留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

GenomeSyn-II: a comparative genomics framework integrating synteny visualization

Zu-Wen Zhou Hong-Yun Zhao Yi-Bo Chai Ru-Peng Zhao Yong-Qing Qian Yuan-Yuan Zhong Yan-Han Shao Ling-Ling Chen Jia-Ming Song

Zu-Wen Zhou, Hong-Yun Zhao, Yi-Bo Chai, Ru-Peng Zhao, Yong-Qing Qian, Yuan-Yuan Zhong, Yan-Han Shao, Ling-Ling Chen, Jia-Ming Song. GenomeSyn-II: a comparative genomics framework integrating synteny visualization[J]. 遗传学报. doi: 10.1016/j.jgg.2026.01.011
引用本文: Zu-Wen Zhou, Hong-Yun Zhao, Yi-Bo Chai, Ru-Peng Zhao, Yong-Qing Qian, Yuan-Yuan Zhong, Yan-Han Shao, Ling-Ling Chen, Jia-Ming Song. GenomeSyn-II: a comparative genomics framework integrating synteny visualization[J]. 遗传学报. doi: 10.1016/j.jgg.2026.01.011
Zu-Wen Zhou, Hong-Yun Zhao, Yi-Bo Chai, Ru-Peng Zhao, Yong-Qing Qian, Yuan-Yuan Zhong, Yan-Han Shao, Ling-Ling Chen, Jia-Ming Song. GenomeSyn-II: a comparative genomics framework integrating synteny visualization[J]. Journal of Genetics and Genomics. doi: 10.1016/j.jgg.2026.01.011
Citation: Zu-Wen Zhou, Hong-Yun Zhao, Yi-Bo Chai, Ru-Peng Zhao, Yong-Qing Qian, Yuan-Yuan Zhong, Yan-Han Shao, Ling-Ling Chen, Jia-Ming Song. GenomeSyn-II: a comparative genomics framework integrating synteny visualization[J]. Journal of Genetics and Genomics. doi: 10.1016/j.jgg.2026.01.011

GenomeSyn-II: a comparative genomics framework integrating synteny visualization

doi: 10.1016/j.jgg.2026.01.011
基金项目: 

This study was supported by the National Natural Science Foundation of China (32570746, U24A20369, and 32100526), Chongqing Technical Innovation and Application Development Special Project (CSTB2024TIAD-KPX0025), Fundamental Research Funds for the Central University (SWU-KR24030), and Innovation Project of Guangxi Graduate Education (YCBZ2024048).

详细信息
    通讯作者:

    Ling-Ling Chen,E-mail:llchen@gxu.edu.cn

    Jia-Ming Song,E-mail:jmsong@swu.edu.cn

GenomeSyn-II: a comparative genomics framework integrating synteny visualization

Funds: 

This study was supported by the National Natural Science Foundation of China (32570746, U24A20369, and 32100526), Chongqing Technical Innovation and Application Development Special Project (CSTB2024TIAD-KPX0025), Fundamental Research Funds for the Central University (SWU-KR24030), and Innovation Project of Guangxi Graduate Education (YCBZ2024048).

  • Buchfink, B., Xie, C., Huson, D.H., 2015. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59-60.
    Goel, M., Schneeberger, K., 2022. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics 38, 2922-2926.
    He, W., Yang, J., Jing, Y., Xu, L., Yu, K., Fang, X., 2023. NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes. Bioinformatics 39, btad121.
    Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., Marra, M.A., 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645.
    Li, H., 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094-3100.
    Mahram, A., Herbordt, M.C., 2015. NCBI BLASTP on high-performance reconfigurable computing systems. ACM Trans. Reconfigurable Technol. Syst. 7, 1-20.
    Marcais, G., Delcher, A.L., Phillippy, A.M., Coston, R., Salzberg, S.L., Zimin, A., 2018. MUMmer4: a fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944.
    Pertea G., Pertea M., 2020. GFF utilities: GffRead and GffCompare. F1000Res 9, ISCB Comm J-304.
    Qian, Y., Zhou, Z., Ouyang, T., Li, D., Li R., Gan, P., Qiao, R., Tan, Y., Qian, M., Liu L., et al., 2025. Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice. Nat. Commun. 16, 7634.
    Shen W., Le S., Li Y., Hu F., 2016. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962.
    Steinegger, M., Soding, J., 2017. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026-1028.
    Sun, H., Tusso, S., Dent, C.I., Goel, M., Wijfjes, R.Y., Baus, L.C., Dong, X., Campoy, J.A., Kurdadze, A., Walkemeier, B., et al., 2025. The phased pan-genome of tetraploid European potato. Nature 642, 389-397.
    Tang, H., Krishnakumar, V., Zeng, X., Xu, Z., Taranto, A., Lomas, J.S., Zhang, Y., Huang, Y., Wang, Y., Yim, W.C., et al., 2024. JCVI: a versatile toolkit for comparative genomics analysis. iMeta 3, 211.
    Wang, Y., Tang, H., DeBarry, J.D., Tan, X., Li, J., Wang, X., Lee, T.-h., Jin, H., Marler, B., Guo, H., et al., 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49.
    Wei, X., Chen, M., Zhang, Q., Gong, J., Liu, J., Yong, K., Wang, Q., Fan, J., Chen, S., Hua, H., et al., 2024. Genomic investigation of 18,421 lines reveals the genetic architecture of rice. Science 385, eadm8762.
    Xie W., Zheng Y., He W., Bi F., Li Y., Dou T., Zhou R., Guo Y., Deng G., Zhang W., et al., 2024. Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control. Plant Com. 5, 100766.
    Yim, W.C., Swain, M.L., Ma, D., An, H., Bird, K.A., Curdie, D.D., Wang, S., Ham, H.D., Luzuriaga-Neira, A., Kirkwood, J.S., et al., 2022. The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome. Plant Cell 34, 4143-4172.
    Zhou, Z., Yu, Z., Huang, X., Liu, J., Guo, Y., Chen, L., Song, J., 2022. GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations. J. Genet. Genomics 49, 1174-1176.
  • 加载中
计量
  • 文章访问数:  33
  • HTML全文浏览量:  16
  • PDF下载量:  0
  • 被引次数: 0
出版历程
  • 收稿日期:  2025-11-30
  • 录用日期:  2026-01-30
  • 修回日期:  2026-01-29
  • 网络出版日期:  2026-02-09

目录

    /

    返回文章
    返回