New Phytol , IF:10.151 , 2024 Jul doi: 10.1111/nph.19949
The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm.
State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
Grain filling in maize (Zea mays) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol, and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.
PMID: 38962989
Plant Biotechnol J , IF:9.803 , 2024 Jul , V22 (7) : P1897-1912 doi: 10.1111/pbi.14309
Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield.
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P.R. China.; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, P.R. China.; Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, P.R. China.
Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.
PMID: 38386569
Sci Total Environ , IF:7.963 , 2024 Jul , V935 : P173413 doi: 10.1016/j.scitotenv.2024.173413
Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L.
Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: dcjin@rcees.ac.cn.
Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L. We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33-0.53 in shoots and 0.39-0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. Specifically, Cr(VI) had a more significant effect on the microbial community structure in the endophytic of Tagetes erecta L. than in the rhizosphere (p < 0.05). The genera Devosia and Methylobacillus were positively correlated with Cr(VI) concentrations. Biomarkers such as Bacilli and Pseudonocardia were identified under the different Cr(VI)-contaminated treatments using LEfSe. In addition, the interaction and stability of the endophytic microbiome were enhanced under Cr(VI) stress. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils.
PMID: 38788956
Sci Total Environ , IF:7.963 , 2024 Aug , V937 : P173422 doi: 10.1016/j.scitotenv.2024.173422
The ethylene response factor gene, ThDRE1A, is involved in abscisic acid- and ethylene-mediated cadmium accumulation in Tamarix hispida.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.; Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China. Electronic address: gaocaiqiu@nefu.edu.cn.
Tamarix hispida is highly tolerant to salt, drought and heavy metal stress and is a potential material for the remediation of cadmium (Cd)-contaminated soil under harsh conditions. In this study, T. hispida growth and chlorophyll content decreased, whereas flavonoid and carotenoid contents increased under long-term Cd stress (25 d). The aboveground components of T. hispida were collected for RNA-seq to investigate the mechanism of Cd accumulation. GO and KEGG enrichment analyses revealed that the differentially expressed genes (DEGs) were significantly enriched in plant hormone-related pathways. Exogenous hormone treatment and determination of Cd(2+) levels showed that ethylene (ETH) and abscisic acid (ABA) antagonists regulate Cd accumulation in T. hispida. Twenty-five transcription factors were identified as upstream regulators of hormone-related pathways. ThDRE1A, which was previously identified as an important regulatory factor, was selected for further analysis. The results indicated that ThABAH2.5 and ThACCO3.1 were direct target genes of ThDRE1A. The determination of Cd(2+), ABA, and ETH levels indicated that ThDRE1A plays an important role in Cd accumulation through the antagonistic regulation of ABA and ETH. In conclusion, these results reveal the molecular mechanism underlying Cd accumulation in plants and identify candidate genes for further research.
PMID: 38796019
Food Res Int , IF:6.475 , 2024 Jul , V187 : P114359 doi: 10.1016/j.foodres.2024.114359
Characterization of the aroma-active compounds in Xiaokeng green tea by three pretreatment methods combined with gas chromatography-olfactometry (GC-O).
State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China; Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei 230036, People's Republic of China; International Joint Laboratory on Tea Chemistry and Health Effects of Ministry of Education, Anhui Agricultural University, Hefei 230036, People's Republic of China.; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China; Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei 230036, People's Republic of China; International Joint Laboratory on Tea Chemistry and Health Effects of Ministry of Education, Anhui Agricultural University, Hefei 230036, People's Republic of China. Electronic address: xiaotingzhai@ahau.edu.cn.; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, People's Republic of China; Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei 230036, People's Republic of China; International Joint Laboratory on Tea Chemistry and Health Effects of Ministry of Education, Anhui Agricultural University, Hefei 230036, People's Republic of China. Electronic address: daiqianying@ahau.edu.cn.
