PHGD: An integrative and user‐friendly database for plant hormone‐related genes

iMeta, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 8, 2024

Plant Hormone Gene Database (PHGD) database platform construction pipeline. First, we collected all reported hormone-related genes in the model plant Arabidopsis thaliana, and combined with existing experimental background, mapped hormone–gene interaction network to provide a blueprint. Next, 469 high-quality genomes. Then, bioinformatics was used identify these plants. Finally, genetic data were programmed be stored website PHGD built. divided into eight modules, namely Home, Browse, Search, Resources, Download, Tools, Help, Contact. We provided resources services facilitate study of hormones. hormones are small amounts organic compounds produced by plants, which can promote or inhibit diverse physiological processes [1-3]. mainly include auxin (AUX), ethylene (ETH), cytokinin (CK), abscisic acid (ABA), gibberellin (GA), brassinosteroids (BRs), jasmonic (JA), strigolactones (SLs), salicylic (SA), melatonin (MT), polypeptide (PEP) [4-6]. Each kind hormone plays its role environmental response, defense growth, development [7]. For example, CKs have been implicated cell division, root bud development, senescence, chloroplast [8]. Polypeptide play important roles adaptation environment, including precursor peptide (PROPEP) [9, 10], phytosulfokine-α (PSK) [11, 12], Ralf-like (RALF) [13], epidermal patterning factor/epidermal factor-like (EPF/EPFL) [14], clavata3/ESR-related (CLE) [15], growth factor (RGF) [16]. MT an different aspects such as salt drought stresses [17, 18]. Moreover, they interact each other form huge regulate various biological [19, 20]. instance, has crosstalk SA, JA, AUX, ABA, further contributed disease resistance [21]. involved variety pathway mechanisms, biosynthesis, metabolism, perception, signal transduction, transport pathways [22, 23]. Therefore, it is very difficult comprehensively analyze complex action mechanism Much work done contribute exploring some four main signaling reported, that is, inhibitor response 1/auxin F-boxes (TIR1/AFBs)-auxin/indole-3-acetic (AUX/IAA)-auxin factors (ARFs) [24], transmembrane kinase 1 (TMK1)-IAA32/34-ARFs [25], TMK1/auxin-binding protein1 (TMK1/ABP1)-rho-related protein from plants 2/6 (ROP2/6)-pin-formeds (PINs) [26], S-phase kinase-associated 2a (SKP2A)-Arabidopsis thaliana homolog e2f c/ATDPB (E2FC/DPB) [27]. Nevertheless, last proposed for many years, but highly controversial requires more evidence In addition, enzymes biosynthesis tryptophan decarboxylase (TDC), tryptamine 5-hydroxylase (T5H), serotonin N-acetyltransferase (SNAT), acetyl methyl transferase (ASMT) [28, 29]. However, transduction still not clear. also needs explored. The mechanisms lots human verification, so large time-consuming work. Another effective approach through big resource integration analysis. At present, only few related databases released about Among them, GSHR (Gene Set-Level Analyses Responses Arabidopsis, http://bioinfo.cemps.ac.cn/GSHR/) information [30]. one (https://plant-hormones.info/) currently unavailable. As far know, date, there no showing distribution 11 large-scale kingdoms, involving pathways. comprehensive described hormones, using methods search Based on deletion lower origin data-sharing established help researchers genes. All A. manually screened literature TAIR (https://www.arabidopsis.org/index.jsp). Initially, performed PubMed, Web Science, Google Scholar keywords "AUX," "ABA," "plant hormone," "phytohormone," "Arabidopsis," "phytohormone pathway." retrieved publications then preliminarily checked eliminate false-positive papers. phytohormone information, Kyoto Encyclopedia Genes Genomes consulted addition literature. sorted out 914 973 publications, crucial (Supporting Information S1: Tables S1 S2). After serial genome collection filtering, species gene annotation this study, 314 dicots, 85 monocots, six magnoliids, three basal angiosperms, gymnosperms, ferns, bryophytes, 39 algae (one glaucophyte, prasinodermophyte new 2020 [31], red algae, 22 green seven charophytes) S3 S4). same time, flowering (408) nonflowering (61) species. gff files, coding sequences (CDSs), examined downloaded according (https://www.plabipd.de/plant_genomes_pn.ep), identifying constructed 11-type components (Figure 1A). Furthermore, multiple effects, defense, stress, heat stomatal closure, branching, vascular included. A total 104 nodes found network. these, 49 lines connected infinitely interactions. regulatory enabled us understand systematically. Combined references, selected thaliana. lonely guy (LOG) isopentenyltransferase (IPT) key rate-limiting synthesis pathway, PURINE PERMEASE (PUP), equilibrative nucleoside transporter (ENT), ATP-binding cassette g14 (ABCG14) proteins pathway. summarized synthetic melatonin, member added recent PMTR1 receptor. PROPEP, PSK, RALF, EPF/EPFL, overexplored. domain Pfam blast (version 34.0) [32] Blast 2.10.1). members family previous reports [32-34], blastp obtain similarity relation component (E value < 1e−5). results, set filter standards higher respectively. reason setting filtering criteria relationships reference genome. Chinese cabbage theoretically times [35]. due amount loss, number identified should 1.2 2 theory, synthesized preliminary identification results determine optimal threshold [36-38] standard components. report, Chara braunii Physcomitrella patens [39]. their S5–7). obtained numbers taxa studied S8–19). 