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The reference genome and full-length transcriptome of pakchoi provide insights into the cuticle formation and heat adaption
Horticulture Research ( IF 7.6 ) Pub Date : 2022-05-31 , DOI: 10.1093/hr/uhac123 Huimin Xu 1 , Chunhua Wang 1 , Guirong Shao 2 , Shasha Wu 1 , Peng Liu 1 , Ping Cao 2 , Peng Jiang 1 , Shubin Wang 1 , Hong Zhu 3 , Xiao Lin 2 , Arfa Tauqeer 1 , Yizhang Lin 2 , Wei Chen 3 , Weiqun Huang 3 , Qingfang Wen 4 , Jiang Chang 1 , Fenglin Zhong 1 , Shuang Wu 1
Horticulture Research ( IF 7.6 ) Pub Date : 2022-05-31 , DOI: 10.1093/hr/uhac123 Huimin Xu 1 , Chunhua Wang 1 , Guirong Shao 2 , Shasha Wu 1 , Peng Liu 1 , Ping Cao 2 , Peng Jiang 1 , Shubin Wang 1 , Hong Zhu 3 , Xiao Lin 2 , Arfa Tauqeer 1 , Yizhang Lin 2 , Wei Chen 3 , Weiqun Huang 3 , Qingfang Wen 4 , Jiang Chang 1 , Fenglin Zhong 1 , Shuang Wu 1
Affiliation
Brassica rapa includes various vegetables with high economic value. Among them, green petiole type pakchoi (B. rapa ssp. chinensis) is one of the major vegetables grown in southern China. Compared with other B. rapa varieties, green petiole type pakchoi shows higher level of heat resistance, which is partially derived from the rich epicuticular wax. Here we sequence a high-quality genome of green petiole type pakchoi, which has been widely used as the parent in breeding. Our results reveal that LTR-RT insertion plays critical roles in promoting the genome expansion and transcriptional diversity of pakchoi genes through preferential insertions, particularly in cuticle biosynthetic genes. After the whole-genome triplication (WGT), over-retained pakchoi genes escape stringent selection pressure, among which a set of cuticle related genes are retained. Using bulked-segregant analysis (BSA) analysis of a heat-resistant pakchoi cultivar, we identify a frame-shift deletion across the third exon and the subsequent intron of BrcCER1 in candidate regions. Using Nanopore long-read sequencing, we analyze the full-length transcriptome of two pakchoi cultivars with opposite sensitivity to high temperature. We find that heat resistant pakchoi cultivar can mitigate heat caused leaf damage by activating unfolded protein response, as well as inhibiting chloroplast development and energy metabolism, which are presumably mediated by both transcriptional regulation and splicing factors. Our study provides valuable resources for Brassica functional genomics and breeding research, and deepens our understanding of plant stress resistance.
更新日期：2022-05-31
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