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Read mapping and transcriptome assembly
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The paired-end raw reads were trimmed and quality controlled by SeqPrep (version 1.1, https://github.com/jstjohn/SeqPrep) and Sickle (version 1.33, https://github.com/najoshi/sickle) with default parameters. Then, clean reads were separately aligned to the Pummelo (Citrus grandis) genome [39] in orientation mode using Tophat2 software [58] (version 2.0.13, http://tophat.cbcb.umd.edu/). The mapped reads of each sample were assembled by Cufflink (version 2.2.1, http://cufflinks.cbcb.umd.edu/) in a reference-based approach.
Copyright and License information: The Author(s). ©2019
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 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.
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