The reference genome and full-length transcriptome of pakchoi provide insights into cuticle formation and heat adaption

Abstract

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.

A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres

“…Moreover, all two gaps of Chiifu v4.0 were in the centromeric regions (Figure S4 ). We further compared Chiifu v4.0 with the other B. rapa genome assemblies based on long‐read sequencing, including a Chinese cabbage (assembly “A03”; Sun et al ., 2022 ), three pak choi (PC‐fu, Xu et al ., 2022 ; NHCC001, Li et al ., 2020 ; ZYCX, Li et al ., 2021c ), a turnip (ECD04, Yang et al ., 2022 ) and a yellow sarson (Z1 v2, Istace et al ., 2021 ). Among them, Chiifu v4.0 had not only the longest contig N50 (38.26 Mb) and the fewest gaps (2) but also the highest values of the BUSCO (99.40%) and LTR assembly index (LAI) score (15.05) (Figures 2 and S5 ; Table 1 ).…”

“…Chiifu v3.5 is the updated annotation of Chiifu v3.0 using full‐length PacBio RNA sequencing technology (Zhang et al ., 2022c ). Recently, other B. rapa morphotypes have been sequenced using PacBio or ONT technologies, such as Chinese cabbage (Sun et al ., 2022 ), pak choi (Li et al ., 2020 , 2021a , c ; Xu et al ., 2022 ), turnip (Park et al ., 2021 ; Yang et al ., 2022 ) and yellow sarson (Istace et al ., 2021 ). In addition, a pan‐genome of B. rapa was released, including 16 genomes assembled using Illumina and PacBio reads (Cai et al ., 2021 ).…”

Auxin homeostasis is maintained by sly‐miR167‐SlARF8A/B‐SlGH3.4 feedback module in the development of locular and placental tissues of tomato fruits

“…The Illumina HiSeq2500 platform was used to construct the libraries according to the standard protocol. Using the fastp software, the raw RNA sequencing reads were first filtered to remove adaptors, low‐quality bases, duplications, and potential contaminations (Xu et al ., 2022). Using H isat 2 (v.2.1.0), we mapped the quality‐filtered reads onto the tomato genome SL2.50 with default settings (Kim et al ., 2015).…”