64 representative taxon display Table S20) determined node based presence counted (408 61 plants) S19). premise avoiding (11 53 counting If present species, define "1," if not, "0" S20). inferred paths statistical result. Here, CK, PEP examples. homologous AUX YUCCA (YUC) distributed proteins) land suggest originated common ancestor receptor TIR1/AFB ABP1 (Chlorella variabilis, Micractinium conductrix, Chlamydomonas reinhardtii), five charophytes (Klebsormidium nitens, C. braunii, Mesotaenium endlicherianum, Penium margaritaceum, Spirogloea muscicola), almost complete perception algae. AUX/IAAs, auxin-upregulated RNA, ARF exist Other critical ROP, Topless, TMK taxa. DPB, E2FC, SKP2A scattered among simultaneously 63 Due high controversy SKP2A/E2FC/DPB explored study. short, our indicate charophytes. AUXIN1 (AUX1)/like AUX1, PIN-formed (PIN)/PIN-likes, ABC families taxa, suggesting glaucophytes. metabolic GRETCHEN HAGEN 3 first followed K. nitens M. well These CK biosynthetic LOG IPT indicates oxidase exists indicating histidine terrestrial histidine-containing phosphotransmitter (AHP) except type-A regulators (ARRs) absent type-B ARRs glaucophytes, prasinodermophytes, charophytes, may originate prasinodermophytes. PUP two (Cyanidiococcus yangmingshanensis Cyanidioschyzon merolae), (Asterochloris glomerata, Chromochloris zofingiensis), ENT ABCG14 taxon. imply PROPEP chlorophytes (A. Coccomyxa subellipsoidea, incerta, eustigma, Edaphochlamys debaryana, Gonium pectorale, (Chlorokybus atmophyticus, P. S. chlorophytes. PSK gymnosperms gymnosperms. RALF EPF/EPFL suggests both TDC had SNAT ASMT synthase homologs (C. zofingiensis, Monoraphidium neglectum), chlorophyte (M. endlicherianum), most did find T5H sequence blast, it. According TDC, SNAT, ASMT, speculated By summarizing above-identified genes, (http://phgd.bio2db.com/) user-friendly web interface referencing [40-42]. includes types 1B). contains synthesis, receptor, signal, integrates functions networks 2A–C). overview interfaces, Contact users easily use 2A). modes "Species" "Pathway" browse 2D). mode, classified locate classification queried view table. "MORE" column table specific name, CDSs, sequences. directly "CDS" "Pro" columns clicking "Bar" "Pie," see ratio download via "Download." bar chart. Users could 2E). displayed pie research. Search contain rich (pfam id, domain, E value, family) (chromosome, start, end, annotation), section, category included 2F). Latin taxonomy, genomic published articles, links details journal, publication year, authors. popular tools, Primer Design, perform analysis 2G). tool conduct CDS alignment. built alignment copying frame uploading Fasta format. developed Design design primers assigned Download demands research 2H). address, email, phone contact any questions 2I). detailed manual video know how 2J). encourage submit enrich database. examples evolutionary AHP belonging cabbage. target page, relevant interest (AHP 3A). file species' page 3B). verification [32], SMART 9, https://smart.embl.de) [43], CDD 3.17, https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) [44], members, consistent report [45]. neighbor-joining method phylogenetic tree MEGA X software [46]. previously [47-49], expansion cabbage, Brassica oleracea, napus carried 3C–E). multiploidy experienced 3F), relationship between B. 1:3:3:6 [49]. showed corresponding lost. six, eight, 16, hybrid sum oleracea equal napus. combination trees, indirect caused hybridization, while direct duplication. To explore trajectory Oryza sativa, Aristolochia fimbriata, Amborella trichopoda, Picea abies, Selaginella moellendorffii, patens, reinhardtii) kingdom platform. Mafft 7.475) [50] FastTree 2.1) construct 3G) [51]. Notung 2.9.1.5) duplication loss [52]. size ancestral [53] 3H). show ancestors reinhardtii contained serious lost zero obtained. Seven moellendorfii lost, obtained, seed angiosperm nine eudicot monocot From exhibits pattern. extensive investigations, integrated studies map components, closely at least providing core interactions overall blueprint regulation development. searches, plants). data, assist people PHGD, effect example. Currently, available GSHR, dedicated service already greatly Compared focuses severely limits whose genomes sequenced far, studying enough terms types. updated since 2018, lacking GSHR. Although makes up above deficiencies, lack functional validation, provides breeders. Researchers in-depth needs. Overall, resources, will future, release innovation research, continue improve update conclusion, Through genomes, continuously newly assembled believe become world. Xiaoming Song conceived project responsible initiation. Song, Shuyan Feng, Zhuo Liu, Xiao Ma supervised managed bioinformatic analyses led Huilong Chen, Ma. Tong Yu, Ma, Fulei Nie. manuscript organized, written, revised Nan Li, Di Guo. Rong Zhou. authors read approved manuscript. This supported National Key Research Development Program China (2023YFF1002000), Natural Science Foundation Distinguished Young Hebei Province (C2022209010), (32172583), (C2021209005, C2021209019), Laboratory Nucleic Research, Tangshan (2022TS003b). declare conflict interest. sets (http://phgd.bio2db.com/). Supplementary materials (figures, tables, scripts, graphical abstract, slides, videos, translated version materials) online DOI iMeta http://www.imeta.science/. sources S2: description S3: classification, source, S4: S5: structural S6: display. S7: S8: ABA pfam identification. S9: S10: BR S11: S12: ETH S13: GA S14: JA S15: SA S16: SL S17: filter. S18: POLYPEPTIDE S19: S20: heatmap Please note: publisher content functionality supporting supplied Any queries (other than missing content) directed author article.

