Pub Date : 2026-03-01Epub Date: 2025-11-21DOI: 10.1016/j.plgene.2025.100561
Chenjuan Jing , Duan Wang , Zhikun Liu , Xuefeng Chen , Yang Zhang , Xiaohong Wu
High levels of organic acids in apricot fruit affect the flavor quality and market scale. Aluminum-activated malate transporters (ALMTs) are key proteins regulating organic acid accumulation in fruits, but their structure and functions in apricot remain understudied. Here, we identified 11 orthologous genes of the ALMT family in the genome of apricot (Prunus armeniaca L.), designated ParALMT1–11. These genes were classified into subfamilies I-V and unevenly distributed across linkage groups LG1/2/6/7/8. Each ParALMT protein contained 5–7 transmembrane domains. Some genes showed tissue-specific expression in apricot roots, stems, leaves, and seeds. The expression dynamics of ParALMT10 and ParALMT11 in apricot fruit were closely associated with organic acid metabolism. ParALMT10 may be a key gene regulating the accumulation of organic acids, particularly malic acid in apricot fruit. This study paves the way for elucidating the metabolic mechanisms of organic acids and improving fruit quality in apricot.
{"title":"Identification of ParALMT genes and their relationship with organic acid accumulation in apricot fruit","authors":"Chenjuan Jing , Duan Wang , Zhikun Liu , Xuefeng Chen , Yang Zhang , Xiaohong Wu","doi":"10.1016/j.plgene.2025.100561","DOIUrl":"10.1016/j.plgene.2025.100561","url":null,"abstract":"<div><div>High levels of organic acids in apricot fruit affect the flavor quality and market scale. Aluminum-activated malate transporters (ALMTs) are key proteins regulating organic acid accumulation in fruits, but their structure and functions in apricot remain understudied. Here, we identified 11 orthologous genes of the ALMT family in the genome of apricot (<em>Prunus armeniaca</em> L.), designated <em>ParALMT1–11</em>. These genes were classified into subfamilies I-V and unevenly distributed across linkage groups LG1/2/6/7/8. Each ParALMT protein contained 5–7 transmembrane domains. Some genes showed tissue-specific expression in apricot roots, stems, leaves, and seeds. The expression dynamics of <em>ParALMT10</em> and <em>ParALMT11</em> in apricot fruit were closely associated with organic acid metabolism. <em>ParALMT10</em> may be a key gene regulating the accumulation of organic acids, particularly malic acid in apricot fruit. This study paves the way for elucidating the metabolic mechanisms of organic acids and improving fruit quality in apricot.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100561"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145624431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-11-17DOI: 10.1016/j.plgene.2025.100560
Ophilia Ibapalei Lyngdoh Mawphlang , M. Bharatheeswaran , Lingaraj Sahoo , Highland Kayang , Eros Kharshiing
The PAS/LOV Protein 1, commonly referred to as PLP1 (also known as LOV/LOV Protein or LLP) is recognized as a novel blue-light photoreceptor in plants, and its homologs have been identified in various species. Nevertheless, the functional role of LLP in plant biology is still unclear. In this report, we have cloned a homolog of LLP from the small-fruited tomato (Solanum lycopersicum var. cerasiforme) and analysed its expression levels under different light, water-deficit and humidity conditions. Determination of relative expression by RT-qPCR show high-intensity blue-light is most effective in inducing LLP expression in the young seedlings as well as in leaves of older plants, indicating that its expression is governed by both light intensity and spectral composition. LLP expression is also enhanced under drought-like conditions but not under conditions of high humidity. This report will further aid our understanding of LLP expression in responses to light and water-deficit conditions in tomato.
