Silpha carinata (Herbst, 1783), and Silpha perforata (Gebler, 1832) (Coleoptera: Staphylinidae) belong to the tribe Silphini, which holds forensic significance due to its species’ rapid colonization of cadavers and relatively long developmental duration. In this study, we reported the complete mitochondrial genomes of S. carinata and S. perforata, representing the first fully sequenced mitochondrial genomes for the genus Silpha. These genomes were acquired via next-generation sequencing and then thoroughly characterized. We examined their sequence structure, base composition, codon usage bias, and the secondary structures of tRNA genes. Phylogenetic trees were generated using Bayesian inference (BI) and maximum likelihood (ML) methods. The results revealed that the mitochondrial genomes (mtDNA) of the two species are 16,322 bp (S. carinata) and 15,469 bp (S. perforata) in length, respectively, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. Their gene arrangement is highly conserved compared to other Coleoptera species. The mtDNA exhibit a significant AT bias, with A+T contents of 74.6% (S. carinata) and 74.4% (S. perforata). Among the 22 tRNA gene secondary structures, the tRNA-Phe and tRNA-His genes of both S. carinata and S. perforata lack the TψC arm. In contrast, all other tRNA genes can fold into the canonical cloverleaf secondary structure. Phylogenetic analyses support the monophyly of the genus Silpha, with S. carinata and S. perforata showing close evolutionary relationships. This research enhances our understanding of mitochondrial genomics and the evolutionary relationships within Silphinae.

Benzylisoquinoline alkaloids (BIAs) are essential secondary metabolites produced by Papaver somniferum, widely recognized for their pharmaceutical importance. This study employs transcriptome sequencing and weighted gene co-expression network analysis (WGCNA) to investigate the spatiotemporal expression patterns and regulatory networks of BIA-related genes across developmental stages and organs. A total of 23 co-expression modules were identified, revealing stage- and organ-specific dynamics in BIA biosynthesis. Key genes such as TYDC, PPO, and GsSRK demonstrated distinct regulatory roles during flowering and fruit maturation. Functional enrichment analysis uncovered critical pathways and transcription factors involved in alkaloid production. These findings enhance our understanding of the molecular regulation of BIAs and provide valuable insights for improving alkaloid yield through metabolic engineering and molecular breeding strategies.

Cultivated lettuce (Lactuca sativa L.) is considered one of the most important economic vegetables worldwide; however, it is subjected to different stresses (salt stress, etc.) during its growth and development, resulting in yield reductions. In this study, we selected cultivated red lettuce and wild lettuce species (Lactuca serriola L.) to investigate the phenotypic and physiological changes in these lettuce under different salt treatment conditions. Functional annotation and enrichment analysis of the differentially expressed genes (DEGs) in the lettuce leaves and roots between the control and salt treatments were performed, identifying the key genes responding to salt stress. The results showed that the growth of the two types of lettuce was limited by salt stress, with decreased leaf area, main root length, biomass, and photosynthesis parameters noted. The cultivated red lettuce and the wild lettuce exhibited similar trends in terms of the variation in their antioxidant enzymatic activity and the content of osmoregulatory compounds in their leaves. The results of our transcriptomic analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway, transporters, cytochrome P450, phenylpropanoid biosynthesis, and isoflavonoid biosynthesis were involved in the response to salt stress in the lettuce seedlings. The red lettuce cultivar showed a greater abundance of DEGs related to secondary metabolite biosynthesis and aquaporins under the salt treatment, resulting in a salinity-tolerant capacity comparable to that of the wild lettuce species. These results reveal important biosynthesis pathways that may play a key role in the salt tolerance of lettuce seedlings and provide key candidate genes that could be functionally characterized further and utilized to genetically improve new salt-tolerant varieties.