Language: Английский

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Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 12, 2025

Cold stress significantly challenges cotton growth and productivity, yet the genetic molecular mechanisms underlying cold tolerance remain poorly understood. We employed RNA-seq iterative weighted gene co-expression network analysis (WGCNA) to investigate transposable element (TE) expression changes at six time points (0 h, 2 4 6 12 24 h). Thousands of differentially expressed genes (DEGs) were identified, exhibiting time-specific patterns that highlight a phase-dependent transcriptional response. While A D subgenomes contributed comparably DEG numbers, numerous homeologous pairs showed differential expression, indicating regulatory divergence. Iterative WGCNA uncovered 125 modules, with some enriched in specific chromosomes or chromosomal regions, suggesting localized hotspots for Notably, transcription factors, including MYB73, ERF017, MYB30, OBP1, emerged as central regulators within these modules. Analysis 11 plant hormone-related revealed dynamic ethylene (ETH) cytokinins (CK) playing significant roles stress-responsive pathways. Furthermore, we documented over 15,000 TEs, TEs forming five distinct clusters. TE families, such LTR/Copia, demonstrated enrichment clusters, their potential role modulators under stress. These findings provide valuable insights into complex networks response cotton, highlighting key components involved regulation. This study provides targets breeding strategies aimed enhancing cotton.

