Table_1_Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in four Ipomoea species.XLSX

The nucleotide-binding site (NBS)-encoding gene is a major type of resistance (R) gene, and its diverse evolutionary patterns were analyzed in different angiosperm lineages. Until now, no comparative studies have been done on the NBS encoding genes in Ipomoea species. In this study, various numbers of NBS-encoding genes were identified across the whole genome of sweet potato (Ipomoea batatas) (#889), Ipomoea trifida (#554), Ipomoea triloba (#571), and Ipomoea nil (#757). Gene analysis showed that the CN-type and N-type were more common than the other types of NBS-encoding genes. The phylogenetic analysis revealed that the NBS-encoding genes formed three monophyletic clades: CNL, TNL, and RNL, which were distinguished by amino acid motifs. The distribution of the NBS-encoding genes among the chromosomes was non-random and uneven; 83.13, 76.71, 90.37, and 86.39% of the genes occurred in clusters in sweet potato, I. trifida, I. triloba, and I. nil, respectively. The duplication pattern analysis reveals the presence of higher segmentally duplicated genes in sweet potatoes than tandemly duplicated ones. The opposite trend was found for the other three species. A total of 201 NBS-encoding orthologous genes were found to form synteny gene pairs between any two of the four Ipomea species, suggesting that each of the synteny gene pairs was derived from a common ancestor. The gene expression patterns were acquired by analyzing using the published datasets. To explore the candidate resistant genes in sweet potato, transcriptome analysis has been carried out using two resistant (JK20 and JK274) and susceptible cultivars (Tengfei and Santiandao) of sweet potato for stem nematodes and Ceratocystis fimbriata pathogen, respectively. A total of 11 differentially expressed genes (DEGs) were found in Tengfei and JK20 for stem nematodes and 19 DEGs in Santiandao and JK274 for C. fimbriata. Moreover, six DEGs were further selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis. The results may provide new insights into the evolution of NBS-encoding genes in the Ipomoea genome and contribute to the future molecular breeding of sweet potatoes.

核苷酸结合位点（nucleotide-binding site, NBS）编码基因是一类主要的抗病（R）基因，此前已有研究针对不同被子植物谱系中该类基因的多样进化模式展开分析。截至目前，尚未有针对番薯属（Ipomoea）物种NBS编码基因的比较研究报道。本研究分别从甘薯（Ipomoea batatas，#889）、三裂叶番薯（Ipomoea trifida，#554）、三浅裂野牵牛（Ipomoea triloba，#571）以及圆叶牵牛（Ipomoea nil，#757）的全基因组中鉴定得到不同数量的NBS编码基因。基因分析显示，CN型与N型NBS编码基因的占比高于其他类型。系统发育分析表明，NBS编码基因可形成三个单系支系：CNL、TNL与RNL，三者可通过氨基酸基序进行区分。NBS编码基因在染色体上的分布并非随机且不均衡：甘薯、三裂叶番薯、三浅裂野牵牛与圆叶牵牛中分别有83.13%、76.71%、90.37%及86.39%的基因以基因簇形式存在。重复模式分析结果显示，甘薯中片段重复基因的数量高于串联重复基因，其余三个物种则呈现相反趋势。在四个番薯属物种的任意两两组合中，共鉴定得到201对NBS编码基因直系同源共线性基因对，表明每一对共线性基因对均源自共同的祖先基因。本研究利用已公开的数据集获取基因表达模式数据。为筛选甘薯的候选抗病基因，本研究针对茎线虫病与甘薯长喙壳菌（Ceratocystis fimbriata）病害分别开展转录组分析：前者采用抗茎线虫病的品种JK20与感病品种滕飞（Tengfei），后者采用抗该病害的品种JK274与感病品种三湘早（Santiandao）。结果显示，在茎线虫病胁迫比较组中，滕飞与JK20间共鉴定得到11个差异表达基因（differentially expressed genes, DEGs）；而在甘薯长喙壳菌胁迫比较组中，三湘早与JK274间共鉴定得到19个DEGs。此外，本研究选取6个DEGs进行定量反转录聚合酶链式反应（quantitative reverse-transcription polymerase chain reaction, qRT-PCR）验证，结果与转录组分析结果一致。本研究结果可为番薯属基因组中NBS编码基因的进化研究提供新视角，并为甘薯的后续分子育种工作提供参考。