Gene family evolution and genome structure analysis

Script for downstream analysis

• 1ortholog_prep/ - Data formatting scripts
• 2synteny_plot/ - Macro-synteny and oxford plots
• 3gene_family_summary/ - Gene family evolution summary
• 4function_anno2tree/ - Functional annotation and enrichment analysis

Citation of scripts:

Yichun. (2022). xieyichun50/Genome-macrosynteny-gene-family-evolution: Genome-macrosynteny-gene-family-evolution-v1.0. Zenodo. DOI: 10.5281/zenodo.6810089

Publications with the script set

• ^So, W.L., ^Nong, W., ^Xie, Y., ^Baril, T., Ma, H., Qu, Z., Haimovitz, J., Swale, T., Gaitan-Espitia, J.D., Lau, K.F., Tobe, S.S., Bendena, W.G., Kai, Z., Hayward, A., & Hui, J.H.L. (2022). Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes. Nature Communications, 13, 1–12. https://doi.org/10.1038/s41467-022-30690-0
• Nong, W., Yu, Y., Aase-Remedios, M.E., Xie, Y., So, W.L., Li, Y., Wong, C.F., Baril, T., Law, S.T.S., Lai, S.Y., Haimovitz, J., Swale, T., Chen, S., Kai, Z., Sun, X., Wu, Z., Hayward, A., Ferrier, D.E.K., & Hui, J.H.L. (2022). Genome of the ramshorn snail Biomphalaria straminea—an obligate intermediate host of schistosomiasis. GigaScience, 11, 1. https://doi.org/10.1093/GIGASCIENCE/GIAC012
• Yu, Y., Nong, W., So, W.L., Xie, Y., Yip, H.Y., Haimovitz, J., Swale, T., Baker, D.M., Bendena, W.G., Chan, T.F., Chui, A.P.Y., Lau, K.F., Qian, P.-Y., Qiu, J.-W., Thibodeau, B., Xu, F., & Hui, J.H.L. (2022). Genome of elegance coral Catalaphyllia jardinei (Euphylliidae). Frontiers in Marine Science, 9, 1–12. https://doi.org/10.3389/fmars.2022.991391
• Lee, I.H.T., Nong, W., So, W.L., Cheung, C.K.H., Xie, Y., Baril, T., Yip, H.Y., Swale, T., Chan, S.K.F., Wei, Y., Lo, N., Hayward, A., Chan, T.F., Lam, H., & Hui, J.H.L. (2023). The genome and sex-dependent responses to temperature in the common yellow butterfly, Eurema hecabe. BMC Biology, 21, 200. https://doi.org/10.1186/s12915-023-01703-1