Language: Английский

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Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants

Molecular Horticulture, Journal Year: 2024, Volume and Issue: 4(1)

Published: April 9, 2024

Abstract The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components the signaling pathway play essential roles in plant growth development. Their large-scale analysis evolutionary trajectory origin currently not known. Here, we identified corresponding ARF Aux/IAA members performed a by scanning 406 genomes. results showed that gene families originated from charophytes. sequences were more conserved than sequences. Dispersed duplications common expansion mode bryophytes, ferns, gymnosperms; however, whole-genome duplication was basal angiosperms, magnoliids, monocots, dicots. Expression regulatory network analyses revealed Arabidopsis thaliana responded to multiple hormone, biotic, abiotic stresses. APETALA2 serum factor-transcription commonly enriched upstream downstream families. Our study provides comprehensive overview trajectories, structural functions, mechanisms, expression patterns, networks these two

Language: Английский

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SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D1623 - D1632

Published: Nov. 11, 2024

The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements sequencing technologies. However, existing databases are limited by incomplete species representation, lack of comprehensive comparative tools the absence systematic pan-genomic analyses. To address these gaps, we developed Information Resource (SoIR, https://soir.bio2db.com), genomics database for family. SoIR integrates from 81 transcriptomic 41 species, encompassing total 3 908 408 gene annotations derived Gene Ontology, nonredundant protein, Pfam, Swiss-Prot TrEMBL databases. resource also 437 115 CRISPR guide sequences, 212 395 transcription factors 19 086 genes associated with methylation modification. In addition species-specific analyses, provides extensive bioinformatics investigating family evolution, phylogenetic relationships karyotype reconstruction across 25 fully sequenced genomes. With advanced Blast, Synteny Sequence Alignment, platform users interactive intuitive visualizations conducting cross-species genomics. As first entire facilitates in-depth analysis, supporting global research initiatives plant functional crop improvement.

Language: Английский

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T2T genome, pan‐genome analysis, and heat stress response genes in Rhododendron species

iMeta, Journal Year: 2025, Volume and Issue: 4(2)

