Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the “protein processing in endoplasmic reticulum” and “plant hormone signal transduction” pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.

Background: Brassicais a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants.TLPfamily genes play important regulatory roles in the growth and development of plants. Therefore, this study used a bioinformatics approach to conduct the systematic comparative genomics analysis ofTLPgene family inB. napusand other three important Brassicaceae crops.Results: Here, we identified a total of 29TLPgenes fromB. napusgenome, and they distributed on 16 chromosomes ofB. napus.The evolutionary relationship showed that these genes could be divided into six groups from Group A to F. We found that the gene corresponding toArabidopsis thaliana AT1G43640was completely lost inB. rapa,B. oleraceaandB. napusafter whole genome triplication. The gene corresponding toAT1G25280was retained in all the three species we analysed, belonging to 1:3:6 ratios. Our analyses suggested that there was a selective loss of some genes that might be redundant after genome duplication. This study proposed that theTLPgenes inB. napusdid not directly expansion compared with its diploid parentsB. rapa, andB. oleracea. Instead, an indirect expansion ofTLPgene family occurred in its two diploid parents. In addition, the study further utilized RNA-seq to detect the expression pattern ofTLPgenes between different tissues and two subgenomes.Conclusions: This study systematically conducted the comparative analyses ofTLPgene family inB. napus, discussed the loss and expansion of genes after genome duplication. It provided rich gene resources for exploring the molecular mechanism ofTLPgene family. Meanwhile, it provided guidance and reference for the research of other gene families inB. napus.

Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental diseases. However, the lack of genomic resources limits the insight into its evolutionary and biological characterization. In the present work, we reported the P. tenuifolia genome, the first genome assembly of the Polygalaceae family. We sequenced and assembled this genome by a combination of Illumnina, PacBio HiFi, and Hi-C mapping. The assembly includes 19 pseudochromosomes covering ~92.68% of the assembled genome (~769.62 Mb). There are 36 463 protein-coding genes annotated in this genome. Detailed comparative genome analysis revealed that P. tenuifolia experienced two rounds of whole genome duplication that occurred ~39–44 and ~18–20 million years ago, respectively. Accordingly, we systematically reconstructed ancestral chromosomes of P. tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species. Based on the transcriptomics data, enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P. tenuifolia were identified. Further analysis demonstrated that whole-genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families, which contributed to the synthesis of triterpenoid saponins. The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae, but also shed light on the synthesis of triterpenoid saponin.

Simple sequence repeats (SSRs) are popular and important molecular markers that exist widely in plants. Here, we conducted a comprehensive identification and comparative analysis of SSRs in 14 tree species. A total of 16, 298 SSRs were identified from 429, 449 genes, and primers were successfully designed for 99.44% of the identified SSRs. Our analysis indicated that tri-nucleotide SSRs were the most abundant, with an average of ~834 per species. Functional enrichment analysis by combining SSR-containing genes in all species, revealed 50 significantly enriched terms, with most belonging to transcription factor families associated with plant development and abiotic stresses such as Myeloblastosis_DNA-bind_4 (Myb_DNA-bind_4), APETALA2 (AP2), and Fantastic Four meristem regulator (FAF). Further functional enrichment analysis showed that 48 terms related to abiotic stress regulation and floral development were significantly enriched in ten species, whereas no significantly enriched terms were found in four species. Interestingly, the largest number of enriched terms was detected in Citrus sinensis (L.) Osbeck, accounting for 54.17% of all significantly enriched functional terms. Finally, we analyzed AP2 and trihelix gene families (Myb_DNA-bind_4) due to their significant enrichment in SSR-containing genes. The results indicated that whole-genome duplication (WGD) and whole genome triplication (WGT) might have played major roles in the expansion of the AP2 gene family but only slightly affected the expansion of the trihelix gene family during evolution. In conclusion, the identification and comprehensive characterization of SSR markers will greatly facilitate future comparative genomics and functional genomics studies.

Stephania japonica is an early-diverging eudicotyledon plant with high levels of cepharanthine, proven to be effective in curing coronavirus infections. Here, we report a high-quality S. japonica genome. The genome size is 688.52 Mb, and 97.37% sequences anchor to 11 chromosomes. The genome comprises 67.46% repetitive sequences and 21,036 genes. It is closely related to two Ranunculaceae species, which diverged from their common ancestor 55.90-71.02 million years ago (Mya) with a whole-genome duplication 85.59-96.75 Mya. We further reconstruct ancestral karyotype of Ranunculales. Several cepharanthine biosynthesis genes are identified and verified by western blot. Two genes (Sja03G0243 and Sja03G0241) exhibit catalytic activity as shown by liquid chromatography-mass spectrometry. Then, cepharanthine biosynthesis genes, transcription factors, and CYP450 family genes are used to construct a comprehensive network. Finally, we construct an early-diverging eudicotyledonous genome resources (EEGR) database. As the first genome of the Menispermaceae family to be released, this study provides rich resources for genomic studies.

Currently, frequent occurrences of abnormal weather events, including drought and extreme temperatures, are impacting plant growth and crop yields globally. Numerous lncRNAs in plants are known to be associated with stress responses, yet only a select few have been validated experimentally. Our prior research identified a set of lncRNAs in Chinese cabbage that were closely related to heat stress response through RNA-seq and bioinformatics analysis. In this study, two lncRNAs (lnc000283 and lnc012465) were selected for genetic transformation in Arabidopsis to elucidate their functions. Arabidopsis plants over-expressing (OE) lnc000283 and lnc012465 accumulated higher levels of anthocyanins in the later growth stage when cultivated in a culture dish. When subjected to heat stress, both OE lnc000283 and OE lnc012465 plants exhibited enhanced thermotolerance, with lnc012465 showing particularly pronounced effects. Moreover, the transgenic Arabidopsis plants demonstrated greater resistance to drought stress compared to the wild type. Under heat or drought treatments, the transgenic plants exhibited significantly higher fresh-to-dry weight ratios, POD activities, green leaf percentages, and survival rates compared to the wild type. Additionally, the transcript levels of Hsp18.1-CI were substantially elevated in the transgenic plants, both before and after heat treatment, and the expression levels of several drought-responsive genes were significantly higher than those in the wild type following drought stress. Altogether, the present results provide new ideas for the breeding of new multi-stress-tolerant varieties.