Cultivated lettuce (Lactuca sativa L.), one of the oldest vegetable crops, serves as an important dietary source of fibers, antioxidants, and bioactive compounds. Enhancing the phytonutrient content in lettuce could offer a potent dietary strategy for disease prevention. However, few studies have addressed the nuclear genome phylogeny, differential gene expression, and metabolite accumulation diversity among cultivated lettuce and wild Lactuca species in China. This study employed an integrated transcriptomic and quasi-targeted metabolomic approach to investigate gene expression patterns and metabolite profiles across cultivated and wild Chinese Lactuca species. Additionally, we reconstructed the first comprehensive phylogeny of Chinese Lactuca species using single-copy orthologs derived from both transcriptomic and genomic data. Phylogenetic analysis repositioned Lactuca canadensis L. and confirmed the position of the winged-achene clade within Lactuca. These winged-achene accessions, especially Lactuca indica L., showed elevated expression of photosynthesis-related genes, enhanced photosynthetic capacity, and higher flavonoid concentrations. The cultivated varieties accumulated higher levels of fructose and glucose, contributing to a sweeter taste, whereas the wild species were enriched in secondary metabolites such as flavonoids, associated with a bitter flavour. L. indica and Lactuca tatarica (L.) C. A. Mey. are proposed as valuable genetic resources for enhancing nutritional quality, disease resistance, and stress tolerance in lettuce breeding. These findings provide fundamental insights into the divergence in photosynthetic performance and flavour-related metabolites among Chinese Lactuca species, and identify promising candidate genes and beneficial metabolites from wild lineages that could be utilized to improve yield, stress resistance, and disease resilience in cultivated lettuce.

Alternative splicing (AS) allows one gene to produce several protein variants, offering valuable predictive insights into cancer and facilitating targeted therapies. Although multi-omics data are used to identify cancer subtypes, AS is rarely utilized for this purpose. Here, we propose a redundancy-reduction contrastive learning-based method (CLCluster) based on copy number variation, methylation, gene expression, miRNA expression, and AS for cancer subtype clustering of 33 cancer types. Ablation experiments emphasize the benefits of using AS data to subtype cancer. We identified 2,921 cancer subtype-related AS events associated with patient survival and conducted multiple analyses including open reading frame annotation, RNA binding protein (RBP)-associated AS regulation, and splicing-related anticancer peptides (ACPs) prediction for therapeutic biomarkers. The CLCluster model is more effective in identifying prognostic-relevant cancer subtypes than other models. The effective annotation of cancer subtype related AS events facilitates the identification of therapeutically targetable biomarkers in patients.

Context Chufa (Cyperus esculentus L. var. sativus Boeck) is an emerging oil crop with significant economic, nutritional, and ecological value. However, few studies have examined the photosynthetic physiological function of chufa, C4 type plant, especially regarding the differences among the three tuber types. Methods This study investigated the photosynthetic characteristics and photosynthate allocation in 8 accessions of 3 types of tubers (round-tuber, large-tuber, and long-tuber). The field tests were conducted over two years in 2022 and 2023 to explore differences in photosynthetic efficiency and agronomic traits. Besides, one accession with the highest yield was selected from each tuber type for further study on the photosynthate allocation using 13C labeling. Results Field tests revealed significant differences among the three tuber types. The long-tuber type of chufa exhibited the lowest photosynthetic capacity, stomatal conductance, tillering number, leaf weight, and 1000-tuber weight, whereas it had a high oil content. The large-tuber type had the largest tuber size and the highest 1000-tuber weight. The round-tuber type showed the highest photosynthetic capacity, gas exchange index, plant height, and yield. The short-term effect of photosynthate transport and distribution followed a similar trend across the three chufa types, with the rate of photosynthate transport being fastest during the tuber initiation stage. However, differences were observed in the long-term effect, indicating distinct distribution strategies among the chufa types, resulting in variations in agronomic traits. Conclusions This study revealed distinct differences in photosynthetic physiology and agronomic traits among the three tuber types of chufa. Additionally, it provided insights into the transport and distribution strategies of photosynthates in chufa across different growth stages and tuber types. Implications These findings offer valuable theoretical and practical insights for chufa cultivar breeding and cultivation management.

