Background: Heterotrimeric G proteins are crucial signaling molecules involved in cell signaling, plant development, and stress response. However, the genome-wide identification and analysis of G proteins in castor (Ricinus communis L.) have not been researched.
Results: In this study, RcG-protein genes were identified using a sequence alignment method and analyzed by bioinformatics and expression analysis in response to salt stress. The results showed that a total of 9 G-protein family members were identified in the castor genome, which were classified into three subgroups, with the majority of RcG-proteins showing homology to soybean G-protein members. The promoter regions of all RcG-protein genes contained antioxidant response elements and ABA-responsive elements. Go enrichment analysis displayed that RcG-protein genes were involved in the G protein-coupled receptor signaling pathway, regulation of root development, and response to the bacterium. Real-time PCR showed varying responses of all RcG-protein genes to salt stress. RcGB1 was notably expressed in both roots and leaves under salt treatment, suggesting that it may be an essential gene associated with salt tolerance in the castor.
Conclusions: This study offers a theoretical framework for exploring G-protein function and presents potential genetic assets for improving crop resilience through genetic enhancement.
背景:异源三聚体 G 蛋白是参与细胞信号传导、植物发育和胁迫响应的重要信号分子。然而,对蓖麻(Ricinus communis L.)中 G 蛋白的全基因组鉴定和分析还没有研究:本研究利用序列比对方法鉴定了 RcG 蛋白基因,并通过生物信息学和表达分析对盐胁迫进行了分析。结果表明,在蓖麻基因组中共鉴定出 9 个 G 蛋白家族成员,并将其分为三个亚组,其中大多数 RcG 蛋白与大豆 G 蛋白成员具有同源性。所有 RcG 蛋白基因的启动子区域都含有抗氧化反应元件和 ABA 反应元件。Go 富集分析表明,RcG 蛋白基因参与了 G 蛋白偶联受体信号通路、根系发育调控和对细菌的反应。实时 PCR 显示,所有 RcG 蛋白基因对盐胁迫的反应各不相同。在盐处理下,RcGB1 在根部和叶片中都有显著表达,这表明它可能是与蓖麻耐盐性相关的一个重要基因:这项研究为探索 G 蛋白的功能提供了一个理论框架,并为通过基因强化提高作物抗逆性提供了潜在的遗传资产。
{"title":"Genome-wide identification of heterotrimeric G protein genes in castor (Ricinus communis L.) and expression patterns under salt stress.","authors":"Mubo Fan, Jiayu Li, Tongjie Zhang, Hongyan Huo, Shiyou Lü, Zhibiao He, Xiaoyu Wang, Jixing Zhang","doi":"10.1186/s12864-024-11027-1","DOIUrl":"10.1186/s12864-024-11027-1","url":null,"abstract":"<p><strong>Background: </strong>Heterotrimeric G proteins are crucial signaling molecules involved in cell signaling, plant development, and stress response. However, the genome-wide identification and analysis of G proteins in castor (Ricinus communis L.) have not been researched.</p><p><strong>Results: </strong>In this study, RcG-protein genes were identified using a sequence alignment method and analyzed by bioinformatics and expression analysis in response to salt stress. The results showed that a total of 9 G-protein family members were identified in the castor genome, which were classified into three subgroups, with the majority of RcG-proteins showing homology to soybean G-protein members. The promoter regions of all RcG-protein genes contained antioxidant response elements and ABA-responsive elements. Go enrichment analysis displayed that RcG-protein genes were involved in the G protein-coupled receptor signaling pathway, regulation of root development, and response to the bacterium. Real-time PCR showed varying responses of all RcG-protein genes to salt stress. RcGB1 was notably expressed in both roots and leaves under salt treatment, suggesting that it may be an essential gene associated with salt tolerance in the castor.</p><p><strong>Conclusions: </strong>This study offers a theoretical framework for exploring G-protein function and presents potential genetic assets for improving crop resilience through genetic enhancement.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1115"},"PeriodicalIF":3.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-20DOI: 10.1186/s12864-024-11029-z
Dorothea Lindtke, Sylvain Lerch, Isabelle Morel, Markus Neuditschko
Background: Crossbreeding beef bulls with dairy cows can improve the economic value and fitness of calves not entering dairy production owing to increased meat yield and heterosis. However, outcrossing might reduce the dosage of alleles that confer local adaptation or result in a higher risk of dystocia due to increased calf size. Given the clear phenotypic differences between beef breeds, the varying phylogenetic distances between beef and dairy breeds, and the genomic variations within breeds, the attainable economic and fitness gains of calves will strongly depend on the selection of sires for crossing. Thus, the aim of this study was to assess genome complementarity between Angus (AAN), Limousin (LIM), or Simmental (SIM) beef bulls and Brown Swiss (BSW) dairy cows by quantifying genomic inbreeding reduction in F1 crosses and identifying genes potentially under BSW-specific selection that might be affected by outcrossing.