Chinese Xiaokeng green tea (XKGT) possesses elegant and fascinating aroma characteristics, but its key odorants are still unknown. In this study, 124 volatile compounds in the XKGT infusion were identified by headspace-solid phase microextraction (HS-SPME), stir bar sorptive extraction (SBSE), and solvent extraction-solid phase extraction (SE-SPE) combined with gas chromatography-mass spectrometry (GC-MS). Comparing these three pretreatments, we found HS-SPME was more efficient for headspace compounds while SE-SPE was more efficient for volatiles with higher boiling points. Furthermore, SBSE showed more sensitive to capture ketones then was effective to the application of pretreatment of aroma analysis in green tea. The aroma intensities (AIs) were further identified by gas chromatography-olfactometry (GC-O). According to the AI and relative odor activity value (rOAV), 27 compounds were identified as aroma-active compounds. Quantitative descriptive analysis (QDA) showed that the characteristic aroma attributes of XKGT were chestnut-like, corn-like, fresh, and so on. The results of network analysis showed that (E, Z)-2,6-nonadienal, nonanal, octanal and nerolidol were responsible for the fresh aroma. Similarly, dimethyl sulfide, (E, E)-2,4-heptadienal, (E)-2-octenal and beta-cyclocitral contributed to the corn-like aroma. Furthermore, indole was responsible for the chestnut-like and soybean-like aroma. This study contributes to a better understanding of the molecular mechanism of the aroma characteristics of XKGT.
PMID: 38763643
Brief Funct Genomics , IF:4.241 , 2024 Jul , V23 (4) : P373-383 doi: 10.1093/bfgp/elad040
EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors.
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 China.; University of Chinese Academy of Sciences, Beijing 100049 China.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.
Reconstructing functional gene regulatory networks (GRNs) is a primary prerequisite for understanding pathogenic mechanisms and curing diseases in animals, and it also provides an important foundation for cultivating vegetable and fruit varieties that are resistant to diseases and corrosion in plants. Many computational methods have been developed to infer GRNs, but most of the regulatory relationships between genes obtained by these methods are biased. Eliminating indirect effects in GRNs remains a significant challenge for researchers. In this work, we propose a novel approach for inferring functional GRNs, named EIEPCF (eliminating indirect effects produced by confounding factors), which eliminates indirect effects caused by confounding factors. This method eliminates the influence of confounding factors on regulatory factors and target genes by measuring the similarity between their residuals. The validation results of the EIEPCF method on simulation studies, the gold-standard networks provided by the DREAM3 Challenge and the real gene networks of Escherichia coli demonstrate that it achieves significantly higher accuracy compared to other popular computational methods for inferring GRNs. As a case study, we utilized the EIEPCF method to reconstruct the cold-resistant specific GRN from gene expression data of cold-resistant in Arabidopsis thaliana. The source code and data are available at https://github.com/zhanglab-wbgcas/EIEPCF.
PMID: 37642217
BMC Plant Biol , IF:4.215 , 2024 Jul , V24 (1) : P641 doi: 10.1186/s12870-024-05366-0
Network analyses predict major regulators of resistance to early blight disease complex in tomato.
Department of Phytopathology and Crop Protection, Institute for Phytopathology, Christian Albrechts University, Kiel, Germany.; Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.; Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.; Department of Phytopathology and Crop Protection, Institute for Phytopathology, Christian Albrechts University, Kiel, Germany. Remco.stam@phytomed.uni-kiel.de.; Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany. Remco.stam@phytomed.uni-kiel.de.
BACKGROUND: Early blight and brown leaf spot are often cited as the most problematic pathogens of tomato in many agricultural regions. Their causal agents are Alternaria spp., a genus of Ascomycota containing numerous necrotrophic pathogens. Breeding programs have yielded quantitatively resistant commercial cultivars, but fungicide application remains necessary to mitigate the yield losses. A major hindrance to resistance breeding is the complexity of the genetic determinants of resistance and susceptibility. In the absence of sufficiently resistant germplasm, we sequenced the transcriptomes of Heinz 1706 tomatoes treated with strongly virulent and weakly virulent isolates of Alternaria spp. 3 h post infection. We expanded existing functional gene annotations in tomato and using network statistics, we analyzed the transcriptional modules associated with defense and susceptibility. RESULTS: The induced responses are very distinct. The weakly virulent isolate induced a defense response of calcium-signaling, hormone responses, and transcription factors. These defense-associated processes were found in a single transcriptional module alongside secondary metabolite biosynthesis genes, and other defense responses. Co-expression and gene regulatory networks independently predicted several D clade ethylene response factors to be early regulators of the defense transcriptional module, as well as other transcription factors both known and novel in pathogen defense, including several JA-associated genes. In contrast, the strongly virulent isolate elicited a much weaker response, and a separate transcriptional module bereft of hormone signaling. CONCLUSIONS: Our findings have predicted major defense regulators and several targets for downstream functional analyses. Combined with our improved gene functional annotation, they suggest that defense is achieved through induction of Alternaria-specific immune pathways, and susceptibility is mediated by modulating hormone responses. The implication of multiple specific clade D ethylene response factors and upregulation of JA-associated genes suggests that host defense in this pathosystem involves ethylene response factors to modulate jasmonic acid signaling.
