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Genes in the row were homologous to each others among different genomes or species.

TraesCS1A01G020200 . TraesCS1A01G020300 TuG1812G0100000287 TraesCS1A01G020400 TuG1812G0100000288 TraesCS1A01G020500 TuG1812G0100000289 TraesCS1A01G023900LC . red*TraesCS1A01G020600 TuG1812G0100000290 TraesCS1A01G020700 TuG1812G0100000291 TraesCS1A01G024000LC . TraesCS1A01G024100LC . blue*TraesCS1A01G020800 TuG1812G0100000292 TraesCS1A01G024200LC . g*TraesCS1A01G020900 TuG1812G0100000293 TraesCS1A01G021000 TuG1812G0100000294 TraesCS1A01G021100 TuG1812G0100000296 TraesCS1A01G021200 TuG1812G0100000297 TraesCS1A01G024300LC TuG1812G0100000298 TraesCS1A01G021300 TuG1812G0100000299 TraesCS1A01G024400LC . TraesCS1A01G021400 TuG1812G0100000300 TraesCS1A01G024500LC TuG1812G0100000293 TraesCS1A01G024600LC . TraesCS1A01G021500 TuG1812G0100000304 TraesCS1A01G024700LC .

Bed file.

chr1A 10005015 10007663 TraesCS1A01G020200 51 - chr1A 10046411 10050382 TraesCS1A01G020300 49 - chr1A 10052199 10055927 TraesCS1A01G020400 62 - chr1A 10067062 10069144 TraesCS1A01G020500 61 + chr1A 10067251 10067551 TraesCS1A01G023900LC 37 - chr1A 10069851 10072312 TraesCS1A01G020600 60 - chr1A 10075208 10084883 TraesCS1A01G020700 62 + chr1A 10090355 10090739 TraesCS1A01G024000LC 28 + chr1A 10090823 10091737 TraesCS1A01G024100LC 29 + chr1A 10126504 10128214 TraesCS1A01G020800 53 + chr1A 10131662 10131968 TraesCS1A01G024200LC 21 + chr1A 10132631 10133075 TraesCS1A01G020900 33 + chr1A 10135658 10136038 TraesCS1A01G021000 33 + chr1A 10150916 10152296 TraesCS1A01G021100 60 + chr1A 10155566 10160405 TraesCS1A01G021200 53 - chr1A 10165781 10166471 TraesCS1A01G024300LC 21 - chr1A 10172748 10173080 TraesCS1A01G021300 41 + chr1A 10176824 10177475 TraesCS1A01G024400LC 26 - chr1A 10210713 10211293 TraesCS1A01G021400 33 - chr1A 10214318 10216296 TraesCS1A01G024500LC 31 - chr1A 10223399 10223771 TraesCS1A01G024600LC 29 - chr1A 10227257 10241556 TraesCS1A01G021500 36 - chr1A 10235663 10236485 TraesCS1A01G024700LC 29 - chr1A 10237060 10237540 TraesCS1A01G024800LC 24 - chr1A 10238068 10238662 TraesCS1A01G024900LC 28 - chr1A 10238791 10239313 TraesCS1A01G025000LC 25 - chr1A 10248094 10249481 TraesCS1A01G025100LC 38 - chr1A 10360107 10360389 TraesCS1A01G025200LC 23 + chr1A 10423318 10424959 TraesCS1A01G021600 33 - chr1A 10469231 10474310 TraesCS1A01G021700 62 - chr1A 10483012 10490956 TraesCS1A01G021800 53 - chr1A 10495328 10500017 TraesCS1A01G021900 36 + chr1A 10585455 10585614 TraesCS1A01G025300LC 30 + Tu1 14209817 14211399 TuG1812G0100000287 0 - Tu1 14217143 14223576 TuG1812G0100000288 0 - Tu1 14218105 14223576 TuG1812G0100000288 0 - Tu1 14240954 14244156 TuG1812G0100000289 0 + Tu1 14244530 14247189 TuG1812G0100000290 0 - Tu1 14248654 14256667 TuG1812G0100000291 0 + Tu1 14248654 14256719 TuG1812G0100000291 0 + Tu1 14248754 14256682 TuG1812G0100000291 0 + Tu1 14300694 14302144 TuG1812G0100000292 0 + Tu1 14314062 14315068 TuG1812G0100000293 0 + Tu1 14317431 14318110 TuG1812G0100000294 0 + Tu1 14365071 14366667 TuG1812G0100000296 0 + Tu1 14369968 14374632 TuG1812G0100000297 0 - Tu1 14379907 14380177 TuG1812G0100000298 0 + Tu1 14395978 14396770 TuG1812G0100000299 0 + Tu1 14400838 14402411 TuG1812G0100000300 0 - Tu1 14440130 14447056 TuG1812G0100000304 0 - Tu1 15821452 15829635 TuG1812G0100000337 0 + Tu1 16004338 16006721 TuG1812G0100000339 0 + Tu1 16004338 16009272 TuG1812G0100000339 0 +

