Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B. Here, we presented three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids. Re sequencing analysis of 45 C. paliurus individuals uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolite biosynthesis. We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes, in particular gibberellin-related genes, associated with the heterodichogamy in C. paliurus species. Our study sheds light on evolutionary history of C. paliurus and provides genomic resources to study the medicinal herbs.

MADS-box transcription factors (TFs) have fundamental roles in regulating floral organ formation and flowering time in flowering plants. In order to understand the function of MIKC-type MADS-box family genes in Cyclocarya paliurus (Batal.) Iljinskaja, we first implemented a genome-wide analysis of MIKC-type MADS-box genes in C. paliurus. Here, the phylogenetic relationships, chromosome location, conserved motif, gene structure, promoter region, and gene expression profile were analyzed. The results showed that 45 MIKC-type MADS-box were divided into 14 subfamilies: BS (3), AGL12 (1), AP3-PI (3), MIKC* (3), AGL15 (3), SVP (5), AGL17 (2), AG (3), TM8 (1), AGL6 (2), SEP (5), AP1-FUL (6), SOC1 (7), and FLC (1). The 43 MIKC-type MADS-box genes were distributed unevenly in 14 chromosomes, but two members were mapped on unanchored scaffolds. Gene structures were varied in the same gene family or subfamily, but conserved motifs shared similar distributions and sequences. The element analysis in promoters’ regions revealed that MIKC-type MADS-box family genes were associated with light, phytohormone, and temperature responsiveness, which may play important roles in floral development and differentiation. The expression profile showed that most MIKC-type MADS-box genes were differentially expressed in six tissues (specifically expressed in floral buds), and the expression patterns were also visibly varied in the same subfamily. CpaF1st24796 and CpaF1st23405, belonging to AP3-PI and SEP subfamilies, exhibited the high expression levels in PA-M and PG-F, respectively, indicating their functions in presenting heterodichogamy. We further verified the MIKC-type MADS-box gene expression levels on the basis of transcriptome and qRT-PCR analysis. This study would provide a theoretical basis for classification, cloning, and regulation of flowering mechanism of MIKC-type MADS-box genes in C. paliurus.

Cyclocarya paliurus is an important medical plant owing to the diverse bioactive compounds in its leaves. However, the heterodichogamy with female and male functions segregation within protandry (PA) or protogyny (PG) may greatly affect seed quality and its plantations for medicinal use. To speculate on the factor playing the dominant role in regulating heterodichogamy in C. paliurus, based on phenotypic observations, our study performed a multi comparison transcriptome analysis on female and male buds (PG and PA types) using RNA-seq. For the female and male bud comparisons, a total of 6753 differentially expressed genes (DEGs) were detected. In addition, functional analysis revealed that these DEGs were significantly enriched in floral development, hormone, and GA-related pathways. As the dominant hormones responsible for floral differentiation and development, gibberellins (GAs) in floral buds from PG and PA types were quantified using HPLC-MS. Among the tested GAs, GA₃ positively regulated the physiological differentiation (S0) and germination (S2) of floral buds. The dynamic changes of GA₃ content and floral morphological features were consistent with the expression levels of GA-related genes. Divergences of GA₃ contents at S0 triggered the asynchronism of physiological differentiation between male and female buds of intramorphs (PA-M vs. PA-F and PG-F vs. PG-M). A significant difference in GA₃ content enlarged this asynchronism at S2. Thus, we speculate that GA₃ plays the dominant role in the formation of heterodichogamy in C. paliurus. Meanwhile, the expression patterns of GA-related DEGs, including CPS, KO, GA20ox, GA2_OX, GID1, and DELLA genes, which play central roles in regulating flower development, coincided with heterodichogamous characteristics. These results support our speculations well, which should be further confirmed.