PAS/LOV蛋白1，通常称为PLP1（也称为LOV/LOV蛋白或LLP）是公认的植物中一种新型蓝光光感受器，其同源物已在多种植物中被鉴定。然而，LLP在植物生物学中的功能作用尚不清楚。在这篇报道中，我们从小果番茄（Solanum lycopersicum var. cerasiformme）中克隆了一个LLP同源物，并分析了其在不同光照、水分亏缺和湿度条件下的表达水平。RT-qPCR相对表达量测定结果显示，高强度蓝光诱导LLP在幼苗和老植株叶片中表达最有效，表明其表达受光强和光谱组成共同控制。LLP的表达在干旱条件下也有增强，而在高湿条件下则没有。该报告将进一步帮助我们了解番茄在光照和缺水条件下LLP的表达。
{"title":"Cloning and expression analyses of the twin LOV protein (LLP) gene under varying light, water-deficit and humidity conditions in the small-fruited tomato (Solanum lycopersicum var. cerasiforme)","authors":"Ophilia Ibapalei Lyngdoh Mawphlang , M. Bharatheeswaran , Lingaraj Sahoo , Highland Kayang , Eros Kharshiing","doi":"10.1016/j.plgene.2025.100560","DOIUrl":"10.1016/j.plgene.2025.100560","url":null,"abstract":"<div><div>The <em>PAS/LOV Protein 1</em>, commonly referred to as <em>PLP1</em> (also known as <em>LOV/LOV Protein</em> or <em>LLP</em>) is recognized as a novel blue-light photoreceptor in plants, and its homologs have been identified in various species. Nevertheless, the functional role of <em>LLP</em> in plant biology is still unclear. In this report, we have cloned a homolog of <em>LLP</em> from the small-fruited tomato (<em>Solanum lycopersicum</em> var. <em>cerasiforme</em>) and analysed its expression levels under different light, water-deficit and humidity conditions. Determination of relative expression by RT-qPCR show high-intensity blue-light is most effective in inducing <em>LLP</em> expression in the young seedlings as well as in leaves of older plants, indicating that its expression is governed by both light intensity and spectral composition. <em>LLP</em> expression is also enhanced under drought-like conditions but not under conditions of high humidity. This report will further aid our understanding of <em>LLP</em> expression in responses to light and water-deficit conditions in tomato.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100560"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145537240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2026-01-16DOI: 10.1016/j.plgene.2026.100576
Hanaa H. El-Shazly , Abdelfattah Badr , Heba Ebeed
Epitranscriptomics has gained attention due to the recent findings and potential utilization in crop breeding. Epitranscriptomics refers to modifications at the RNA level, which may be considered reversible chemical or enzymatic changes to the transcriptome without introducing changes into the RNA sequence but are functionally significant. These RNA modifications are known to have a far-reaching influence on plant development and adaptation to changing environment. This review summarizes the current epitranscriptomic landscape in plants, highlighting major RNA modifications and their regulatory enzymes, and discusses recent advances in understanding their roles in key physiological and developmental processes. Particular emphasis is placed on epitranscriptomic regulation of plant responses to abiotic and biotic stresses and its contribution to stress memory and phenotypic plasticity under climate change scenarios. Furthermore, we explore the translational potential of epitranscriptomics in sustainable crop improvement, including its integration with genome editing and molecular breeding strategies. Collectively, this review provides an updated and critical perspective on how epitranscriptomic mechanisms can be harnessed to enhance crop resilience and productivity.
{"title":"The emerging role of the plant epitranscriptome in regulating development and stress responses","authors":"Hanaa H. El-Shazly , Abdelfattah Badr , Heba Ebeed","doi":"10.1016/j.plgene.2026.100576","DOIUrl":"10.1016/j.plgene.2026.100576","url":null,"abstract":"<div><div>Epitranscriptomics has gained attention due to the recent findings and potential utilization in crop breeding. Epitranscriptomics refers to modifications at the RNA level, which may be considered reversible chemical or enzymatic changes to the transcriptome without introducing changes into the RNA sequence but are functionally significant. These RNA modifications are known to have a far-reaching influence on plant development and adaptation to changing environment. This review summarizes the current epitranscriptomic landscape in plants, highlighting major RNA modifications and their regulatory enzymes, and discusses recent advances in understanding their roles in key physiological and developmental processes. Particular emphasis is placed on epitranscriptomic regulation of plant responses to abiotic and biotic stresses and its contribution to stress memory and phenotypic plasticity under climate change scenarios. Furthermore, we explore the translational potential of epitranscriptomics in sustainable crop improvement, including its integration with genome editing and molecular breeding strategies. Collectively, this review provides an updated and critical perspective on how epitranscriptomic mechanisms can be harnessed to enhance crop resilience and productivity.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100576"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2026-01-08DOI: 10.1016/j.plgene.2026.100572
Tao Zhou, Muhetaer Zhare, Gulimire Kakeshe, Ayimire Maolamu, Hadier Yishake, Yue Pan
Many plants display striking juvenile reddening phenomenon due to the accumulation of anthocyanins in juvenile shoots (young leaves) but not in adult tissues. Anthocyanins are beneficial for fragile shoots to defend against biotic and abiotic stresses, and have ornamental and edible value. Although the biosynthesis pathways and regulatory factors of plant anthocyanins have been well identified in the past few decades, the reasons and molecular regulatory mechanisms for the tissue-specific enrichment of anthocyanins in young leaves have not been elucidated.
