功能基因表达是连接基因编码信息与蛋白质产物的一个基本生命过程, 基因表达水平被视为介于基因型与表现型之间的一种数量性状, 在植物应对气候和环境变化时发挥重要作用。该文首先系统综述了植物基因表达调控因子研究进展, 包括转录因子和小RNA等在基因表达调控中的作用。其次, 探讨了基于基因表达数据进行全基因组关联分析(GWAS)估计调控因子基因的表达数量性状基因座(eQTLs)位置以及该方法的局限性。随后从理论上分析了在突变、漂变、选择和迁移过程中的种内基因表达变异与检验方法, 在突变-漂变过程中以及在基于系统发育树的漂变-选择过程中的种间基因表达进化与检测方法。最后, 探讨了植物交配系统对基因表达进化的调控, 自交降低了有效群体大小、突变率、基因重组及外源花粉竞争, 改变了配子与合子阶段的自然选择功效等, 从而间接调控种内基因表达变异和种间基因表达进化。全文综合评述了目前的理论和实际研究进展及存在的问题, 有助于深入理解植物基因表达调控和进化机制。

Understanding how East Asian subtropical evergreen broad-leaved forests (EBLFs) have evolved over time is not only vital for biodiversity conservation but also facilitates predictive modeling of ecosystem services under global change scenarios. During recent decades, numerous studies have been devoted to investigating the evolution of EBLFs. However, there are often contradictory interpretations of the different taxa associated with different geological events and environmental backgrounds. Here, we synthesize several key aspects of the spatiotemporal evolution of EBLFs. First, the EBLFs emerged concomitantly with the development of Asian monsoon systems, occurring no earlier than the Eocene. While the southernmost region was inhabited by tropical elements, EBLFs are not the direct relic of boreotropical flora because of the presence of a broad arid belt at that time. Rather, they represent a unique assemblage including boreotropical relics, tropical floras and deciduous broad-leaved forests. Second, the evolution of EBLFs should not be contextualized within an enclave, the adjacent vegetation systems to elucidate the potential connections between EBLFs and other biomes should be considered to avoid an isolated phenomenon. Third, the adaptive response of EBLFs to environmental changes caused by anthropogenic disturbance in subtropical regions remains understudied. Such a knowledge gap must be addressed to develop effective conservation strategies to sustain the ecosystem amid the dual pressure of climate change and human activity in the future. Finally, current research has predominantly focused on the dominant tree species in EBLFs, whereas comprehensive understanding requires expanding the investigation of associated flora, including understory trees and herbaceous plants. This review not only consolidates contemporary perspectives on the evolution of EBLFs but also proposes a framework to navigate the Anthropocene challenges. By bridging historical patterns with future projections, we aim to catalyze transformative research on EBLFs’ resilience and sustainable management, fostering further research and development regarding the resurgence.

The genus Micromonospora, a globally distributed actinomycete inhabiting diverse ecosystems, is widely recognized for its remarkable biosynthetic capacity and role as a prolific source of bioactive natural products. However, the members of the genus Micromonospora from extreme environments remain largely unstudied. In this study, we isolated 15 Micromonospora spp. strains from samples collected in desert and marine habitats. Based on polyphasic taxonomy approaches eight strains were identified and represent four novel species. Genome mining of the newly isolated strains revealed substantial biosynthetic potential for terpenes (n = 70, 22.9% of total biosynthetic gene clusters [BGCs]) and polyketides (n = 60, 19.6% of total BGCs). Subsequent pan-genomic analysis identified substantial numbers of terpene-related (n = 745, 33.8% of total biosynthetic genes [BGs]) and polyketide-related (n = 728, 33.0%) BGs in the core genome, highlighting their core biosynthetic potential. To further investigate their metabolic capacity, fermentation and metabolomic profiling were conducted to assess the secondary metabolite production capacity of all 15 strains. The results revealed a diverse array of alkaloids (averaging 75.3, 33.4% of total annotated secondary metabolites) and amino acid-derived peptides (averaging 56.3, 25.0% of total). These findings also highlight significant metabolic variations among strains and underscore the pivotal role of fermentation conditions in shaping their metabolic profiles. This study advances the taxonomic and functional understanding of Micromonospora spp. and presents a multi-omics framework combining genome mining and metabolomics to explore the biosynthetic potential of wild-type strains from extreme habitats.