The HAP clade, mainly including Helichrysum Mill, Anaphalis DC., and Pseudognaphalium Kirp., is a major component of tribe Gnaphalieae (Asteraceae). In this clade, Anaphalis represents the largest genus of Asian Gnaphalieae. The intergeneric relationships among Anaphalis and its related genera and the infrageneric taxonomy of this genus are complex and remain controversial. However, there are few studies that have focused on these issues. Herein, based on the current most comprehensive sampling of the HAP clade, especially Anaphalis, we conducted phylogenetic analyses using chloroplast (cp) genome and nuclear ribosomal DNA (nrDNA) to evaluate the relationships within HAP clade, test the monophyly of Anaphalis, and examine the infrageneric taxonomy of this genus. Meanwhile, the morphological characters were verified to determine the circumscription and infrageneric taxonomy system of Anaphalis. Additionally, the biogeographical history, diversification processes, and evolution of crucial morphological characters were estimated and inferred. Our phylogenetic analyses suggested that Anaphalis is polyphyletic because it nested with Helichrysum and Pseudognaphalium. Two and four main clades of Anaphalis were identified in cp genome and nrDNA trees, respectively. Compared with nrDNA trees, the cp genome trees were more effective for phylogenetic resolution. After comprehensively analyzing morphological and phylogenetic evidence, it was concluded that the achene surface ornamentation and leaf base showed less homoplasy and supported the two Anaphalis lineages that were inferred from cp genome. Our biogeographical analyses based on cp genome indicated that HAP clade underwent rapid diversification from late Miocene to Pliocene. The two Anaphalis lineages appeared to have originated in Africa, then spread to Western and Southern Asia, and subsequently moved into Southwestern China forming a diversity center. The dispersal patterns of the two Anaphalis lineages were different. One dispersed around the world, except in Africa and South America. The other one dispersed to Eastern and Southeastern Asia from the ancestral origin region.

The genus Trigonotis comprises nearly 60 species mainly distributed in East and Southeast Asia.China has the largest number of Trigonotis species in the world,with a total of 44 species,of which 38 are endemic.Nutlet morphology is useful for the taxonomic delimitation of Trigonotis.However,there are still controversial circumscriptions of nutlet shape in some species.In previous studies,interspecies phylogenetic relationships were inferred using few DNA markers and very few taxa,which possibly led to erroneous or incomplete conclusions.In this study,the nutlet morphology of 39 Trigonotis taxa and the characteristics of 34 complete chloroplast genomes（29 taxa） were investigated and analyzed.Then,the phylogenetic relationships were discussed within this genus based on complete chloroplast genomes.To the best of our knowledge,this study is the first comprehensive analysis of nutlet morphology and complete chloroplast genome of Trigonotis.Based on nutlet morphology,Trigonotis can be divided into two groups:Group 1,hemispherical or oblique tetrahedron with carpopodiums,and Group 2,inverted tetrahedron without carpopodiums.The chloroplast genome of Trigonotis exhibited a typical quadripartite structure,including 84-86 protein-coding,37 transfer RNA,and 8 ribosomal RNA genes,with a total length of 147,247-148,986 bp.Genes in the junctions were well conserved in Trigonotis,similar to those in other Boraginaceae s.str.species.Furthermore,Trigonotis chloroplast genomes showed relatively high diversity,with more conserved genic regions than intergenic regions;in addition,we detected 14hot spots（Pi＞ 0.005） in non-coding regions.Phylogenetic analyses based on chloroplast genome data identified highly resolved relationships between Trigonotis species.Specifically,Trigonotis was divided into two clades with strong support:one clade included species with hemispherical or oblique tetrahedron nutlets with carpopodiums and bracts,whereas the other clade included species with inverted tetrahedron nutlets without carpopodiums or bracts.Our results may inform future taxonomic,phylogenetic,and evolutionary studies on Boraginaceae.