In this review, we searched for clues related to anthocyanin enrichment in young tissues and emphasized the key role of major growth related regulatory factors in anthocyanin biosynthesis in plant seedlings.
{"title":"Why juvenile reddening occurs in many plants","authors":"Tao Zhou, Muhetaer Zhare, Gulimire Kakeshe, Ayimire Maolamu, Hadier Yishake, Yue Pan","doi":"10.1016/j.plgene.2026.100572","DOIUrl":"10.1016/j.plgene.2026.100572","url":null,"abstract":"<div><div>Many plants display striking juvenile reddening phenomenon due to the accumulation of anthocyanins in juvenile shoots (young leaves) but not in adult tissues. Anthocyanins are beneficial for fragile shoots to defend against biotic and abiotic stresses, and have ornamental and edible value. Although the biosynthesis pathways and regulatory factors of plant anthocyanins have been well identified in the past few decades, the reasons and molecular regulatory mechanisms for the tissue-specific enrichment of anthocyanins in young leaves have not been elucidated.</div><div>In this review, we searched for clues related to anthocyanin enrichment in young tissues and emphasized the key role of major growth related regulatory factors in anthocyanin biosynthesis in plant seedlings.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100572"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2026-01-07DOI: 10.1016/j.plgene.2026.100569
Shijie Zhang, Zhiguo Zhang, Qiaoping Qin
Climate change heightens the risk of seawater submergence in coastal areas. Hemerocallis fulva L., known as daylily, is an important horticultural and medicinal plant with a high abiotic stress tolerance capacity and potential for coastal stabilization. However, the molecular regulatory responses of daylily to seawater submergence are still largely unexplored. In this study, daylily cultivar ‘Autumn Red’ plants were subjected to seawater logging stress (SLS), and time-series root transcriptional changes were explored using PacBio Iso-seq techniques. Compared with the control (0 h), we detected 3168, 4924, and 5525 differentially expressed genes (DEGs) in daylily roots at 6 h, 24 h, and 72 h post-SLS, respectively. Oxidation−reduction process, Glutathione hydrolase activity, Glutathione catabolic process, Taurine and hypotaurine metabolism, Phenylpropanoid biosynthesis, and Arachidonic acid metabolism were the main induced metabolic processes in daylily following SLS. Some key continuously up-regulated genes related to antioxidant system, ion regulation, hormone transduction, photosynthesis, and secondary metabolite synthesis that may play important roles in daylily tolerance to SLS were identified. In addition, 119 transcription factor family genes, including AP2/ERF, bHLH, C2H2, AUX/IAA, bZIP, and MYB, which may regulate SLS-responsive mechanisms in daylily, were screened. An in-depth study on the dynamic changes of bZIPs under seawater treatment revealed that conserved structural features alongside species-specific and functional divergence in salt stress responses. Class III bZIPs demonstrated sustained upregulation for salt tolerance, while others exhibited variable expression despite having similar structures. These findings enhance our understanding of daylily's tolerance to SLS and could facilitate its cultivation in coastal and saline regions.
