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Preprint

Gene synteny and structure variation

HW Hongwei Wang
SS Silong Sun
LK Lingrang Kong

Last updated date: Nov 30, 2022 Views: 947 Forks: 0

original An abbreviated version of this protocol was published in Science
Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat
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The brief protocol for gene synteny and structure variation analysis was listed below:

  1. Protein sequences of annotated high-confidence genes from Thinopyrum elongatum (https://ngdc.cncb.ac.cn/gwh/Assembly/965/show) and Triticum aestivum (IWGSC v1.1) were reciprocally aligned using BLASTP with an e-value cutoff of 1e-05.
  2. The reciprocal best hit for each alignment was used to build whole genome collinearity between Th. elongatum and three T. aestivum sub-genomes by MCScanX with default parameters (data S1). 
  3. jcvi software (https://github.com/tanghaibao/jcvi) was used to show the synteny result and detect large structure variations between Th. elongatum and all T. aestivum sub-genomes. As these two species were diverged 5 Mya, we just searched large inversions using annotated genes in this study, which can be found in the analysis temporary file “*.anchors.simple”, which included the syntenic block information with inversion showed “-” direction.
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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Wang, H, Sun, S and Kong, L(2022). Gene synteny and structure variation. Bio-protocol Preprint. bio-protocol.org/prep2065.
  2. Wang, H., Sun, S., Ge, W., Zhao, L., Hou, B., Wang, K., Lyu, Z., Chen, L., Xu, S., Guo, J., Li, M., Su, P., Li, X., Wang, G., Bo, C., Fang, X., Zhuang, W., Cheng, X., Wu, J., Dong, L., Chen, W., Li, W., Xiao, G., Zhao, J., Hao, Y., Xu, Y., Gao, Y., Liu, W., Liu, Y., Yin, H., Li, J., Li, X., Zhao, Y., Wang, X., Ni, F., Ma, X., Li, A., Xu, S. S., Bai, G., Nevo, E., Gao, C., Ohm, H. and Kong, L.(2020). Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat . Science 368(6493). DOI: 10.1126/science.aba5435

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