Comparative transcriptome analysis of Sweetpotato ( Ipomoea batatas L.) and discovery of genes involved in starch biosyn
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Plant Biotechnology Reports (2020) 14:713–723 https://doi.org/10.1007/s11816-020-00647-0
ORIGINAL ARTICLE
Comparative transcriptome analysis of Sweetpotato (Ipomoea batatas L.) and discovery of genes involved in starch biosynthesis Meng Kou1,2 · Zai‑Xing Su1 · Yun‑Gang Zhang1 · Qiang Li1,2 Received: 11 October 2020 / Revised: 2 November 2020 / Accepted: 4 November 2020 / Published online: 12 November 2020 © Korean Society for Plant Biotechnology 2020
Abstract Sweetpotato, Ipomoea batatas L., Convolvulaceae, rich in starch, is a major staple economically important root crop worldwide. Limited functional genomics resources and whole genome studies could be improved through the development of next-generation sequencing technologies. Illumina sequencing of three sweetpotato varieties, Xushu 18, Xu 781 and Xushu 25, including de novo transcriptome assembly, functional annotation, and differential expression of potential starch biosynthesis-related genes are described. A total of 2508, 1807 and 3169 Mb clean reads were generated for Xushu 18, Xu 781 and Xushu 25, and were assembled into 32,112, 35,788 and 36,955 unigenes with an average length of 787, 802 and 824 bp, respectively. BLAST against the NCBI non-redundant protein, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) databases have classified these unigenes into functional categories for understanding gene functions and regulation pathways. The proportion of up-regulated DEGs was lower than that of the down-regulated DEGs among three sweetpotato cultivars. The similar proportion of the up/down-regulated gene number was presented between Xushu 25 and one of its parents (Xushu18 and Xu 781). Moreover, 14 unigenes related to starch biosynthesis in Xushu 18 and Xu 781were searched out from the transcriptome sequencing data. Furthermore, gene expression of these genes in storage root during different developing stages was also investigated, 6 types of gene expression patterns were summarized. The novel sequence dataset developed in this study will be helpful for the further genetic characterization and studies of starch biosynthesis in sweetpotato. Keywords Sweetpotato · Transcriptome · RNA-seq · Starch biosynthesis · Gene expression
Introduction
Meng Kou and Zai-Xing Su contribute equally to this manuscript. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11816-020-00647-0) contains supplementary material, which is available to authorized users. * Qiang Li [email protected] 1
Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou 221131, China
School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
2
Sweetpotato [Ipomoea batatas (L.) Lam.] is the world’s seventh most important food crop after maize, rice, wheat, potatoes, cassava and barley (FAO 2018). It is ada
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