Suaeda australis is a typical halophyte due to its high salt tolerance. The WRKY gene family plays crucial roles in responding to salt stress, yet reports on WRKY genes in S. australis are scarce. In this study, we identified 47 WRKY genes in the S. australis genome. We then conducted comprehensive analyses, including investigations into their chromosomal locations, gene structures, phylogenetic relationships, promoter regions, conserved motifs, and expression profiles. The 47 WRKY genes were classified into three main groups (with six subfamilies). Among nine chromosomes, S. australis displayed an unequal pattern of distribution. The analysis of regulatory elements revealed that WRKY promoters were associated with light responsiveness, anaerobic induction, drought inducibility, meristem expression, and gibberellin responsiveness. Expression pattern analyses highlighted the role of several SaWRKYs, including Sau00527, Sau00681, Sau18413, Sau19293, Sau00810, Sau05901, Sau09209, Sau12457, and Sau14103. These genes exhibited higher expression levels under ST2 compared to ST1, indicating a significant response to salt stress. Higher SOD, POD, and CAT activity, as well as increased MDA and H₂O₂ content, were observed in ST2, in line with the expression patterns and our RTq-PCR results. Our study offers a profound understanding of the evolutionary development of S. australis WRKY members, clarifying their vital functions in responding to salt stress. Along with crucial genomic data, these findings establish a solid foundation for investigating the mechanisms of salt-stress regulation in S. australis. This research holds substantial scientific and ecological importance, offering potential contributions to the conservation of S. australis and the utilization of saline soil resources.

Sebastes schlegelii is one of the most commercially important marine fish in the northwestern Pacific. However, little information about the genome-wide genetic characteristics is available for S. schlegelii individuals from the Bohai and Yellow Seas. In this study, a total of 157,778, 174,480, and 188,756 single-nucleotide polymorphisms from Dalian (DL), Yantai (YT), and Qingdao (QD) coastal waters of China were, respectively, identified. Sixty samples (twenty samples per population) were clustered together, indicating shallow structures and close relationships with each other. The observed heterozygosity, expected heterozygosity, polymorphism information content, and nucleotide diversity ranged from 0.14316 to 0.17684, from 0.14035 to 0.17145, from 0.20672 to 0.24678, and from 7.63 × 10⁻⁶ to 8.77 × 10⁻⁶, respectively, indicating the slight difference in genetic diversity among S. schlegelii populations, and their general genetic diversity was lower compared to other marine fishes. The population divergence showed relatively low levels (from 0.01356 to 0.01678) between S. schlegelii populations. Dispersing along drifting seaweeds, as well as the ocean current that flows along the western and northern coasts of the Yellow Sea and southward along the eastern coast of China might be the major reasons for the weak genetic differentiation. These results form the basis of the population genetic characteristics of S. schlegelii based on GBS (Genotyping by Sequencing). In addition to basic population genetic information, our results provid a theoretical basis for further studies aimed at protecting and utilizing S. schlegelii resources.

Cyclocarya paliurus (Batal) Iljinskaja is mainly used for harvesting leaves as materials for tea production and ingredients for the food industry. As its most important component, the contents of its total or specific flavonoids are supposed to vary at different ploidy levels. In the present study, two ploidy levels of C. paliurus are used to study their metabolome and transcriptome profiles. Though the total content of the flavonoids in leaves that were collected in September (the main harvesting season) presented insignificant differences between the two ploidies, flavonoid glucuronides were significantly accumulated in the tetraploid C. paliurus. Several structural genes related to the biosynthesis of these flavonoid glucuronides were expressed differentially, including PAL, 4CL, CHS, and CpUGTs. A weighted gene co-expression network analysis (WGCNA) revealed that nine genes were highly correlated with the flavonoid glucuronide contents. Furthermore, 3 CpMYB39 and 3 CpUGT71 were highly associated with this accumulation of flavonoid glucuronides in tetraploid C. paliurus. These results can provide a new perspective on how different polyploid levels alter the quantitative and qualitative patterns of the secondary metabolite production in C. paliurus.