{"title":"Molecular adaptation analysis of Hemerocallis fulva roots to seawater-logging stress in a simulated natural environment","authors":"Shijie Zhang, Zhiguo Zhang, Qiaoping Qin","doi":"10.1016/j.plgene.2026.100569","DOIUrl":"10.1016/j.plgene.2026.100569","url":null,"abstract":"<div><div>Climate change heightens the risk of seawater submergence in coastal areas. <em>Hemerocallis fulva</em> L<em>.</em>, known as daylily, is an important horticultural and medicinal plant with a high abiotic stress tolerance capacity and potential for coastal stabilization. However, the molecular regulatory responses of daylily to seawater submergence are still largely unexplored. In this study, daylily cultivar ‘Autumn Red’ plants were subjected to seawater logging stress (SLS), and time-series root transcriptional changes were explored using PacBio Iso-seq techniques. Compared with the control (0 h), we detected 3168, 4924, and 5525 differentially expressed genes (DEGs) in daylily roots at 6 h, 24 h, and 72 h post-SLS, respectively. Oxidation−reduction process, Glutathione hydrolase activity, Glutathione catabolic process, Taurine and hypotaurine metabolism, Phenylpropanoid biosynthesis, and Arachidonic acid metabolism were the main induced metabolic processes in daylily following SLS. Some key continuously up-regulated genes related to antioxidant system, ion regulation, hormone transduction, photosynthesis, and secondary metabolite synthesis that may play important roles in daylily tolerance to SLS were identified. In addition, 119 transcription factor family genes, including AP2/ERF, bHLH, C2H2, AUX/IAA, bZIP, and MYB, which may regulate SLS-responsive mechanisms in daylily, were screened. An in-depth study on the dynamic changes of bZIPs under seawater treatment revealed that conserved structural features alongside species-specific and functional divergence in salt stress responses. Class III bZIPs demonstrated sustained upregulation for salt tolerance, while others exhibited variable expression despite having similar structures. These findings enhance our understanding of daylily's tolerance to SLS and could facilitate its cultivation in coastal and saline regions.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100569"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145938819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-20DOI: 10.1016/j.plgene.2025.100567
Alistar Moy, Kabwe Nkongolo
Plants use DNA methylation to quickly adjust gene activity in response to environmental stressors helping them adapt and survive. Conifers have large genomes and unique metal responses, making conifer DNA methylation research highly compelling. This study evaluated how excess nickel exposure affects methylation patterns and identified differentially methylated regions (DMRs) in Pinus banksiana. Reduced representation bisulfite sequencing (RRBS) was used to assess global methylation changes in nickel-treated seedlings. Nickel sulfate minimally affected overall global methylation; however, it induced significant levels of methylation within specific, localized regions of the genome. The increase in global CG methylation was largely due to hypermethylated DMRs that had methylation levels exceeding 80 %. The observed global hypermethylation was localized predominantly to constitutively hypermethylated regions. A total of 1173 DMRs were found to be hypermethylated, while 239 were hypomethylated. Notably, 97 % of these DMRs were intergenic and displayed high levels of CG methylation, leading to the suggestion that they may be located within transposable elements (TEs). All gene-annotated Differentially Methylated Regions (DMRs) spanned two distinct areas of the gene body, potentially suggesting a strong bias toward gene upregulation. DMR-covered genes, associated with stress mitigation, encode proteins including DEAD-box ATP-dependent RNA helicase, calcium/calmodulin-dependent protein kinase, and UDP-glycosyltransferase. Methylation analyses reveal epigenetic changes that can help discover how P. banksiana resist nickel and adapt long-term to contamination. For this study, RRBS was a suitable compromise because it allowed for precise analysis of specific, relevant regions.