Published: March 5, 2025

This study reports the first high-quality telomere-to-telomere (T2T) Rhododendron liliiflorum genome with 11 chromosomes that are gap free. The 24 telomeres and all 13 centromeres detected in this genome, which reached highest quality gold level. In addition, other three species were sequenced assembled to chromosomal Based on 15 genomes, we conducted a pan-genome analysis of genus Rhododendron. Combining whole transcriptome sequencing, identified several key genes miRNAs related heat stress, further verified by transgenic experiments. Our findings provide rich resources for comparative functional genomics studies species. belongs Ericaceae, is one largest woody plants. There approximately 1000 worldwide, China an important distribution center [1]. They underwent evolutionary radiations Himalaya-Hengduan Mountains, world's biodiversity hotspots [2]. highly prized horticulture due their ornamental value. Global climate change causes rise temperatures, while stress can influence growth development plants [3, 4]. However, typically adapted cooler climates. Multi-omics molecular techniques be used explore response mechanism, great significance breeding heat-tolerant varieties expanding cultivation range. Although genomic have been separately Rhododendrons, genomes large-scale still lacking, limits our understanding genetic diversity gene mining [5-14]. T2T more complete comprehensive information [15]. Therefore, aims resolve genome. Then, analysis, identifying lots structural variations (SVs), provided Here, perform de novo sequencing four (Rhododendron liliiflorum, decorum, platypodum, concinnum) PacBio HiFi, Oxford Nanopore Technology (ONT), Illumina, Hi-C technology (Figure 1A, Tables S1–6). estimated size K-mer was 759.08, 581.05, 593.47, 1356.22 Mb R. concinnum, respectively, flow-cytometry (Table S1, Figure 1B). We found concinnum almost twice as large analyzed chromosome karyotype using flow cytometry, time, discovered tetraploid 2n = 4x 52, distinctly different from diploid (2n 2x 26) 1C, Table S1). 793.25, 649.87, 652.27, 1321.11 anchored ratio over 97.90% among 1D, S5). obtained scaffold N50 48.68 S6). Core Eukaryotic Genes Mapping Approach value 95.63% 99.56%, Benchmarking Universal Single-Copy Orthologs (BUSCO) 96.65% 97.34%, reads mapping rate exceeded 99.40% S7). Most importantly, consists chromosomes, S1A, S8–S11). Eleven gap-free telomere telomere, two only gap. contig 58.56 Mb, larger than most previous [1, 6, 7, 12]. completeness assessed BUSCO (96.65%), consistency (QV) 43.71 Genome LTR assembly index (LAI) 21.15 S1B), indicating it has level (LAI ≥ 20) [16]. Repetitive sequences accounted 49.10% repetitive long-terminal repeats (LTRs) 1E, S11). A total 41,406, 41,084, 40,556, 83,203 predicted S12). Over 97.15% detected, high prediction S13). 92.16% annotated NR, eggNOG, GO, KEGG, TrEMBL, KOG, Swissprot, Pfam databases S14). 2355, 4862, 2852, 9511 noncoding RNAs S15). Rhododendron, renowned its diverse floral displays, drawn significant scientific attention, being decoded recent years since delavayi released [13]. Several reported, such griersonianum [11], Henanense [9], Irroratum [6], kiyosumense [10], Ripense Vialii [8], nivale [5], williamsianum [12]. These laying groundwork [17-20]. these along previously published 1F, S16). T2T-level selected reference. super-pangenome expanded adding 394.57 14,424 genes. number families across 45,731, including 5734 core families, 37,027 dispensable 2970 private (Figures 1G S2A, S17). An UpSet plot show relationships family sharing uniqueness Finally, constructed map presence absence based clustering 1H). Among there species-specific irroratum (1705) S17, S2B). enrichment indicated "Sesquiterpenoid triterpenoid biosynthesis" "Linoleic acid metabolism" pathways significantly enriched S3). 121,185 identified, ovatum had (9847) Functional flower color fragrance enriched, limonene pinene degradation S4). identification single nucleotide polymorphisms (SNPs), insertions deletions (InDels), SVs reference 1I–L SNPs (1,876,446) InDels (447,281) 1I, S18–19). showed contained "Carbon "Biosynthesis amino acids" pathways. SVs, reaching 7694 S20). Meanwhile, subdivided into duplication (DUP), translocation (TRANS), inversion (INV), former's quantity latter S6–S7). distinct pattern compared those or InDels, focusing RNA polymerase mRNA surveillance pathway. 