A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order, Lepidoptera (butterflies and moths) are central to terrestrial ecosystems and serve as important models for biologists studying ecology and evolutionary biology. However, for such an insect group, the higher-level phylogenetic relationships among its superfamilies remain poorly resolved. Here, we increased taxon sampling among Lepidoptera (37 superfamilies and 68 families containing 263 taxa), obtaining a series of amino-acid data sets from 69 680 to 400 330 aa in length for phylogenomic reconstructions. Using these data sets, we explored the effect of different taxon sampling with significant increases in gene loci on tree topology using maximum-likelihood (ML) and Bayesian inference (BI) methods. Moreover, we also tested the effectiveness of topology robustness among the three ML-based models. The results demonstrated that taxon sampling is an important determinant in tree robustness of accurate phylogenetic estimation for species-rich groups. Site-wise heterogeneity was identified as a significant source of bias, causing inconsistent phylogenetic positions among ditrysian lineages. The application of the posterior mean site frequency (PMSF) model provided reliable estimates for higher-level phylogenetic relationships of Lepidoptera. Phylogenetic inference presented a comprehensive framework among lepidopteran superfamilies, and revealed some new sister relationships with strong supports (Papilionoidea is sister to Gelechioidea, Immoidea is sister to Galacticoidea, and Pyraloidea is sister to Hyblaeoidea, respectively). The current study provides essential insights for future phylogenomic investigations in species-rich lineages of Lepidoptera and enhances our understanding on phylogenomics of highly diversified groups.

Although considerable progress has recently been made in the phylogeny of Hymenasplenium, the genus remains poorly investigated; specifically, the diversification and historical biogeography of the genus have been little studied. Here, we infer an updated plastid DNA phylogeny and the first large-scale nuclear DNA phylogeny to understand the biogeography of the genus. The plastid phylogeny includes 312 accessions from across the genus′ distribution range (ca. 121% increase of the latest sampling), with special attention paid to island accessions from 14 Indian Ocean and Pacific islands, whereas the nuclear phylogeny includes 161 accessions of the Afro–Eurasian species. We identify one new major clade and two new subclades. Reticulate evolution was revealed both among subclades and among species in the Afro–Eurasian. Our divergence-time analyses show that most of the extant species diversity has arisen from diversification after the Oligocene despite a Cretaceous origin of the genus. Ancestral area reconstruction revealed that vicariance likely played a major role in building biogeographic patterns at deep evolutionary scales (the Afro–Eurasian clade and the American clade) in Hymenasplenium, while the intercontinental disjunctions within the Afro–Eurasian clade among Asia, Africa, and Oceania might have resulted from frequent long-distance dispersal events from Asia to Oceania and Africa.

Recent phylogenomic studies have confirmed that Scirtidae is one of the earliest-diverging groups of polyphagan beetles. Cretaceous fossils and genome-scale data have shown promise in elucidating the evolutionary history of Scirtidae. However, knowledge about the Mesozoic diversity of scirtids remains limited, and a recent phylogenomic study of Australasian Scirtinae failed to consider among-site compositional heterogeneity. In this study, we present a refined phylogeny of Scirtinae by analyzing ultraconserved element data under the better-fitting site-heterogeneous CAT-GTR+G4 model. A new scirtine fossil, Serracyphon philipsi gen. et sp. nov., is reported from mid-Cretaceous Kachin amber. This fossil is characterized by serrate antennae, uncarinated antennomere 1, absence of subocular carinae, and absence of a buttonhole on subgenal ridges. The placement of Serracyphon is evaluated within our updated phylogenomic framework for scirtine evolution. Additionally, we critically reevaluate the taxonomy of the “Scirtes” fossils previously described from the Eocene of the Isle of Wight.

番茄(Solanum lycopersicum)在生长发育过程中常受到低温和干旱等多种非生物胁迫的影响。WRKY转录因子参与调控植物多种非生物胁迫响应过程, 而SlWRKY45在番茄非生物胁迫中的功能尚不清楚。基因表达分析发现, 低温、干旱和ABA处理均可显著诱导SlWRKY45的表达; 过表达SlWRKY45可提高番茄对干旱和低温的耐受性; 在干旱和低温处理下, 过表达株系的光合指标、抗氧化酶活性和脯氨酸(Pro)含量显著高于野生型(WT), 活性氧(ROS)和丙二醛(MDA)含量显著低于WT。转录组数据分析显示, SlWRKY45主要通过调控抗氧化酶活性和胁迫响应途径介导番茄对低温胁迫的响应。双荧光素酶报告基因检测发现, SlWRKY45可直接激活SlPOD1的表达。酵母双杂交(Y2H)和双分子荧光互补(BiFC)试验结果表明, SlWRKY45与SlWRKY46存在相互作用。综上表明, SlWRKY45可能通过直接调控抗氧化酶途径增强转基因番茄的抗逆性, 为番茄的遗传改良提供了重要的候选基因资源。