{"title":"DNA methylation analysis of Jack pine (Pinus banksiana) under nickel stress reveals a highly targeted epigenetic response","authors":"Alistar Moy, Kabwe Nkongolo","doi":"10.1016/j.plgene.2025.100567","DOIUrl":"10.1016/j.plgene.2025.100567","url":null,"abstract":"<div><div>Plants use DNA methylation to quickly adjust gene activity in response to environmental stressors helping them adapt and survive. Conifers have large genomes and unique metal responses, making conifer DNA methylation research highly compelling. This study evaluated how excess nickel exposure affects methylation patterns and identified differentially methylated regions (DMRs) in <em>Pinus banksiana</em>. Reduced representation bisulfite sequencing (RRBS) was used to assess global methylation changes in nickel-treated seedlings. Nickel sulfate minimally affected overall global methylation; however, it induced significant levels of methylation within specific, localized regions of the genome. The increase in global CG methylation was largely due to hypermethylated DMRs that had methylation levels exceeding 80 %. The observed global hypermethylation was localized predominantly to constitutively hypermethylated regions. A total of 1173 DMRs were found to be hypermethylated, while 239 were hypomethylated. Notably, 97 % of these DMRs were intergenic and displayed high levels of CG methylation, leading to the suggestion that they may be located within transposable elements (TEs). All gene-annotated Differentially Methylated Regions (DMRs) spanned two distinct areas of the gene body, potentially suggesting a strong bias toward gene upregulation. DMR-covered genes, associated with stress mitigation, encode proteins including DEAD-box ATP-dependent RNA helicase, calcium/calmodulin-dependent protein kinase, and UDP-glycosyltransferase. Methylation analyses reveal epigenetic changes that can help discover how <em>P. banksiana</em> resist nickel and adapt long-term to contamination. For this study, RRBS was a suitable compromise because it allowed for precise analysis of specific, relevant regions.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100567"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145839485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-11-27DOI: 10.1016/j.plgene.2025.100563
Neelesh Patra , Susamoy Sarkar , Mrinal K. Maiti
The fatty acid elongase1 (FAE1) genes of allotetraploid Brassica juncea are the key determinants of high erucic acid (EA, C22:1) accumulation in its seed oil. Although our previous work demonstrated near-zero EA content in Indian mustard oil through CRISPR/Cas9 knockout of the two homeoalleles, BjFAE1.1 and BjFAE1.2; the specific contribution of each isozyme towards EA biosynthesis remains elusive. This study investigates the heterologous expression of BjFAE1.1 and BjFAE1.2 from high-EA B. juncea cultivar JD6 in two metabolically distinct eukaryotic microbial hosts: the green microalga Chlamydomonas reinhardtii and the budding yeast Saccharomyces cerevisiae. Despite confirmed mRNA/protein expression, neither BjFAE1 isozyme produced detectable C20:1 or C22:1 very-long-chain fatty acids (VLCFAs) in transgenic lines of C. reinhardtii. In contrast, expression in S. cerevisiae resulted in significant de novo biosynthesis of VLCFAs, C20:1 (∼9–11 %) and C22:1 (∼17–19 %), confirming their enzymatic activity as functional β-ketoacyl-CoA synthase. Furthermore, substrate feeding experiments in yeast further validated their capability to elongate oleoyl-CoA (C18:1-CoA) to erucoyl-CoA (C22:1-CoA) via eicosenoyl-CoA (C20:1-CoA) intermediate, with BjFAE1.1 showing slightly higher activity, as indicated by the enhanced VLCFA accumulation. These findings substantiate the critical influence of the heterologous host's cellular environment on the functionality of plant lipid metabolism enzymes and underscore the challenges for VLCFA production in microalgal platform.
