*Article* **Transcriptomics Analysis of Heat Stress-Induced Genes in Pepper (***Capsicum annuum* **L.) Seedlings**

**Fei Wang †, Yanxu Yin †, Chuying Yu, Ning Li, Sheng Shen, Yabo Liu, Shenghua Gao, Chunhai Jiao \* and Minghua Yao \***

> Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; wangfei\_raymond@163.com (F.W.); yinyanxu2008@126.com (Y.Y.); yuchuying@126.com (C.Y.); n.li@msn.com (N.L.); shengshen199711@163.com (S.S.); liu13125048135@163.com (Y.L.); gaoshenghua1986@126.com (S.G.)

**\*** Correspondence: jiaoch@hotmail.com (C.J.); yaomh\_2008@126.com (M.Y.); Tel.: +86-27-87380819 (M.Y.)

† These authors contributed equally to this work.

**Abstract:** Pepper (*Capsicum annuum* L.) is one of the most economically important crops worldwide. Heat stress (HS) can significantly reduce pepper yield and quality. However, changes at a molecular level in response to HS and the subsequent recovery are poorly understood. In this study, 17-03 and H1023 were identified as heat-tolerant and heat-sensitive varieties, respectively. Their leaves' transcript abundance was quantified using RNA sequencing to elucidate the effect of HS and subsequent recovery on gene expression. A total of 11,633 differentially expressed genes (DEGs) were identified, and the differential expression of 14 randomly selected DEGs was validated using reverse-transcription polymerase chain reaction. Functional enrichment analysis revealed that the most enriched pathways were metabolic processes under stress and photosynthesis and light harvesting during HS and after recovery from HS. The most significantly enriched pathways of 17-03 and H1023 were the same under HS, but differed during recovery. Furthermore, we identified 38 heat shock factors (Hsps), 17 HS transcription factors (Hsfs) and 38 NAC (NAM, ATAF1/2, and CUC2), and 35 WRKY proteins that were responsive to HS or recovery. These findings facilitate a better understanding of the molecular mechanisms underlying HS and recovery in different pepper genotypes.

**Keywords:** pepper; transcriptomics; heat stress; transcription factor