PMID: 38971719
Microorganisms , IF:4.128 , 2024 Jul , V12 (7) doi: 10.3390/microorganisms12071348
Structure and Diversity of Endophytic Bacteria in Maize Seeds and Germinating Roots.
Guizhou Academy of Agriculture Sciences, Guiyang 550025, China.; School of Karst Science, Guizhou Normal University, Guiyang 550025, China.; College of Animal Science, Guizhou University, Guiyang 550025, China.; School of Life Sciences, Guizhou Normal University, Guiyang 550025, China.; State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
Seed endophytes in maize, which facilitate the transmission of microorganisms from one plant generation to the next, may play a crucial role in plant protection and growth promotion. This study aimed to investigate the effects of various maize varieties on the communities of endophytic bacteria in seeds and germinating roots. This study utilized Illumina high-throughput sequencing technology to examine the structural and diversity differences of endophytic bacterial communities within seed maize (BY1507), silage maize (QQ446), and wild maize (Teosinte) in both seeds and germinating roots. The results showed that 416 bacterial genera were detected, with Pantoea, Lachnospiraceae, Pararhizobium, Enterobacteriaceae, Stenotrophomonas, and Pseudonocardia being the most prevalent (relative abundance > 10%) at the genus level. No significant difference was observed in diversity indices (Chao1, ACE, Shannon, and Simpson) of seed endophytes among BY1507, QQ446, and Teosinte. The Shannon and Simpson indices for the germinating root endophyte from the wild variety (Teosinte) were significantly higher than the domesticated varieties (BY1507 and QQ446). PCoA revealed a notable overlap in the endophytic bacterial communities from the seeds of BY1507, QQ446, and Teosinte. Yet, clustering patterns were found. Co-occurrence network analysis showed that BY1507, QQ446, and Teosinte share a notable proportion of shared endophytic bacteria (>30%) between the seeds and germinating roots. This investigation elucidates the characteristics of endophytic microbial communities of seeds and germinating roots with seed maize, silage maize, and wild maize, offering data for future research on the physiological ecological adaptation of these endophytic microbial communities.
PMID: 39065116
BMC Genomics , IF:3.969 , 2024 Jul , V25 (1) : P666 doi: 10.1186/s12864-024-10549-y
Metabolomic and transcriptomic analyses of peach leaves and fruits in response to pruning.
College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China.; National Engineering Research Center for Agriculture in Northern Mountainous Areas, Agricultural Technology Innovation Center in Mountainous Areas of Hebei Province, Hebei Agricultural University, Baoding, Hebei, 071000, China.; College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China. yychj@hebau.edu.cn.; College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China. tianyi@hebau.edu.cn.; National Engineering Research Center for Agriculture in Northern Mountainous Areas, Agricultural Technology Innovation Center in Mountainous Areas of Hebei Province, Hebei Agricultural University, Baoding, Hebei, 071000, China. tianyi@hebau.edu.cn.
BACKGROUND: Pruning is an important cultivation management option that has important effects on peach yield and quality. However, the effects of pruning on the overall genetic and metabolic changes in peach leaves and fruits are poorly understood. RESULTS: The transcriptomic and metabolomic profiles of leaves and fruits from trees subjected to pruning and unpruning treatments were measured. A total of 20,633 genes and 622 metabolites were detected. Compared with those in the control, 1,127 differentially expressed genes (DEGs) and 77 differentially expressed metabolites (DEMs) were identified in leaves from pruned and unpruned trees (pdLvsupdL), whereas 423 DEGs and 29 DEMs were identified in fruits from the pairwise comparison pdFvsupdF. The content of three auxin analogues was upregulated in the leaves of pruned trees, the content of all flavonoids detected in the leaves decreased, and the expression of almost all genes involved in the flavonoid biosynthesis pathway decreased. The phenolic acid and amino acid metabolites detected in fruits from pruned trees were downregulated, and all terpenoids were upregulated. The correlation analysis revealed that DEGs and DEMs in leaves were enriched in tryptophan metabolism, auxin signal transduction, and flavonoid biosynthesis. DEGs and DEMs in fruits were enriched in flavonoid and phenylpropanoid biosynthesis, as well as L-glutamic acid biosynthesis. CONCLUSIONS: Pruning has different effects on the leaves and fruits of peach trees, affecting mainly the secondary metabolism and hormone signalling pathways in leaves and amino acid biosynthesis in fruits.
PMID: 38961329
Plants (Basel) , IF:3.935 , 2024 Jul , V13 (14) doi: 10.3390/plants13141905
Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L.
Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia.; Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.
In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.
PMID: 39065433
Insect Mol Biol , IF:3.585 , 2024 Aug , V33 (4) : P387-404 doi: 10.1111/imb.12908
Polygenic adaptation of a cosmopolitan pest to a novel thermal environment.
State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China.; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China.; Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China.; Institute of Plant Protection Fujian Academy of Agricultural Sciences, Fuzhou, China.; BGI Research, Sanya, China.; Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada.
The fluctuation in temperature poses a significant challenge for poikilothermic organisms, notably insects, particularly in the context of changing climatic conditions. In insects, temperature adaptation has been driven by polygenes. In addition to genes that directly affect traits (core genes), other genes (peripheral genes) may also play a role in insect temperature adaptation. This study focuses on two peripheral genes, the GRIP and coiled-coil domain containing 2 (GCC2) and karyopherin subunit beta 1 (KPNB1). These genes are differentially expressed at different temperatures in the cosmopolitan pest, Plutella xylostella. GCC2 and KPNB1 in P. xylostella were cloned, and their relative expression patterns were identified. Reduced capacity for thermal adaptation (development, reproduction and response to temperature extremes) in the GCC2-deficient and KPNB1-deficient P. xylostella strains, which were constructed by CRISPR/Cas9 technique. Deletion of the PxGCC2 or PxKPNB1 genes in P. xylostella also had a differential effect on gene expression for many traits including stress resistance, resistance to pesticides, involved in immunity, trehalose metabolism, fatty acid metabolism and so forth. The ability of the moth to adapt to temperature via different pathways is likely to be key to its ability to remain an important pest species under predicted climate change conditions.
PMID: 38488345
Photosynth Res , IF:3.573 , 2024 Jul doi: 10.1007/s11120-024-01103-8
Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium.
Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA.; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.; Competence Network IBD, Hopfenstrasse 60, 24103, Kiel, Germany.; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.; Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Plant and Microbial Biology, University of California, Berkeley, CA, 99354, USA. sabeeha@berkeley.edu.; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA. sabeeha@berkeley.edu.; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA. sabeeha@berkeley.edu.; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. sabeeha@berkeley.edu.; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. sabeeha@berkeley.edu.
Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.
PMID: 39017982
PeerJ , IF:2.984 , 2024 , V12 : Pe17649 doi: 10.7717/peerj.17649
Identifying highly connected sites for risk-based surveillance and control of cucurbit downy mildew in the eastern United States.
Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC, United States.; Department of Statistics, Oregon State University, Corvallis, OR, United States.; Department of Mathematics, City University of New York, City College, New York, NY, United States.; Agricultural Research Service, U.S. Department of Agriculture, Corvallis, OR, United States.; Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States.
OBJECTIVE: Surveillance is critical for the rapid implementation of control measures for diseases caused by aerially dispersed plant pathogens, but such programs can be resource-intensive, especially for epidemics caused by long-distance dispersed pathogens. The current cucurbit downy mildew platform for monitoring, predicting and communicating the risk of disease spread in the United States is expensive to maintain. In this study, we focused on identifying sites critical for surveillance and treatment in an attempt to reduce disease monitoring costs and determine where control may be applied to mitigate the risk of disease spread. METHODS: Static networks were constructed based on the distance between fields, while dynamic networks were constructed based on the distance between fields and wind speed and direction, using disease data collected from 2008 to 2016. Three strategies were used to identify highly connected field sites. First, the probability of pathogen transmission between nodes and the probability of node infection were modeled over a discrete weekly time step within an epidemic year. Second, nodes identified as important were selectively removed from networks and the probability of node infection was recalculated in each epidemic year. Third, the recurring patterns of node infection were analyzed across epidemic years. RESULTS: Static networks exhibited scale-free properties where the node degree followed a power-law distribution. Betweenness centrality was the most useful metric for identifying important nodes within the networks that were associated with disease transmission and prediction. Based on betweenness centrality, field sites in Maryland, North Carolina, Ohio, South Carolina and Virginia were the most central in the disease network across epidemic years. Removing field sites identified as important limited the predicted risk of disease spread based on the dynamic network model. CONCLUSIONS: Combining the dynamic network model and centrality metrics facilitated the identification of highly connected fields in the southeastern United States and the mid-Atlantic region. These highly connected sites may be used to inform surveillance and strategies for controlling cucurbit downy mildew in the eastern United States.