{"title":"Heterologous expression of fatty acid elongase1 homeoalleles of Brassica juncea reveals robust erucic acid biosynthesis in Saccharomyces and highlights metabolic constraints in Chlamydomonas","authors":"Neelesh Patra , Susamoy Sarkar , Mrinal K. Maiti","doi":"10.1016/j.plgene.2025.100563","DOIUrl":"10.1016/j.plgene.2025.100563","url":null,"abstract":"<div><div>The <em>fatty acid elongase1</em> (<em>FAE1</em>) genes of allotetraploid <em>Brassica juncea</em> are the key determinants of high erucic acid (EA, C22:1) accumulation in its seed oil. Although our previous work demonstrated near-zero EA content in Indian mustard oil through CRISPR/Cas9 knockout of the two homeoalleles, <em>BjFAE1.1</em> and <em>BjFAE1.2</em>; the specific contribution of each isozyme towards EA biosynthesis remains elusive. This study investigates the heterologous expression of <em>BjFAE1.1</em> and <em>BjFAE1.2</em> from high-EA <em>B. juncea</em> cultivar JD6 in two metabolically distinct eukaryotic microbial hosts: the green microalga <em>Chlamydomonas reinhardtii</em> and the budding yeast <em>Saccharomyces cerevisiae</em>. Despite confirmed mRNA/protein expression, neither BjFAE1 isozyme produced detectable C20:1 or C22:1 very-long-chain fatty acids (VLCFAs) in transgenic lines of <em>C. reinhardtii</em>. In contrast, expression in <em>S. cerevisiae</em> resulted in significant <em>de novo</em> biosynthesis of VLCFAs, C20:1 (∼9–11 %) and C22:1 (∼17–19 %), confirming their enzymatic activity as functional β-ketoacyl-CoA synthase. Furthermore, substrate feeding experiments in yeast further validated their capability to elongate oleoyl-CoA (C18:1-CoA) to erucoyl-CoA (C22:1-CoA) via eicosenoyl-CoA (C20:1-CoA) intermediate, with BjFAE1.1 showing slightly higher activity, as indicated by the enhanced VLCFA accumulation. These findings substantiate the critical influence of the heterologous host's cellular environment on the functionality of plant lipid metabolism enzymes and underscore the challenges for VLCFA production in microalgal platform.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100563"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145691273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-12-13DOI: 10.1016/j.plgene.2025.100566
Qing Du , Ziyi Rong , Yanjuan Guan , Chang Zhang , Liqiang Wang , Xiangyang Zhou , Chuanbei Jiang , Haidong Gao , Bin Wang , Haimei Chen , Chang Liu
To compare the distinction and evolutionary relationship of the four studied Leonurus species in the Lamiaceae family, we identified them from physical characteristics, compared their intrinsic sequences, and phylogenetic relationships through the chloroplast genomes and Internal Transcribed Spacer 2 (ITS2) in the nuclear genomes. Among them, the chloroplast genome of L. pseudomacranthus was newly sequenced and analyzed. The results revealed that they are standard circular structure with the four regions and the total length ranged from 151,236 bp to 151,689 bp, including the identical number of 37 tRNAs and 8 rRNAs. The unique trans-spliced rps12 genes can be caught sight of L. sibiricus andL. pseudomacranthus. The isoleucine (AUU) and cysteine (UGC) were the most and least abundant amino acid with the codons ending with the most bases of A/U. Among the ycf1, ycf2, and matK genes, there are significantly more editing sites. The nine hotspot divergent regions and five specific Coding sequence (CDS) genes were systematically counted with the highest nucleotide diversity. The two chosen IGS regions (M1: rps15-ycf1 and M2: atpH-atpI) were cloned, thus finding that twenty-two specific variable SNP sites and three variable Indel sites for distinguishing between the four species. In the aftermath of evolutional analysis together with the nine characters, the four Leonurus species were significantly clustered into one significant clade. In contrast, they were located at different sub-branchs and differentiated, especially the species of L. cardiaca gathered separately into one group due to the specific morphology based on the sequences of 75 shared nucleotide and 19 ITS2 DNA. Thus above results can directly offer the phenotypic feature, molecular polymorphism of nucleotide, and evolutionary development to distinguish the four Leonurus species.
