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. 2022 Dec 9;10:216. doi: 10.1186/s40168-022-01422-9

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© The Author(s) 2022

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. 7 — Phylogenetic analysis and characterization of vertically transmitted rice seed endophytes. a Maximum likelihood phylogeny of 21 isolates of Pantoea with 20 type strains based on the concatenated multiple alignment of the 1258 single-copy orthologous genes. Shimodaira-Hasegawa test support values (percentage of 1000 replications) greater than 75% were indicated at branching nodes. Selected biosynthetic, secretion system-related and catabolic genes or gene clusters were predicted using the genome sequences of the Pantoea isolates. b Maximum likelihood phylogeny of 27 isolates of Xanthomonas with 22 type strains based on the concatenated multiple alignment of the 892 single-copy orthologous genes. Selected biosynthetic, secretion system-related, and catabolic genes or gene clusters were predicted using the genome sequences of the Xanthomonas isolates. SM, secondary metabolites; PSS, protein secretion systems; ENZ, digestive enzymes. Dark green and brown boxes represent the presence and absence of a gene or gene cluster within a genome, respectively. The bootstrap values greater than 80 are not displayed