PMID: 39056053
3 Biotech , IF:2.406 , 2024 Jul , V14 (7) : P174 doi: 10.1007/s13205-024-04019-1
Transcriptomic and metabolomic profiling reveals molecular regulatory network involved in flower development and phenotypic changes in two Lonicera macranthoides varieties.
College of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208 Hunan Province China. GRID: grid.488482.a. ISNI: 0000 0004 1765 5169; Key Laboratory of Germplasm Resources and Standardized Planting of Hunan Large-Scale Genuine Medicinal Materials, Changsha, 410208 Hunan Province China.; Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha, 410208 Hunan Province China. ROR: https://ror.org/05ckg3w11. GRID: grid.454772.7. ISNI: 0000 0004 5901 2284
Due to the medicinal importance of the flowers of Xianglei type (XL) Lonicera macranthoides, it is important to understand the molecular mechanisms that underlie their development. In this study, we elucidated the transcriptomic and metabolomic mechanisms that underlie the flower development mechanism of two L. macranthoides varieties. In this study, 3435 common differentially expressed unigenes (DEGs) and 1138 metabolites were identified. These common DEGs were mainly enriched in plant hormone signal transduction pathways. Metabolomic analysis showed that amino acids were the main metabolites of differential accumulation in wild-type (WT) L. macranthoides, whereas in XL, they were flavonoids and phenylalanine metabolites. Genes and transcription factors (TFs), such as MYB340, histone deacetylase 1 (HDT1), small auxin-up RNA 32 (SAUR32), auxin response factor 6 (ARF6), PIN-LIKES 7 (PILS7), and WRKY6, likely drive metabolite accumulation. Plant hormone signals, especially auxin signals, and various TFs induce downstream flower organ recognition genes, resulting in a differentiation of the two L. macranthoides varieties in terms of their developmental trajectories. In addition, photoperiodic, autonomous, and plant hormone pathways jointly regulated the L. macranthoides corolla opening. SAUR32, Arabidopsis response regulator 9 (ARR9), Gibberellin receptor (GID1B), and Constans-like 10 (COL10) were closely related to the unfolding of the L. macranthoides corolla. These findings offer valuable understanding of the flower growth process of L. macranthoides and the excellent XL phenotypes at the molecular level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-024-04019-1.
PMID: 38855147
Zhongguo Zhong Yao Za Zhi , 2024 Jul , V49 (13) : P3473-3483 doi: 10.19540/j.cnki.cjcmm.20240413.101
[Identification and functional characterization of candidate genes involved in biosynthesis of ginsenoside Rg_1].
School of Life Sciences, Jilin Agricultural University Changchun 130118, China.; School of Life Sciences, Jilin Agricultural University Changchun 130118, China Jilin Agricultural University,Research Center for Ginseng Genetic Resources Development and Utilization,Jilin Province Changchun 130118, China.
Panax ginseng is a perennial herb with the main active compounds of ginsenosides. Among the reported ginsenosides, ginsenoside Rg_1 not only has a wide range of medicinal functions and abundant content but also is one of the major ginsenoside for the quality evaluation of this herb in the Chinese Pharmacopoeia. The main biosynthesis pathway of ginsenoside Rg_1 in P. ginseng has been clarified, which lays a foundation for the comprehensive and in-depth analysis of the biosynthesis and regulatory mechanism of ginseno-side Rg_1. However, the biosynthesis of ginsenoside Rg_1 is associated with other complex processes involving a variety of regulatory genes and catalyzing enzyme genes, which remain to be studied comprehensively. With the transcriptome data of 344 root samples from 4-year-old P. ginseng plants and their corresponding ginsenoside Rg_1 content obtained in the previous study, this study screened out 217 differentially expressed genes(DEGs) with Rg_1 content changes by DEseq2 analysis in R language. Furthermore, the weighted gene co-expression network analysis(WGCNA) revealed 40 hub genes among the DEGs.Pearsoncorrelation analysis was further perforned to yield 20 candidate genes significantly correlated with ginsenoside Rg_1 content, and these genes were annotated to multiple metabolic processes including primary metabolism and secondary metabolism. Finally, the treatment of P. ginseng adventitious roots with methyl jasmonate indicated that 16 of these genes promoted the biosynthesis of ginsenoside Rg_1 in response to methyl jasmonate induction. Finally, one of the 16 genes was randomly selected to verify the function of the gene by genetic transformation and qRT-PCR and to confirm the rationality of the methodology of this study. The above results lay a foundation for studying the mechanism for regulation on the synthesis of ginsenoside Rg_1 and provide genetic resources for the industrial production of ginsenoside Rg_1.
PMID: 39041119