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. 2023 Feb 28;18:7. doi: 10.1186/s13062-023-00362-0

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© The Author(s) 2023

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 4 — Heatmap of pairwise Jaccard Index among the 45 GFs with significantly associated GFs. The Jaccard Index represents the extend of overlap between the associated GFs. Higher Jaccard Index (closer to 1 or in red color) means higher overlap of the associated GFs between two GFs, which could suggest the two GFs could be closely related. We highlight three clusters with at least three GFs sharing common associated GFs. These clusters contain GF_29643[b4730/yahV], GF_4841 [b1472/yddL] and GF_8394 [b1392/paaE] (cluster I), GF_15208 [b4778/yecV], GF_801 [b4615/yibV], GF_8481 [b4776/ynfU] and GF_10326 [b4749/ynfR] (cluster II) and GF_9576 [b2642/yfjW], GF_9575 [b2629/yfjM], GF_10334 [b2638/yfjU], GF_2127 [b4729/ykgV], GF_29089 [b4780/yodE] and GF_29267 [b1567/ydfW] (cluster III). The cluster II genes belong to Qin and rac cryptic prophages, whereas cluster III genes are known to be part of cryptic prophages CP4-57 and CP4-6. Cryptic prophages have been suggested to play an important role in bacterial cell physiology including bacterial cell growth, biofilm formation and environmental stress resistance [60]