70,759 LTRs species, (7323) S21). experienced outbreak insertion event during last 1 million (Mya), delavayi, molle, outbreaks. Two events occurred at 1.53 2.94 Mya, earlier performed obtain shared within each cluster. results 2622 could clustered, platypodum having (531). specific (109), no williamsianum. diagram proportion 1M). Furthermore, density middle greater ends 1N). Through collinearity generally exhibit good 1O). blocks 336 (R. henanense vs. delavayi) 692 prattii). Additionally, some transpositions terminal regions 7 simsii henanense. To heat-resistant regulatory mechanisms under treatment CK, 3 days (H3) 6 (H6) 2A, S22). 50,648 mRNAs, 17,476 lncRNAs, 448 miRNAs, 6299 circRNAs 2B). 632 21 differently expressed H3, H6 treatments 2C). representative pairs target verification treatment. Expression upregulated h after treatment, expression small downregulated. investigate effects miR177 RdbHLH153 (Rhdel02G0118700) miR49 RdMYB1R1 (Rhdel08G0208700) expression, respectively. Firefly luciferase fused C-terminal RdMYB1R1, inserted SK vectors 2D). Results sites slightly altered 2E). infiltrated areas Nicotiana benthamiana leaves mixtures RdbHLH153/RdMYB1R1 empty vector (mixed together), (RdMYB1R1 miR49). All induction signals, whereas overexpressed abolish signals produced 2E–G). roles Arabidopsis lines overexpressing generated floral-dip method S23). After 36 better WT 2H). seedlings returned normal conditions 5 days, turn alive, became yellowish. result play enhancing tolerance. DAB NBT staining revealed contents H2O2 O−2 RdbHLH153/RdMYB1R1-OE decreased comparing 2I). nine researchers underlying formation Kiyosumense database none them level, especially deciphered Compared released, higher behind various morphotypes. conclusion, report completed, tetraploid. Pan-genome structure heat-stress-related estimation, Data control data processing assisted Telomere-to-Telomere Genomic sequence annotation Gene prediction, evaluation, Noncoding extraction Graph-based construction noncore Variant Long-terminal (LTR) time visualization Plant materials Library Analysis mRNAs Dual-luciferase transient system Generation plant Detection reactive oxygen (ROS). Xiaojing Wang: Conceptualization; curation; investigation; funding acquisition; supervision; writing—original draft; project administration; writing—review editing; resources; validation; visualization; formal analysis. Ping Zhou: Validation; analysis; editing. Xiaoyu Hu: Yun Bai: draft. Chenhao Zhang: methodology. Yanhong Fu: Formal Ruirui Huang: Writing—review curation. Niu Suzhen: Investigation; Xiaoming Song: methodology; software. work supported National Natural Science Foundation Project (32260097, 32172583), Key Research Development Program (2023YFF1002000), Tangshan Plan (24130219C), Distinguished Young Scholar Hebei Province (C2022209010). BioMarker Corporation. apologize not able cite additional owing space limitations. authors declare conflict interest. No animals humans involved study. deposited NCBI submission SUB15033098, BioProject accession PRJNA1215314 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1215314). scripts saved GitHub (https://github.com/songxm-ncst/Rhododendron). datasets also curated download interface TEGR (http://www.tegr.com.cn) latin name. Supplementary (methods, figures, tables, graphical abstract, slides, videos, Chinese translated version update materials) may online DOI iMeta http://www.imeta.science/. S1: assessment liliiflorum. S2: S3: KEGG S4: cluster genomes. S5: shows homology rearrangement between S6: length (SVs) types, (TRANS) S7: (INV) type Statistics annotation. illumina Hiseq platform survey Pacbio HiFi platform. ONT HIC. HIC CEGMA S8: informatioin S9: position S10: centromere S11: statistics repeat classification S12: S13: S14: annotations S15: ncRNA S16: S17: core, dispensable, S18: SNP S19: INDEL S20: SV S21: S22: Whole S23: Transgenic dual assay primers Please note: publisher responsible content functionality any supporting supplied authors. Any queries (other missing content) should directed corresponding author article.

