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Abstract Background Suaeda australis is one of typical halophyte owing to high levels of salt tolerance. In addition, the bZIP gene family assumes pivotal functions in response to salt stress. However, there are little reports available regarding the bZIP gene family in S. australis. Results In this study, we successfully screened 44 bZIP genes within S. australis genome. Subsequently, we conducted an extensive analysis, encompassing investigations into chromosome location, gene structure, phylogenetic relationship, promoter region, conserved motif, and gene expression profile. The 44 bZIP genes were categorized into 12 distinct groups, exhibiting an uneven distribution among the 9 chromosomes of S. australis chromosomes, but one member (Sau23745) was mapped on unanchored scaffolds. Examination of cis-regulatory elements revealed that bZIP promoters were closely related to anaerobic induction, transcription start, and light responsiveness. Comparative transcriptome analysis between ST1 and ST2 samples identified 2,434 DEGs, which were significantly enriched in some primary biological pathways related to salt response-regulating signaling based on GO and KEGG enrichment analysis. Expression patterns analyses clearly discovered the role of several differently expressed SabZIPs, including Sau08107, Sau08911, Sau11415, Sau16575, and Sau19276, which showed higher expression levels in higher salt concentration than low concentration and a response to salt stress. These expression patterns were corroborated through RT-qPCR analysis. The six differentially expressed SabZIP genes, all localized in the nucleus, exhibited positive regulation involved in the salt stress response. SabZIP14, SabZIP26, and SabZIP36 proteins could bind to the promoter region of downstream salt stress-related genes and activate their expressions. Conclusions Our findings offer valuable insights into the evolutionary trajectory of the bZIP gene family in S. australis and shed light on their roles in responding to salt stress. In addition to fundamental genomic information, these results would serve as a foundational framework for future investigations into the regulation of salt stress responses in S. australis.

Abstract Remora albescens, also known as white suckerfish, recognized for its distinctive suction-cup attachment behavior and medicinal significance. In this study, we produced a high-quality chromosome-level genome assembly of R. albescens through the integration of 23.87 Gb PacBio long reads, 64.54 Gb T7 short reads, and 88.63 Gb Hi-C data. Initially, we constructed a contig-level genome assembly totaling 605.30 Mb with a contig N50 of 23.12 Mb. Subsequently, employing Hi-C technology, approximately 99.68% (603.38 Mb) of the contig-level genome was successfully assigned to 23 pseudo-chromosomes. Through the integration of homologous-based predictions, ab initio predictions, and RNA-sequencing methods, we successfully identified a comprehensive set of 22,445 protein-coding genes. Notably, 96.36% (21,629 genes) of these were effectively annotated with functional information. The genome assembly achieved an estimated completeness of 98.1% according to BUSCO analysis. This work promotes the applicability of the R. albescens genome, laying a solid foundation for future investigations into genomics, biology, and medicinal importance within this species.

The classification of the Uranoscopidae species is controversial and the Ichthyscopus pollicaris belonging to Uranoscopidae was first reported in 2019. In the present study, the whole genome sequence of I. pollicaris were generated by PacBio and Illumina platforms for the first time. After de novo assembly and correction of the high-quality PacBio data, a 527.25 Mb I. pollicaris genome with an N50 length of 11.25 Mb was finally generated. Meanwhile, 170.41 Mb repeating sequence, 21,263 genes, 784 miRNAs, 2,225 tRNAs, 3004 rRNAs, and 1422 snRNAs were annotated in I. pollicaris genome. Furthermore, 3,168 single-copy orthologous genes were applied to reconstructed the phylogenetic relationship between I. pollicaris and other 11 species. The draft genome sequences have been deposited in NCBI database with the accession number of PRJNA1071810.

The construction of high-quality genomes is fundamental for molecular studies of species. Currently, there are no published genome sequences within the Uranoscopidae family, and research on the genomic characteristics of this family is lacking. In this study, genomic analyses of seven species from the Uranoscopidae family which captured from the southeastern coast of China were conducted using next-generation sequencing technology. The results revealed that the genomic characteristics of the seven species are relatively similar. The genome sizes of the seven Uranoscopidae species ranged from 536.00 Mb to 652.49 Mb, with repeat sequence proportions between 20.09% and 36.64%, and heterozygosity levels ranging from 0.41% to 0.88%. The assembled draft genomes exhibited GC contents of these species ranging from approximately 42.14% to 43.53%. Furthermore, the mitochondrial sequences for the seven species were assembled, with sizes ranging from 14,966 to 18,446 bp. The evolutionary relationships between different species were depicted through the mapping of conserved genes, whole-genome variances and mitochondrial genome sequences. Besides, the historical effective population sizes of all species experienced rapid expansion after the Last Interglacial Period, with three species undergoing bottleneck effects. In conclusion, this study provides a reference for the subsequent construction of high-quality genomes for species within the Uranoscopidae family and offers a rich data resource for further evolutionary research.