干旱是全球农林生产面临的主要非生物胁迫之一。植物通过调控共生微生物群落，形成了多层次的抗旱适应机制，其协同作用机制主要可概括为以下5个方面：(1)通过分泌胞外多糖(EPS)在植物表面形成保护性生物膜，增强保水性和土壤结构稳定性；(2)合成脯氨酸等渗透调节物质维持细胞渗透稳态；(3)产生抗氧化物质清除活性氧，缓解过氧化损伤；(4)分泌植物激素(如生长素)及1-氨基环丙烷-1-羧酸脱氨酶(ACCD)，调控内源激素代谢平衡；(5)释放挥发性有机化合物、激素及酶等信号分子，激活植物对干旱的适应能力。未来研究需聚焦于宿主特异性抗旱微生物菌群，解析叶际-根际微生物组的协同调控网络，最终通过微生物组工程评价其在农业中的应用效果。

Floral color and odor serve as attractants for pollinators. It remains unclear how changes in these traits in color-change species interact with pollinators and impact a plant's reproductive success. Lonicera calcarata flowers change from white (Night 1 [N1] and Day 1 [D1]) through yellow (Night 2 [N2]) and orange (Day 2 [D2]) to orange-red (Night 3 [N3] and Day 3 [D3]). Our research showed that floral characters, stigma activity, nectar production and floral spectral reflectance decreased through the flowering phases. Floral odor mainly comprised fatty acids, aldehydes, monoterpenes and alcohols, especially n-hexadecanoic acid, hexadecanal and 3-carene. Floral odor peaked on N1 and N3, largely due to the presence of fatty acids. The emission of n-hexadecanoic acid was higher on N1 and N3 compared with other phases, while hexadecanal emission remained constant throughout the flowering stages. The emission of 3-carene was highest on N1. Lonicera calcarata was mainly pollinated by the moth Chorodna strixaria, the butterfly Acosmeryx naga and three bumblebees (Bombus melanurus, B. eximius, B. sonani) and they all preferred to visit white (younger) flowers. Moths had a preference for 3-carene and no significant preference for n-hexadecanoic acid and hexadecanal. Seed sets of nocturnal pollination and control treatments were not significantly different. Lonicera calcarata could produce seeds by self-pollination; cross-pollination significantly increased the seed set. Floral color guides pollinators to visit younger flowers with more floral rewards and higher stigma activity. Different chemical compounds in floral odor may not only attract pollinators but also avoid herbivore damage.

近年来, 植物抗病免疫研究取得了突破性进展, 包括病原识别、免疫信号转导及植物-病原-介体-环境互作等。这些研究不仅增强了我们对植物抗病免疫的理解, 还为分子育种和分子遗传学研究奠定了坚实的基础。近期, 国内多家单位相继在植物免疫机制研究中取得了令人振奋的新突破, 从植物应对病原的识别机制、次级代谢产物参与植物抗病反应过程、 禾本科作物的抗病模块和基于人工智能的抗病小肽设计等不同层面对植物免疫反应的分子机制进行了深入解析。随着CRISPR/Cas9基因编辑技术和人工智能的快速发展, 这些研究成果将有助于创制具有抗病特性的新种质, 从而加速抗病作物新品种的培育过程, 对于抗病生物育种和国家粮食安全具有重要意义。

ABF转录因子是能够特异识别并结合ABA响应元件(ABRE)的碱性亮氨酸拉链蛋白的统称, 参与ABA信号转导。通过对甘蓝型油菜(Brassica napus) BnaABF2基因编码蛋白进行分析, 亚细胞定位结果显示, BnaABF2蛋白定位于细胞核; 酵母系统转录活性分析表明, BnaABF2无转录激活活性; qRT-PCR检测发现, BnaABF2在叶中的表达量最高。此外, 还发现ABA处理、模拟干旱和盐胁迫能够诱导BnaABF2的表达; BiFC结果显示, BnaMPK1/2/6/7/9/12/13能与BnaABF2相互作用。Dual-LUC结果表明, BnaMPK7可能通过磷酸化增强BnaABF2对下游靶基因的转录调控。该研究初步探索了转录因子BnaABF2的基本特性与互作蛋白, 对理解其功能与机制具有一定的理论价值。