The infrageneric taxonomy system, species delimitation, and interspecies systematic relationships of Leontopodium remain controversial and complex. However, only a few studies have focused on the molecular phylogeny of this genus. In this study, the characteristics of 43 chloroplast genomes of Leontopodium and its closely related genera were analyzed. Phylogenetic relationships were inferred based on chloroplast genomes and nuclear ribosomal DNA (nrDNA). Finally, together with the morphological characteristics, the relationships within Leontopodium were identified and discussed. The results showed that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved in terms of gene number, gene order, and GC content. The most remarkable differences among the three genera were the length of the complete chloroplast genome, large single-copy region, small single-copy region, and inverted repeat region. In addition, the chloroplast genome structure of Leontopodium exhibited high consistency and was obviously different from that of Filago and Gamochaeta in some regions, such as matk, trnK (UUU)-rps16, petN-psbM, and trnE (UUC)-rpoB. All the phylogenetic trees indicated that Leontopodium was monophyletic. Except for the subgeneric level, our molecular phylogenetic results were inconsistent with the previous taxonomic system, which was based on morphological characteristics. Nevertheless, we found that the characteristics of the leaf base, stem types, and carpopodium base were phylogenetically correlated and may have potential value in the taxonomic study of Leontopodium. In the phylogenetic trees inferred using complete chloroplast genomes, the subgen. Leontopodium was divided into two clades (Clades 1 and 2), with most species in Clade 1 having herbaceous stems, amplexicaul, or sheathed leaves, and constricted carpopodium; most species in Clade 2 had woody stems, not amplexicaul and sheathed leaves, and not constricted carpopodium.

为了分析栽培莴苣Lactuca sativa'Salinas'和野生莴苣Lactuca saligna的线粒体基因组密码子使用特征差异,对2种莴苣的线粒体基因组编码序列进行密码子使用偏好性研究,比较其密码子偏好性形成的影响因素和演化过程.结果表明:栽培莴苣和野生莴苣线粒体编码基因的总GC含量分别为43.43％和42.54％,富含A/T碱基.2种莴苣的有效密码子数(ENC)都在36.61～61.00,密码子偏好性较弱.中性绘图分析表明,2种莴苣线粒体编码基因的第1、2位和第3位碱基GC含量较为保守,选择是影响2种莴苣线粒体基因密码子使用偏好性的主要因素.PR2-plot分析表明,2种莴苣线粒体基因第3位碱基更偏好使用嘧啶碱基.ENC-plot分析结果显示,2种莴苣的线粒体基因密码子偏好性主要受到选择压力影响.对2种莴苣的相对同义密码子使用度(RSCU)分析表明,栽培莴苣和野生莴苣分别有28个和29个高频密码子,除亮氨酸外,2种莴苣的高频密码子均以A/U结尾.2种莴苣线粒体编码基因的密码子使用偏好性总体上较接近,但最优密码子存在较大差异.这种差异可能是因为2种莴苣的低表达基因库差异造成的,也可能与选择压力及人工育种对栽培莴苣线粒体基因组进化的影响有关.

Swertia L. is a large genus in Swertiinae (Gentianaceae). In China, many Swertia species are used as traditional Tibetan medicines, known as "Zangyinchen" or "Dida". However, the phylogenetic relationships among Swertia medicinal plants and their wild relatives have remained unclear. In this study, we sequenced and assembled 16 complete chloroplast (cp) genomes of 10 Swertia species, mainly distributed in Qinghai Province, China. The results showed that these species have typical structures and characteristics of plant cp genomes. The sizes of Swertia cp genomes are ranging from 149,488 bp to 154,097 bp. Most Swertia cp genomes presented 134 genes, including 85 protein coding genes, eight rRNA genes, 37 tRNA genes, and four pseudogenes. Furthermore, the GC contents and boundaries of cp genomes are similar among Swertia species. The phylogenetic analyses indicated that Swertia is a complex polyphyletic group. In addition, positive selection was found in psaI and petL genes, indicating the possible adaptation of Qinghai Swertia species to the light environment of the Qinghai-Tibet plateau. These new cp genome data could be further investigated to develop DNA barcodes for Swertia medicinal plants and for additional systematic studies of Swertia and Swertiinae species.