Language: Английский

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plantGIR: a genomic database of plants

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(12)

Published: Dec. 1, 2024

Language: Английский

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Genome-Wide Analysis of the NBS-LRR Gene Family and SSR Molecular Markers Development in Solanaceae

Horticulturae, Journal Year: 2024, Volume and Issue: 10(12), P. 1293 - 1293

Published: Dec. 4, 2024

The Solanaceae family occupies a significant position, and the study of resistance genes within this is extremely valuable. Therefore, our goal to examine disease based on high-quality representative genomes crops, develop corresponding Simple Sequence Repeat (SSR) molecular markers. Among nine species, we identified 819 NBS-LRR genes, which were further divided into 583 CC-NBS-LRR (CNL), 54 RPW8-NBS-LRR (RNL), 182 TIR-NBS-LRR (TNL) genes. Whole genome duplication (WGD) has played very important role in expansion crops. Gene structure analysis showed striking similarity conserved motifs suggests common ancestral origin, followed by evolutionary differentiation amplification. clustering events like rearrangement contribute their scattered chromosomal distribution. Our findings reveal that majority across all examined species predominantly localize termini. indicates impact most recent whole triplication (WGT) Moreover, constructed Protein–Protein Interaction (PPI) networks for identifying 3820 potential PPI pairs. Notably, 97 displayed clear interactive relationships, highlighting processes. A total 22,226 SSRs detected from species. these SSRs, screened 43 NBS-LRR-associated SSRs. lays foundation exploration SSR development genetic mapping related

Language: Английский

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Progress in metabolic engineering of Yarrowia lipolytica for the synthesis of terpenes

BioDesign Research, Journal Year: 2024, Volume and Issue: 6

Published: Jan. 1, 2024

Terpenes are natural secondary metabolites with isoprene as the basic structural unit; they widely found in nature and have potential applications advanced fuels, pharmaceutical ingredients, agricultural chemicals. However, traditional methods inefficient for obtaining terpenes because of complex processes, low yields, environmental unfriendliness. The unconventional oleaginous yeast

Language: Английский

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Transcriptomic Analysis of Wheat Under Multi LED Light Conditions

Plants, Journal Year: 2024, Volume and Issue: 14(1), P. 46 - 46

Published: Dec. 27, 2024

Light is a vital environmental cue that profoundly influences the development of plants. LED lighting offers significant advantages in controlled growth environments over fluorescent lighting. Under monochromatic blue light, wheat plants exhibited reduced stature, accelerated spike development, and shortened flowering period with increased light intensity promoting an earlier heading date. In this study, we conducted comprehensive transcriptome analysis to investigate molecular mechanisms underlying plants’ response varying conditions. We identified 34 types transcription factors (TFs) highlighted dynamic changes key families such as WRKY, AP2/ERF, MYB, bHLH, NAC, which play crucial roles light-induced gene regulation. Additionally, study revealed differential effects red on expression levels genes related hormones cytokinin (CK) salicylic acid (SA) synthesis well pathways flavonoid biosynthesis, circadian rhythms, chlorophyll synthesis, flowering. Particularly, upregulated involved contrasting downregulation observed under light. Furthermore, enhanced anthocyanin synthesis-related genes, CHS, underscoring its role accumulation. These findings provide valuable insights into how quality impacts crop development.

Language: Английский

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The genomic database of fruits: A comprehensive fruit information database for comparative and functional genomic studies

Agriculture Communications, Journal Year: 2024, Volume and Issue: 2(2), P. 100041 - 100041

Published: May 24, 2024

Fruit has an important role in human nutrition and health; therefore, the systematic study of fruit genomic data is essential. The Genomic Database Fruits (TGDF, http://tgdf.bio2db.com/), established through whole-genome analyses 44 species, a comprehensive, user-friendly database. TGDF contains wealth functional genes, including 11,350 flowering 3,161 auxin signaling 2,164 anthocyanin synthesis 1,464 abscisic acid (ABA) 10,931 cell division expansion 1,786 starch 294 size 6,311 sugar transporter genes. Additionally, 1,433,368 CRISPR guide sequences from various genomes, along with information on homologous genes duplication types for species. 6,417,060 gene annotations sourced TrEMBL, SwissProt, Nr, Gene Ontology databases, tools such as Sequence Fetch, BLAST, Synteny, JBrowse bioinformatics analyses. Transcriptomic were also collected collated fruits, details instruments, tissues, or growth stages. This resource first collection data. Users can easily download sequences, annotations, analysis results TGDF, which will be updated continually. We anticipate that become primary comparative studies.

Language: Английский

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