The Solanaceae family contains many agriculturally important crops, including tomato, potato, pepper, and tobacco, as well as other species with potential for agricultural development, such as the orphan crops groundcherry, wolfberry, and pepino. Research progress varies greatly among these species, with model crops like tomato being far ahead. This disparity limits the broader agricultural application of other Solanaceae species. In this study, we constructed an interspecies pan-genome for the Solanaceae family and identified various gene retention patterns. Our findings reveal that the activity of specific transposable elements is closely associated with gene fractionation and transposition. The pan-genome was further resolved at the level of T subgenomes, which were generated by Solanaceae-specific paleo-hexaploidization (T event). We demonstrate substantial gene fractionation (loss) and divergence events following ancient duplications. For example, all class A and E flower model genes in Solanaceae originated from two tandemly duplicated genes, which expanded through the γ and T events before fractionating into 10 genes in tomato, each acquiring distinct functions critical for fruit development. Based on these results, we developed the Solanaceae Pan-Genome Database (SolPGD, http://www.bioinformaticslab.cn/SolPGD), which integrates datasets from both inter- and intra-species pan-genomes of Solanaceae. These findings and resources will facilitate future studies of solanaceous species, including orphan crops.

Rubus corchorifolius (Shanmei or mountain berry, 2n = 14) is widely distributed in China, and its fruits possess high nutritional and medicinal values. Here, we reported a high-quality chromosome-scale genome assembly of Shanmei, with contig size of 215.69 Mb and 26,696 genes. Genome comparison among Rosaceae species showed that Shanmei and Fupenzi (Rubus chingii Hu) were most closely related, followed by blackberry (Rubus occidentalis), and that environmental adaptation-related genes were expanded in the Shanmei genome. Further resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan, Hunan, Jiangxi, and Sichuan in China revealed that among these samples, the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral population. Moreover, the Yunnan population underwent strong selection based on the nucleotide diversity, linkage disequilibrium, and historical effective population size analyses. Furthermore, genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways, indicating the genetic basis of adaptation of Shanmei to the local environment. The high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

Polyploidization plays a crucial role in plant evolution and is becoming increasingly important in breeding. Structural variations and epigenomic repatterning have been observed in synthetic polyploidizations. However, the mechanisms underlying the occurrence and their effects on gene expression and phenotype remain unknown. Here, we investigated genome-wide large deletion/duplication regions (DelDups) and genomic methylation dynamics in leaf organs of progeny from the first eight generations of synthetic tetraploids derived from Chinese cabbage (Brassica rapa L. ssp. pekinensis) and cabbage (Brassica oleracea L. var. capitata). One- or two-copy DelDups, with a mean size of 5.70 Mb (400 kb to 65.85 Mb), occurred from the first generation of selfing and thereafter. The duplication of a fragment in one subgenome consistently coincided with the deletion of its syntenic fragment in the other subgenome, and vice versa, indicating that these DelDups were generated by homoeologous exchanges (HEs). Interestingly, the larger the genomic syntenic region, the higher the frequency of DelDups, further suggesting that the pairing of large homoeologous fragments is crucial for HEs. Moreover, we found that the active transcription of continuously distributed genes in local regions is positively associated with the occurrence of HE breakpoints. In addition, the expression of genes within DelDups exhibited a dosage effect, and plants with extra parental genomic fragments generally displayed phenotypes biased toward the corresponding parent. Genome-wide methylation fluctuated remarkably, which did not clearly affect gene expression on a large scale. Our findings provide insights into the early evolution of polyploid genomes, offering valuable knowledge for polyploidization-based breeding.

Background: Pepper (Capsicum annuum L.) is a widely cultivated vegetable crop worldwide, with its rich fruit colors providing unique visual traits and economic value. This study investigated the genetic basis of the immature green fruit color by constructing a F₂ segregating population derived from a cross between yellow fruit C20 and green fruit C62 parent lines. Methods: Bulked segregant analysis sequencing (BSA-seq) was performed to identify genomic regions associated with fruit color. Candidate genes were pinpointed through functional annotation and genetic variation analysis, supported by SNP markers, genotype analysis, and transcriptome profiling. Results: Two genomic regions associated with fruit color were identified on chromosomes 1 (14.55–20.85 Mb) and 10 (10.15–22.85 Mb), corresponding to previously reported loci pc1 and pc10.1. Two chlorophyll synthesis-related genes, CaAPRR2 and CaGLK2, were identified as candidate regulators of fruit color. Mutations in these genes include a premature stop codon in both CaGLK2 and CaAPRR2. The mutation of CaAPRR2 and CaGLK2 jointly regulate the yellow fruit trait in pepper, with CaGLK2 being the major gene and CaAPRR2 being the minor gene. Transcriptome analysis showed that the expression levels of the two genes increased during the green ripening stage of the parent fruits, with higher expression levels of CaGLK2. Conclusions: This study identifies CaGLK2 and CaAPRR2 as key regulators of immature green fruit color in pepper, with CaGLK2 playing a predominant role. These findings provide a theoretical foundation and data support for elucidating the molecular regulatory mechanisms of fruit color and advancing marker-assisted breeding in pepper.

Background/Objectives: Pepper (Capsicum annuum L.) is a widely grown vegetable and spice crop worldwide. This study aims to reveal the differences of metabolites among pepper accessions from different regions and explore candidate genes related to metabolites of pepper. Methods: The metabolome and transcriptome of 36 pepper accessions were determined by widely targeted metabolomics analysis and RNA sequencing technology, and the differential metabolites and differential genes among C. annuum from four important pepper production and consumption provinces of China, Hunan, Guizhou, Yunnan and Sichuan, were analyzed. Results: Flavonoids are the main characteristic metabolites that distinguish pepper accessions from Yun_Gui_Chuan Group and Hunan Group. The aglycones of characteristic flavonoids in each group are different; in Yun_Gui_Chuan Group mainly are luteolin, quercetin, chrysoeriol and isorhamnetin; in Hunan Group mainly are apigenin. Transcriptome data showed that two genes related to flavonoid 3′-monooxygenase differed significantly between the two groups of chili peppers, and we speculated that they may be the core enzymes regulating their flavonoid profile. And an SNP mutation located in gene Cgla06g001871 showed a strong correlation with pepper accessions from Yun_Gui_Chuan Group, which can be used as a DNA marker to identify pepper accessions from Yun_Gui_Chuan Group, and provide strong support for regional specialty variety conservation. In addition, we also analyzed the metabolites related to the taste and nutrition of pepper accessions in the four provinces, and the results showed that the sugar content of pepper accessions from Guizhou was low and the capsaicinoids content of pepper accessions from Sichuan was low, while no significant difference was found in acid and vitamin contents among pepper accessions from the four provinces. Conclusions: The metabolome and transcriptome of 36 pepper accessions from four important pepper production and consumption provinces of China were determined, and the characteristic metabolites and expressed genes of pepper accessions from each province were analyzed.