:2385
  • Xin H†, Zhang T†, Han Y, Wu YF, Shi JS, Xi ML*, and Jiang JM. Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides. Chromosoma 2018, 127(3):313-321

• Cotton:

  • Yan H, Han JL, Jin SK, Han ZG, Si ZF, Yan SY, Xuan LS, Yu GR, Guan XY, Fang L*, Wang K*, Zhang TZ.* Post-polyploidization centromere evolution in cotton. Nature Genetics 2025, DOI:https://doi.org/10.1038/s41588-025-02115-3
  • Liu YL, Wang XY, Wei YY, Liu Z, Lu QW, Liu F, Zhang T*, Peng RH*. Chromosome Painting Based on Bulked Oligonucleotides in Cotton Frontier in Plant Science 2020, 11:802

• Sugarcane:

  • Zhang Q†, Qi YY†, Pan HR†, Tang HB, Wang G, Hua XT, Wang YJ, Lin LY, Li Z, Li YH, Yu F, Yu ZH, Huang YJ, Wang TY, Ma PP, Dou MJ, Sun ZY, Wang YB, Wang HB, Zhang XT, Yao W, Wang YT, Liu XL, Wang MJ, Wang JP, Deng ZH, Xu JS, Yang QH, Liu ZJ, Chen BS, Zhang MQ, Ming R, Zhang JS*. Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum Nature Genetics 2022, 54:885-896
  • Yu ZH, Huang YJ, Yu XK, Deng ZH, Chai J, Liu JR, Gong ZY, Yao W, Zhang JS, Zhang MQ, Yu F* and Jiang JM. (Formation and centromere inactivation of fusion chromosomes in two allotetraploid species from the Saccharum complex)[https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.70369]. New Phytologist 2025. https://doi.org/10.1111/nph.70369

• Potato, Tomato, Eggplant, Tzimbalo and Pepper:

  • Braz GT†, He L†, Zhao HN†, Zhang T†, Semrau K, Rouillard JM, Torres GA, Jiang JM*. Comparative oligo-FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics 2018, 208(2):513-523

• Cucumber, Muskmelon and other Cucumis:

  • Han YH†, Zhang T†, Thammapichai P, Weng YQ, and Jiang JM*. Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics 2015, 200(3):771-779
  • Zhao QZ, Bai YL, Cheng CY, Yu XQ, Lou QF* and Chen JF*. Chromosome-specific oligo-painting provides insights into the cytogenetic basis of karyotypic stasis in paleo-allotetraploid Cucurbita. Horticulture Research 2025. https://doi.org/10.1093/hr/uhaf179

• Chicken:

  • Huang Z†, Xu ZX†, Bai H†, Huang YJ, Kang N, Ding XT, Liu J, Luo HR, Yang CT, Chen WJ, Guo QX, XUE LZ, ZhangXP, Xu L, Chen ML, Fu HG, Chen YL, Yue ZC, Fukagawa T, Liu SL, Chang GB*, Xu LH*. Evolutionary analysis of a complete chicken genome Proceedings of the National Academy of Sciences of the United States of America 2023, 120(8)e2216641120

• Switchgrass, Banana and etc ...

https://github.com/zhangtaolab/Chorus2