Leontopodium R. Brown ex Cass.belongs to the tribe Gnaphalieae in the family Asteraceae; it comprises approximately 60 species worldwide, of which 40 are distributed in China. The morphological characteristics of the achene are relatively stable and can be used as taxonomic criteria for species classification within Asteraceae. In this study, scanning electron microscopy (SEM) was used to observe the achene micromorphological characteristics of 28 species and 1 variety of Chinese Leontopodium . The results showed that the achenes of Leontopodium species were elliptical or narrow elliptical, approximately 0.7–1.6-mm long × 0.1–0.6-mm wide. The surface ornamentation was reticulate or rippled with clavate twin hairs or smooth. The carpopodium base was constricted or unconstricted. Based on these characteristics, we provided a new key for Chinese Leontopodium taxa. The characteristics of the achene trichome, surface ornamentation, and carpopodium show important taxonomic value at different taxonomic levels, leading us to arrive at the following conclusions. 1. The shape of the achene trichome is valuable for the taxonomic delimitation of taxa between Leontopodium and related genera. 2. The achene surface ornamentation can be categorized into two types and is a taxonomic tool for classification at the section level within Leontopodium . 3. The characteristics of the carpopodium and trichome density can serve as important features under the section level. Thus, achene micromorphological characteristics provide significant morphological evidence that could play an important role in resolving various taxonomic problems within Leontopodium related Asteraceae.

This study generated and analyzed complete plastome and internal transcribed spacer (ITS) data of 46 Lactuca species, 13 African endemic (AE) Lactuca species, and 15 species from eight related genera in Lactucinae. The new plastome and nuclear ITS sequences were then used to reconstruct the phylogenetic relationships of Lactuca species. The whole-plastome data were used to estimate divergence time and ancestral area reconstruction of the identified major Lactuca lineages. The results showed that Lactuca species are generally similar in plastome size, Guanine and Cytosine (GC) content, gene structure, and categories, although crop lettuce (Lactuca sativa L.) and its gene pool relatives were found to have one unique pseudogene (ψ ndhF), and accD, atpF, cemA, clpP, and rpl22 showed signs of positive selection. Our phylogenomic analysis demonstrated that Lactuca is monophyletic after excluding Lactuca alatipes Collett and Hemsl and AE Lactuca species. AE Lactuca species are morphologically distinct from core Lactuca lineage and need to be excluded from Lactua. The core Lactuca species most likely originated from Asia-Temperate W ~6.82 Mya and then dispersed globally and formed nine clades. Finally, the lettuce gene pool concept was amended according to the phylogenetic and historical biogeographic analyses. This study revised the circumscription of Lactuca, revealed robust phylogenetic relationships within the genus, and provided insights into Lactucinae phylogeny. The lettuce gene pool species could be used as potential genetic resources for lettuce breeding.

Lactuca L. is the central genus of Lactucinae (Cichorieae; Asteraceae), containing cultivated lettuce and its wild relatives. In this study, we used Scanning Electron Microscope, Plain Stereo Microscope and Automated Digital Microscope to observe, record and discuss the achene characters and surface micro-features ofLactuca (including taxa of ex-Pterocypsela Shih) and Notoseris Shih species. The taxon sampling consisted of fifteen globally distributed Lactuca species and Chinese originated Notoseris species. The results indicated that the morphological and micro-morphological features of achenes were of great importance to identify Lactuca species at the genus and species level. We conclude that two key features, the presence or absence of beak and the arrangement and shape of epidermal cells, can be used to distinguish Lactuca from Notoseris. The shape and margin of the achene body, the beak length and the number of ribs on either side of achene are key features to classify Lactuca species. The ornamentation of epidermal cells can also provide extra evidence to determine closely related Lactuca species. The interspecific relationships among the Lactuca species based on achene features are consistent with the results of previously molecular systematics of these species.

Anaphalis DC. is the largest genus in Asian Gnaphalieae, and China, containing 54 known species, is one of the largest centers of Anaphalis diversity. In the present study, the achene micro-morphology of 39 Chinese Anaphalis taxa were studied in detail using scanning electron microscopy (SEM). The results showed that the Chinese Anaphalis could be classified into two groups based on achene surface ornamentation viz. reticulate-claviform (Group I) and ligulate protuberant (Group II). Achene micro-morphological characteristics were useful for the delimitation of interspecific and supraspecific classification within Anaphalis.