{"title":"Morphological characteristics, molecular identification, and phylogenetic analysis of the four Leonurus species used for the treatment of gynecological diseases","authors":"Qing Du , Ziyi Rong , Yanjuan Guan , Chang Zhang , Liqiang Wang , Xiangyang Zhou , Chuanbei Jiang , Haidong Gao , Bin Wang , Haimei Chen , Chang Liu","doi":"10.1016/j.plgene.2025.100566","DOIUrl":"10.1016/j.plgene.2025.100566","url":null,"abstract":"<div><div>To compare the distinction and evolutionary relationship of the four studied <em>Leonurus</em> species in the Lamiaceae family, we identified them from physical characteristics, compared their intrinsic sequences, and phylogenetic relationships through the chloroplast genomes and Internal Transcribed Spacer 2 (ITS2) in the nuclear genomes. Among them, the chloroplast genome of <em>L</em>. <em>pseudomacranthus</em> was newly sequenced and analyzed. The results revealed that they are standard circular structure with the four regions and the total length ranged from 151,236 bp to 151,689 bp, including the identical number of 37 tRNAs and 8 rRNAs. The unique trans-spliced <em>rps</em>12 genes can be caught sight of <em>L. sibiricus and</em> <em>L</em>. <em>pseudomacranthus</em>. The isoleucine (AUU) and cysteine (UGC) were the most and least abundant amino acid with the codons ending with the most bases of A/U. Among the <em>ycf</em>1, <em>ycf</em>2, and <em>mat</em>K genes, there are significantly more editing sites. The nine hotspot divergent regions and five specific Coding sequence (CDS) genes were systematically counted with the highest nucleotide diversity. The two chosen IGS regions (M1: <em>rps</em>15-<em>ycf</em>1 and M2: <em>atp</em>H-<em>atp</em>I) were cloned, thus finding that twenty-two specific variable SNP sites and three variable Indel sites for distinguishing between the four species. In the aftermath of evolutional analysis together with the nine characters, the four <em>Leonurus</em> species were significantly clustered into one significant clade. In contrast, they were located at different sub-branchs and differentiated, especially the species of <em>L</em>. <em>cardiaca</em> gathered separately into one group due to the specific morphology based on the sequences of 75 shared nucleotide and 19 ITS2 DNA. Thus above results can directly offer the phenotypic feature, molecular polymorphism of nucleotide, and evolutionary development to distinguish the four <em>Leonurus</em> species.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100566"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145883742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-11-23DOI: 10.1016/j.plgene.2025.100562
Xiao-Fang Hou , Di Sang , Wen-Qian Song , Yu-Fan Chen , Shu-Fan Liu , Min Huang , Hao Cheng , Xuan Huang , Zi-Qin Xu
Plants defend against multiple pathogens by activating different signaling pathways. However, the molecular mechanisms underlying the antagonistic responses, where enhanced resistance to one pathogen is often accompanied by increased susceptibility to another, remain poorly understood. This study explores the functional role of the NtabSPL6–4 gene in Arabidopsis thaliana, with a focus on its involvement in regulating plant growth, development, and immune responses. The results show that the NtabSPL6–4 protein is mainly localized in the nucleus. Compared with the wild-type plants, NtabSPL6–4-overexpressing Arabidopsis plants exhibited delayed flowering, increased leaf number, and larger leaf area. Transcriptome analysis under Botrytis cinerea infection showed that differentially expressed genes were mainly enriched in the jasmonic acid (JA) and salicylic acid (SA) signaling pathways. Functional experiments revealed that NtabSPL6–4 enhances plant sensitivity to Pseudomonas syringae by down-regulating the expression of PR1 and PR5, while activating JA pathway-related genes to increase resistance to fungal pathogens. Chromatin immunoprecipitation (ChIP) assays further demonstrated that NtabSPL6–4 binds to the promoter region of ACX1, regulating JA levels. This modulation reduces the accumulation of reactive oxygen species (ROS) and hydrogen peroxide, limits cell damage, and decreases the severity of leaf lesions, thereby contributing to enhanced resistance against fungal infection. These results suggest that NtabSPL6–4 has a dual regulatory role in plant immunity, enhancing resistance to fungal pathogens while increasing susceptibility to bacterial pathogens.