Set Layout

# x, y, rotation, ha, va, color, ratio, label 0.55, 0.6, 0, left, center, m, 1, Chinese_Spring chr1A 0.55, 0.5, 0, left, center, #fc8d62, 0.5, Triticum_urartu Tu1 # edges e, 0, 1

Axes background   darkgrid dark ticks whitegrid white
Physical dot density   300dpi 600dpi 800dpi 1000dpi
Generate image of format   pdf svg svgz png eps ps emf raw rgba
Font name   Arial Helvetica Palatino Schoolbook
Contrasting color scheme   PiYG  BrBG  PRGn  PuOr  RdBu  RdGy  RdYlBu  RdYlGn  Spectral 
Add scale bar to the plot   False  True 
Style of syntenic wedges   curve  line 
Figure size `width`x`height` in inches   8x7 

This webtool used the MCscan (python-version) in 'jcvi'. Haibao Tang et al. (2015). jcvi: JCVI utility libraries. Zenodo. 10.5281/zenodo.31631

If you use wild emmer genome, please cite:
Avni, R., Nave, M., Barad, O., Baruch, K., Twardziok, S.O., Gundlach, H., et al. (2017). Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357(6346), 93-97.
doi: 10.1126/science.aan0032

If you use qingke genome, please cite:
Dai, F., Wang, X., Zhang, X.Q., Chen, Z., Nevo, E., Jin, G., et al. (2018). Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley. Plant Biotechnol J 16(3), 760-770.
doi: 10.1111/pbi.12826

If you use Chinese Spring genome (labeling with IWGSC1.0), please cite:
International Wheat Genome Sequencing, C., investigators, I.R.p., Appels, R., Eversole, K., Feuillet, C., Keller, B., et al. (2018). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361(6403).
doi: 10.1126/science.aar7191

If you use Triticum urartu genome, please cite:
Ling, H.Q., Ma, B., Shi, X., Liu, H., Dong, L., Sun, H., et al. (2018). Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 557(7705), 424-428.
doi: 10.1038/s41586-018-0108-0

If you use Aegilops tauschii genome, please cite:
Luo, M.C., Gu, Y.Q., Puiu, D., Wang, H., Twardziok, S.O., Deal, K.R., et al. (2017). Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551(7681), 498-502.
doi: 10.1038/nature24486

If you use Durum wheat genome, please cite:
Maccaferri, M., Harris, N.S., Twardziok, S.O., Pasam, R.K., Gundlach, H., Spannagl, M., et al. (2019). Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet 51(5), 885-895.
doi: 10.1038/s41588-019-0381-3

If you use barley genome, please cite:
Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S.O., Wicker, T., et al. (2017). A chromosome conformation capture ordered sequence of the barley genome. Nature 544(7651), 427-433.
doi: 10.1038/nature22043

If you use wild emmer genome V2, gene and protein sequences, please cite:
Zhu, T., Wang, L., Rodriguez, J.C., Deal, K.R., Avni, R., Distelfeld, A., et al. (2019). Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps. G3 (Bethesda) 9(3), 619-624.
doi: 10.1534/g3.118.200902



For more information and any question, please contact : WheatOmics