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. 2017 Aug 22;7:9098. doi: 10.1038/s41598-017-09680-6

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© The Author(s) 2017

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Synteny analysis between G. hirsutum and G. arboretum. (A) The Blastn result between the G. arboreum gene Cotton_A_04120 and a novel transcript in G. hirsutum XLOC_012978. The red rectangles indicate alignment regions with high scores. The lower panel presents profiles of H3K4me3 and RNA-seq surrounding XLOC_012978 in SVG software. (B) Detail of the reverse synteny regions between chromosome Chr7 (37,868,000 to 37,859,000) in G. arboreum and A01 (1,108,000 to 1,118,000) in G. hirsutum. (C) Detail of the known genes and novel transcripts in the (B) synteny region. XLOC_002006 and XLOC_002007 are novel transcripts in G. hirsutum. The novel transcript Cotton_A_novel_09121 in G. arboreum shares a reverse collinearity relationship with XLOC_002006. The known gene Cotton_A_00075 in G. arboreum shares a reverse collinearity relationship with XLOC_002007.