Microalgae’s adaptability and resilience to Earth’s diverse environments have evolved these photosynthetic microorganisms into a biotechnological source of industrially relevant physiological functions and biometabolites. Despite this, microalgae-based industries only exploit a handful of species. This lack of biodiversity hinders the expansion of the microalgal industry. Microalgal bioprospecting, searching for novel biological algal resources with new properties, remains a low throughput and time-consuming endeavour due to inefficient workflows that rely on non-selective sampling, monoalgal culture status and outdated, non-standardized characterization techniques. This review will highlight the importance of microalgal bioprospecting and critically explore commonly employed methodologies. We will also explore current advances driving the next generation of smart algal bioprospecting focusing on novel workflows and transdisciplinary methodologies with the potential to enable high-throughput microalgal biodiscoveries. Images adapted from (Addicted04 in Wikipedia File: Australia on the globe (Australia centered).svg. 2014.; Jin et al. in ACS Appl Bio Mater 4:5080–5089, 2021; Kim et al. in Microchim Acta 189:88, 2022; Tony et al. in Lab on a Chip 15, 19:3810–3810; Thermo Fisher Scientific INC. in CTS Rotea Brochure).

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a “two-step domestication” process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Transgenic and gene-editing technologies are essential for gene functional analysis and crop improvement. However, the pleiotropic effects and unknown mechanisms of morphogenic genes have hindered their broader application. In this study, we employed the one-step de novo shoot organogenesis (DNSO) method, and demonstrated that overexpression of the morphogenic gene Arabidopsis thanalia GROWTH-REGULATING FACTOR 5 (AtGRF5) significantly enhanced genetic transformation efficiency in cucurbit crops by promoting callus proliferation and increasing dense cells during regeneration. High-resolution time-series transcriptomics and single-cell RNA sequencing revealed that AtGRF5 overexpression induced auxin-related genes and expanded stem cell populations during cucumber DNSO. Using DNA-affinity purification sequencing (DAP-seq) in combination with spatiotemporal differential gene expression analysis, we identified CsIAA19 as a key downstream target of AtGRF5, with its modulation playing a pivotal role in regeneration. Rescuing CsIAA19 in AtGRF5-overexpressing explant reversed the enhanced callus proliferation and regeneration. To address growth defects caused by AtGRF5 overexpression, we developed an abscisic acid-inducible AtGRF5 expression system, significantly improving transformation and gene-editing efficiency across diverse genotypes while minimizing pleiotropic effects. In summary, this research provides mechanistic insights into AtGRF5-mediated transformation and offers a practical solution to overcome challenges in cucurbit crop genetic modification.

Due to the high cost of whole-genome sequencing and the sampling difficulty of transcriptome sequencing in non-model plants, evolutionary studies often depend on next-generation sequencing (NGS) data. Nonetheless, current approaches typically focus on assembling chloroplast genomes or a few nuclear loci, leaving much of the genomic information from NGS underexploited. In this study, we employed multigenomic data sets and advanced analytical pipelines to reconstruct a robust phylogenetic framework for 39 Bupleurum. Nuclear gene data sets and organellar genomes derived from NGS were analyzed. We successfully reconstructed a robust phylogenetic framework for East Asia (EA) Bupleurum, in which two clades were strongly supported and all intersectional relationships were resolved. Phylogenetic discordance was mainly caused by incomplete lineage sorting and hybridization. Divergence dating estimated the origin of Bupleurum at ∼50.76 Ma, with the two subgenera (Penninervia and Bupleurum) diverging at 42.26 Ma. The EA lineages emerged around 22.85 Ma, with Group I diverging at 11 Ma and Group II at 8.72 Ma. Notably, diversification rates remained stable within both EA groups. Combined with geological events and gene–environment correlations, precipitation seasonality (PSN) showed the strongest phylogenetic signals with the Single Copy Orthologue (SCO) tree. The arid event in Central Asia may have driven the adaptation of EA Bupleurum (especially in EA Group II species) to arid, sun-exposed environments. By integrating phylogenetics, geology, and environmental data, this study provides a comprehensive understanding of the evolutionary history and adaptive strategies of Bupleurum in EA, offering valuable insight into the interplay between genetic and ecological factors in plant diversification.

MYB transcription factors (TFs), one of the largest TF families in plants, are involved in various plant-specific processes as the central regulators, such as in phenylpropanoid metabolism, cell cycle, formation of root hair and trichome, phytohormones responses, reproductive growth and abiotic or biotic stress responses. Here we summarized multiple roles and explained the molecular mechanisms of MYB TFs in plant development and stress adaptation. The exploration of MYB TFs contributes to a better comprehension of molecular regulation in plant development and environmental adaptability.

