Abstract Studies have shown that abundant and various flavonoids accumulate in chili pepper (Capsicum), but there are few reports on the genes that govern chili pepper flavonoid biosynthesis. Here, we report the comprehensive identification of genes encoding type III polyketide synthase (PKS), an important enzyme catalyzing the generation of flavonoid backbones. In total, 13, 14 and 13 type III PKS genes were identified in each genome of C. annuum, C. chinense and C. baccatum, respectively. The phylogeny topology of Capsicum PKSs is similar to those in other plants, as it showed two classes of genes. Within each class, clades can be further identified. Class II genes likely encode chalcone synthase (CHS) as they are placed together with the Arabidopsis CHS gene, which experienced extensive expansions in the genomes of Capsicum. Interestingly, 8 of the 11 Class II genes form three clusters in the genome of C. annuum, which is likely the result of tandem duplication events. Four genes are not expressed in the tissues of C. annuum, three of which are located in the clusters, indicating that a portion of genes was pseudogenized after tandem duplications. Expression of two Class I genes was complementary to each other, and all the genes in Class II were not expressed in roots of C. annuum. Two Class II genes (CA00g90790 and CA05g17060) showed upregulated expression as the chili pepper leaves matured, and two Class II genes (CA05g17060 and CA12g20070) showed downregulated expression with the maturation of fruits, consistent with flavonoid accumulation trends in chili pepper as reported previously. The identified genes, sequences, phylogeny and expression information collected in this article lay the groundwork for future studies on the molecular mechanisms of chili pepper flavonoid metabolism.

中文翻译：

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辣椒III型聚酮合酶基因的计算机识别及其在辣椒中的表达模式

摘要 研究表明，辣椒（Capsicum）中积累了丰富多样的黄酮类化合物，但关于控制辣椒黄酮类生物合成基因的报道较少。在这里，我们报告了编码 III 型聚酮化合物合酶 (PKS) 的基因的综合鉴定，PKS 是一种重要的酶，催化黄酮类骨架的生成。总共在 C. annuum、C. chinense 和 C. baccatum 的每个基因组中分别鉴定了 13、14 和 13 个 III 型 PKS 基因。辣椒 PKS 的系统发育拓扑与其他植物中的相似，因为它显示了两类基因。在每个类中，可以进一步识别进化枝。II 类基因可能编码查尔酮合酶 (CHS)，因为它们与拟南芥 CHS 基因放在一起，后者在辣椒基因组中经历了广泛的扩展。有趣的是，11 个 II 类基因中的 8 个在 C. annuum 基因组中形成三个簇，这可能是串联重复事件的结果。4 个基因在 C. annuum 组织中未表达，其中 3 个位于簇中，表明部分基因在串联重复后被假基因化。两个Ⅰ类基因表达互补，Ⅱ类基因在青蒿根中均未表达。随着辣椒叶的成熟，两个 II 类基因（CA00g90790 和 CA05g17060）的表达上调，两个 II 类基因（CA05g17060 和 CA12g20070）随着果实的成熟而表达下调，这与之前报道的辣椒中黄酮类化合物积累趋势一致。确定的基因、序列、