{"title":"Functional analysis of tobacco NtabSPL6–4 in fungal pathogen resistance","authors":"Xiao-Fang Hou , Di Sang , Wen-Qian Song , Yu-Fan Chen , Shu-Fan Liu , Min Huang , Hao Cheng , Xuan Huang , Zi-Qin Xu","doi":"10.1016/j.plgene.2025.100562","DOIUrl":"10.1016/j.plgene.2025.100562","url":null,"abstract":"<div><div>Plants defend against multiple pathogens by activating different signaling pathways. However, the molecular mechanisms underlying the antagonistic responses, where enhanced resistance to one pathogen is often accompanied by increased susceptibility to another, remain poorly understood. This study explores the functional role of the <em>NtabSPL6–4</em> gene in <em>Arabidopsis thaliana</em>, with a focus on its involvement in regulating plant growth, development, and immune responses. The results show that the NtabSPL6–4 protein is mainly localized in the nucleus. Compared with the wild-type plants, <em>NtabSPL6–4</em>-overexpressing Arabidopsis plants exhibited delayed flowering, increased leaf number, and larger leaf area. Transcriptome analysis under <em>Botrytis cinerea</em> infection showed that differentially expressed genes were mainly enriched in the jasmonic acid (JA) and salicylic acid (SA) signaling pathways. Functional experiments revealed that <em>NtabSPL6–4</em> enhances plant sensitivity to <em>Pseudomonas syringae</em> by down-regulating the expression of <em>PR1</em> and <em>PR5</em>, while activating JA pathway-related genes to increase resistance to fungal pathogens. Chromatin immunoprecipitation (ChIP) assays further demonstrated that NtabSPL6–4 binds to the promoter region of <em>ACX1</em>, regulating JA levels. This modulation reduces the accumulation of reactive oxygen species (ROS) and hydrogen peroxide, limits cell damage, and decreases the severity of leaf lesions, thereby contributing to enhanced resistance against fungal infection. These results suggest that <em>NtabSPL6–4</em> has a dual regulatory role in plant immunity, enhancing resistance to fungal pathogens while increasing susceptibility to bacterial pathogens.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100562"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145624430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Flowering represents the phenological response of plants to environmental cues, serving as a critical developmental phase that dictates the reproductive success of plants. Numerous over-wintering plants require vernalization to induce flowering, yet the shifting climate patterns in recent years have disrupted their flowering phenology. Different vernalization requirements in wild radish make them ideal for exploring the adaptations of vernalization-responsive plants to warmer winter. Transcriptomic analysis was conducted to investigate the flowering regulation pathways and molecular mechanism in wild radish with different vernalization requirements. A total of 2369 genes were identified as significantly differentially expressed genes (DEGs) across various time points. Vernalization upregulated floral activators VIN3 and AGL19 while downregulating repressors such as WRKY34/MSP3 and MAF5/AGL68, leading to suppression of FLC. Notably, even without cold exposure, facultative lineages exhibited elevated VIN3 and AGL19 and reduced repressors (FRI, MAF5/AGL68, FES1). Enrichment analysis highlighted photosynthesis-related pathways. Obligate vernalization types flower through the vernalization pathway, whereas facultative ones utilize photoperiod, gibberellin, and temperature pathways under non-vernalizing conditions. These findings improve understanding of floral adaptation to warming winters and offer insights for crop resilience and production under global climate change.
{"title":"Natural variation in the plasticity of flowering time across Raphanus sativus var. raphanistroides characterized by different vernalization requirements","authors":"Qingxiang Han , Pengbo Hao , Tomomi Wakabayashi , Shota Sakaguchi , Hiroaki Setoguchi","doi":"10.1016/j.plgene.2025.100565","DOIUrl":"10.1016/j.plgene.2025.100565","url":null,"abstract":"<div><div>Flowering represents the phenological response of plants to environmental cues, serving as a critical developmental phase that dictates the reproductive success of plants. Numerous over-wintering plants require vernalization to induce flowering, yet the shifting climate patterns in recent years have disrupted their flowering phenology. Different vernalization requirements in wild radish make them ideal for exploring the adaptations of vernalization-responsive plants to warmer winter. Transcriptomic analysis was conducted to investigate the flowering regulation pathways and molecular mechanism in wild radish with different vernalization requirements. A total of 2369 genes were identified as significantly differentially expressed genes (DEGs) across various time points. Vernalization upregulated floral activators <em>VIN3</em> and <em>AGL19</em> while downregulating repressors such as <em>WRKY34</em>/<em>MSP3</em> and MAF5/AGL68, leading to suppression of <em>FLC</em>. Notably, even without cold exposure, facultative lineages exhibited elevated <em>VIN3</em> and <em>AGL19</em> and reduced repressors (<em>FRI</em>, <em>MAF5/AGL68</em>, <em>FES1</em>). Enrichment analysis highlighted photosynthesis-related pathways. Obligate vernalization types flower through the vernalization pathway, whereas facultative ones utilize photoperiod, gibberellin, and temperature pathways under non-vernalizing conditions. These findings improve understanding of floral adaptation to warming winters and offer insights for crop resilience and production under global climate change.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"45 ","pages":"Article 100565"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145747749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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