由大丽轮枝菌(Verticillium dahliae)引起的黄萎病是棉花(Gossypium hirsutum)生产中最主要的威胁之一, 其可导致棉花大幅减产和纤维品质严重下降。前期对接种大丽轮枝菌的拟南芥(Arabidopsis thaliana)进行转录组分析, 表明DIR1类蛋白基因AT3G53980.2受病原菌强烈诱导表达。该研究发现, 棉花脂质转移蛋白编码基因GhDIR1 (Gh_A09G180700.1)与AT3G53980.2表现出高度的同源性。生物信息学分析表明, GhDIR1开放阅读框(ORF)为351 bp, 编码116个氨基酸残基。亚细胞定位结果显示GhDIR1定位于细胞膜。分析GhDIR1在大丽轮枝菌V991侵染后的表达模式, 发现其能快速响应大丽轮枝菌侵染。利用病毒诱导的基因沉默(VIGS)技术下调该基因表达后, 棉花对黄萎病菌的抗性显著降低。野生型和GhDIR1沉默植株转录组测序结果表明, 差异表达基因主要在类黄酮生物合成、倍半萜和三萜生物合成以及α-亚麻酸代谢3个途径富集; 同时, 荧光定量PCR结果表明, 3个途径中的6个关键基因(GhCHS、GhDFR、GhCAD、GhSEQ、GhLOX和GhAOC)在GhDIR1沉默植株中均下调表达, 与转录组数据一致。推测GhDIR1可能通过介导类黄酮和萜类化合物的合成途径, 并调节茉莉酸(JA)等植物激素的次级代谢来激活相关信号通路, 进而影响植株抗病性。综上, GhDIR1作为棉花抗黄萎病的正向调控因子, 通过参与多种激素和抗病信号网络调控植物的免疫反应。

Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan-Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax.

Inferring general biogeographic patterns in the sub-Antarctic region has been challenging due to the disparate geological origins of its islands and archipelagos—ranging from Gondwanan fragments to uplifted seafloor and more recently formed volcanic islands—and the remoteness of these island systems, spread around the austral continental landmasses. Here, we conduct phylogenetic reconstruction, divergence time estimation, and Bayesian Island Biogeographic analyses to reconstruct the spatio–temporal colonization histories of seven vascular plant lineages, which are either widespread across the sub-Antarctic region (Acaena magellanica, Austroblechnum penna-marina, Azorella selago, Notogrammitis crassior) or restricted to an extremely remote sub-Antarctic province (Colobanthus kerguelensis, Polystichum marionense, Pringlea antiscorbutica). Our results reveal high biological connectivity within the sub-Antarctic region, with southern landmasses (Australia, New Zealand, South America) as key sources of sub-Antarctic plant diversity since the Miocene, supporting long-distance dispersal as the primary colonization mechanism rather than tectonic vicariance. Despite the geographic isolation of the sub-Antarctic islands, eastward and westward colonization events have maintained this connectivity, likely facilitated by eastward-moving marine and wind currents, short-term weather systems, and/or dispersal by birds. Divergence time estimates indicate that most species diverged within the Plio–Pleistocene, with crown ages predating the Last Glacial Maximum, suggesting that sub-Antarctic archipelagos acted as refuges for biodiversity. Our findings highlight the role of one of the most remote sub-Antarctic archipelagos as both a refugium and a source of (re)colonization for continental regions. These results underscore the urgent need for establishing priority conservation plans in the sub-Antarctic, particularly in the face of climate change.

The integration of phytochemistry into forensic science has emerged as a groundbreaking frontier, providing unprecedented insights into nature's secrets through the precise application of phytochemical fingerprinting of phytotoxins as a cutting-edge approach. This study explores the dynamic intersection of phytochemistry and forensic science, highlighting how the unique phytochemical profiles of toxic plants and their secondary metabolites, serve as distinctive markers for forensic investigations. By utilizing advanced techniques such as Ultra-High-Performance Liquid Chromatography (UHPLC) and High-Resolution Mass Spectrometry (HRMS), the detection and quantification of plant-derived are made more accurate in forensic contexts. Real-world case studies are presented to demonstrate the critical role of plant toxins in forensic outcomes and legal proceedings. The challenges, potential, and future prospects of integrating phytochemical fingerprinting of plant toxins into forensic science were discussed. This review aims to illuminate phytochemical fingerprinting of plant toxins as a promising tool to enhance the precision and depth of forensic analyses, offering new insights into the complex stories embedded in plant toxins.