Abstract Cyclocarya paliurus, an endemic species in the genus Juglandaceae with the character of heterodichogamy, is one of triterpene-rich medicinal plants in China. To uncover the genetic mechanisms behind the special characteristics, we sequenced the genomes of two diploid (protandry, PA-dip and protogyny, PG-dip) and one auto-tetraploid (PA-tetra) C. paliurus genomes. Based on 134.9 (~225x), 75.5 (~125x) and 271.8 Gb (~226x) subreads of PacBio platform sequencing data, we assembled 586.62 Mb (contig N50 = 1.9 Mb), 583.45 Mb (contig N50 = 1.4 Mb), and 2.38 Gb (contig N50 = 430.9 kb) for PA-dip, PG-dip and PA-tetra genome, respectively. Furthermore, 543.53, 553.87, and 2168.65 Mb in PA-dip, PG-dip, and PA-tetra, were respectively anchored to 16, 16, and 64 pseudo-chromosomes using over 65.4 Gb (~109x), 68 Gb (~113x), and 264 (~220x) Hi-C sequencing data. Annotation of PA-dip, PG-dip, and PA-tetra genome assembly identified 34,699, 35,221, and 34,633 protein-coding genes (90,752 gene models) or allele-defined genes, respectively. In addition, 45 accessions from nine locations were re-sequenced, and more than 10 × coverage reads were generated.

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.

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. Resequencing 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.

Abstract Background DNA methylation is one of the most abundant epigenetic modifications, which plays important roles in flower development, sex differentiation, and regulation of flowering time. Its pattern is affected by cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase). At present, there are no reports on C5-MTase and dMTase genes in heterodichogamous Cyclocarya paliurus. Results In this study, 6 CpC5-MTase and 3 CpdMTase genes were identified in diploid (2n = 2 × = 32) C. paliurus, while 20 CpC5-MTase and 13 CpdMTase genes were identified in autotetraploid (2n = 4 × = 64). 80% of identified genes maintained relatively fixed positions on chromosomes during polyploidization. In addition, we found that some DRM subfamily members didn’t contain the UBA domain. The transcript abundance of CpC5-MTase and CpdMTase in male and female flowers of two morphs (protandry and protogyny) from diploidy was analyzed. Results showed that all genes were significantly up-regulated at the stage of floral bud break (S2), but significantly down-regulated at the stage of flower maturation (S4). At S2, some CpC5-MTase genes showed higher expression levels in PG-M than in PG-F, whereas some CpdMTase genes showed higher expression levels in PA-M than in PA-F. In addition, these genes were significantly associated with gibberellin synthesis-related genes (e.g. DELLA and GID1), suggesting that DNA methylation may play a role in the asynchronous floral development process through gibberellin signal. Conclusions These results broaden our understanding of the CpC5-MTase and CpdMTase genes in diploid and autotetraploid C. paliurus, and provide a novel insight into regulatory mechanisms of DNA methylation in heterodichogamy.

Pampus belongs to the Perciformes, Stromateoidei, and Stromateidae and are widely distributed throughout the Indian Ocean and the Western Pacific. In this study, we employed next-generation sequencing to generate comprehensive genomic data for Pampus punctatissimus and Pampus echinogaster and subsequently compared the obtained genomic information with the published data of Pampus argenteus. P. echinogaster was identified to be the largest genome size (602 Mb), heterozygosity (1.38%), and repetitive sequence ratio (33.06%), while similar genome sizes between P. punctatissimus (540 Mb) and P. argenteus (550 Mb) were observed. A total of 402,921 and 628,298 SSRs were identified for P. punctatissimus and P. echinogaster, respectively. Additionally, 1,876, 638, and 394 single-copy homologous genes were identified from P. punctatissimus, P. echinogaster, and P. argenteus, respectively. The KEGG enrichment results of the unique single-copy genes to the three species were significantly different in genetic information processing, protein processing, and metabolic functions. The complete mitochondrial genomes of P. punctatissimus and P. echinogaster were successfully assembled, and the resulting phylogenetic relationships align with the currently reported taxonomic status of species in the Stromateoidei. Additionally, population size analysis using PSMC revealed that P. punctatissimus experienced one bottleneck effect, while P. echinogaster underwent two bottleneck events during the Pleistocene Glacial Epoch.

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.

Cyclocarya paliurus (Batal.) Iljinskaja, a monotypic species in Cyclocarya of Juglandaceae, is regarded as one of important medical plants in China. In order to reveal the alterations in chloroplast (cp) genome with nuclear genome duplication, we presented the complete cp genomes of C. paliurus, and firstly analyzed on the basis of ploidy type (tetraploid and diploid C. paliurus). The total length of the cp genome of tetraploid and diploid C. paliurus is 160,938 and 161,105 bp, respectively. Both type genome consist of a large single-copy (LSC) region (90,221 and 90,391 bp), a small single-copy (SSC) region (18,593 and 18,590 bp), and an pair of invert repeats (IRs) regions (26,062 and 26,062 bp). Tetraploid and diploid plastid genome contain 132 and 137 genes, 87 and 88 protein-coding genes, 37 and 39 tRNA genes, and both eight rRNA genes, respectively. Closely phylogenetic relationship by analyzing 23 cp genomes suggests that tetraploid C. paliurus probably originated from diploid 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, GA2OX, 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.

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.

[Objectives] This study was conducted to investigate the genetic diversity of 20 lotus (Nelumbo nucifera Gaertn) samples. [Methods] On this optimal ISSR amplification system, 16 primers were screened with good polymorphism. and the DNA was used to amplify the 20 plant samples. [Results] The 16 primers produced 225 loci, of which 170 were polymorphic, and the polymorphic loci percentage was up to 75. 56% . The genetic similarity coefficients between the 20 varieties ranged from 0.5778 to 0.9511. which were calculated by POPGENE32. The 20 varieties by UPMGA analysis could be clustered into 2 groups, the first of which included Baiyangdian red lotus and Donggua lotus, and other varieties was included in the second group. [Conclusions] ISSK molecular markers could be effectively used in genetic diversity and fingerprint analysis for differenly lotus varieties. [ABSTRACT FROM AUTHOR]