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

doi:10.1016/j.jgg.2026.01.011

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GenomeSyn-II: a comparative genomics framework integrating synteny visualization

doi: 10.1016/j.jgg.2026.01.011

a. State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China;
b. Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China;
c. Yazhouwan National Laboratory, Sanya 572025, China

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).

Received Date: 2025-11-30
Accepted Date: 2026-01-30
Rev Recd Date: 2026-01-29

Available Online: 2026-02-09

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References

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.

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