As important post-translational modifications, protein cysteine modifications (PCMs) occurring at cysteine thiol group play critical roles in the regulation of various biological processes in eukaryotes. Due to the rapid advancement of high-throughput proteomics technologies, a large number of PCM events have been identified but remain to be curated. Thus, an integrated resource of eukaryotic PCMs will be useful for the research community. In this work, we developed an integrative database for protein cysteine modifications in eukaryotes (iCysMod), which curated and hosted 108 030 PCM events for 85 747 experimentally identified sites on 31 483 proteins from 48 eukaryotes for 8 types of PCMs, including oxidation, S-nitrosylation (-SNO), S-glutathionylation (-SSG), disulfide formation (-SSR), S-sulfhydration (-SSH), S-sulfenylation (-SOH), S-sulfinylation (-SO2H) and S-palmitoylation (-S-palm). Then, browse and search options were provided for accessing the dataset, while various detailed information about the PCM events was well organized for visualization. With human dataset in iCysMod, the sequence features around the cysteine modification sites for each PCM type were analyzed, and the results indicated that various types of PCMs presented distinct sequence recognition preferences. Moreover, different PCMs can crosstalk with each other to synergistically orchestrate specific biological processes, and 37 841 PCM events involved in 119 types of PCM co-occurrences at the same cysteine residues were finally obtained. Taken together, we anticipate that the database of iCysMod would provide a useful resource for eukaryotic PCMs to facilitate related researches, while the online service is freely available at http://icysmod.omicsbio.info.

The first complete mitochondrial genome (mt) of Paraprenanthes diversifolia (Vaniot) N. Kilian (Cichorieae; Asteraceae) was sequenced and successfully assembled in this study. The full length of the mt genome is 360,751 bp, containing 73 genes (33 protein-coding genes, 29 tRNA genes, 6 rRNA genes, and 5 protein-coding genes containing internal stop codons). There are two pairs of long (over 1000 bp) repeat regions in the mt genome of P. diversifolia. The phylogenetic analysis indicated that P. diversifolia has a close relationship with other Lactucinae species.

Opisthopappus taihangensis (Ling) Shih is a monotypic species (Anthemideae, Asteraceae) and an endemic endangered plant of China. In this study, we sequenced the complete chloroplast genome of O. taihangensis using Illumina HiSeq X Ten platform. The total length of O. taihangensis chloroplast genome is 151,089 bp, including a large single-copy region of length 82,877 bp, a small single-copy region of length 18304 bp, and a pair of 24,954-bp inverted repeat regions. The chloroplast genome of O. taihangensis has 132 genes, including 87 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. The overall GC content of the whole genome was 37.5%. The phylogenetic analysis revealed a close relationship between O. taihangensis and Chrysanthemum boreale.

Halenia elliptica D.Don (Gentianaceae) is one of the genuine medicinal species in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of H. elliptica using Illumina HiSeq X Ten platform. The length of its complete cp genome is 153,341?bp, containing four sub-regions; a large single-copy region (LSC) of 82,811?bp and a small single-copy region (SSC) of 18,278?bp, which are separated by a pair of inverted repeat regions (IRs) of 26,126bp each. The complete cp genome of H. elliptica contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the cp genome is 38.1%. The phylogenetic analysis, based on 15?cp genomes, suggested that H. elliptica is closely related to Halenia corniculata (L.) Cornaz and Swertia species.

Flaveria bidentis (L.) Kuntze (Asteraceae) is one of the most hazardous invasive alien plant species and spread rapidly in China. In this study, the complete chloroplast genome of F. bidentis was sequenced using Illumina HiSeq X Ten platform. The results showed that the length of chloroplast genome of F. bidentis is 152, 230 bp, including a small single-copy region (18,362 bp), a large single-copy region (83,798 bp) and two inverted repeat regions (25,035 bp). The chloroplast genome contains 115 unique genes, including 81 protein-coding genes, four rRNA genes, and 30 tRNA genes. In total, we found 32 tandem repeats, 34 dispersed repeats and 36 SSRs in the chloroplast genome of F. bidentis. Phylogenetic analysis revealed that F. bidentis was in an independent clade and did not belong to the tribe Heliantheae Cass.