Results: Low-pass sequencing data from 181 cows, 34 bulls, and 301 of their F1 progeny, and body weight and carcass composition measurements of 248 F1s were obtained. The high genomic inbreeding levels detected in the BSW cows were substantially reduced in the crossbreds, with only minor differences between the sire breeds. In the BSW cows, 585 candidate genes under selection were identified, overrepresenting genes associated with milk, meat and carcass, and production traits. Only a few genes were strongly differentiated at nonsynonymous variants between the BSW and beef breeds, including four tightly clustered genes (FAM184B, NCAPG, DCAF16, and LCORL) nearly fixed for alternate alleles in the BSW cows but mostly heterozygous or homozygous for the reference alleles in the AAN and LIM bulls. The alternate allele dosage at these genes significantly correlated with reduced carcass weight and protein mass in F1s.
Conclusion: Some of the few genes that were highly divergent between the BSW and beef breeds at nonsynonymous variants were likely under strong selection for reduced carcass weight in the BSW breed, potentially due to trade-offs between beef and dairy productions. As alleles with opposing effects still segregate in beef cattle, marker-assisted selection of mating pairs may be used to modulate the desired phenotypes and simultaneously decrease genomic inbreeding.
背景:肉用公牛与奶牛杂交可提高肉产量和异交率,从而提高未进入奶牛生产的犊牛的经济价值和体质。然而,杂交可能会降低赋予本地适应性的等位基因的剂量,或因犊牛体型增大而导致犊牛难产的风险增加。鉴于肉牛品种之间存在明显的表型差异,肉牛和奶牛品种之间存在不同的系统发育距离,以及品种内部存在基因组变异,犊牛可获得的经济和体能收益在很大程度上取决于杂交母本的选择。因此,本研究的目的是评估安格斯(AAN)、利木赞(LIM)或西门塔尔(SIM)肉牛与布朗瑞士(BSW)奶牛之间的基因组互补性,方法是量化 F1 杂交中基因组近交减少的情况,并确定可能受 BSW 特异性选择影响的基因:结果:获得了 181 头奶牛、34 头公牛及其 301 头 F1 后代的低通测序数据,以及 248 头 F1 后代的体重和胴体成分测量数据。在 BSW 奶牛中检测到的高基因组近亲繁殖水平在杂交品种中大大降低,父本品种之间仅有微小差异。在 BSW 奶牛中,发现了 585 个候选基因,其中与乳、肉、胴体和生产性状相关的基因所占比例过高。只有少数基因的非同义变异在 BSW 和肉牛品种之间存在强烈差异,其中包括四个紧密聚类的基因(FAM184B、NCAPG、DCAF16 和 LCORL),这些基因在 BSW 奶牛中几乎为固定的等位基因,但在 AAN 和 LIM 公牛中大多为参考等位基因的杂合子或同合子。这些基因的等位基因剂量与F1s胴体重量和蛋白质质量的降低有显著相关性:结论:在 BSW 和肉牛品种之间存在高度差异的非同义变异的少数基因中,有一些可能是由于肉牛和奶牛生产之间的权衡而导致 BSW 品种的胴体重量降低。由于具有相反效应的等位基因在肉牛中仍会发生分离,因此可利用标记辅助选择交配对来调节所需的表型,同时减少基因组近亲繁殖。
{"title":"Assessment of genome complementarity in three beef-on-dairy crossbreds reveals sire-specific effects on production traits with comparable rates of genomic inbreeding reduction.","authors":"Dorothea Lindtke, Sylvain Lerch, Isabelle Morel, Markus Neuditschko","doi":"10.1186/s12864-024-11029-z","DOIUrl":"10.1186/s12864-024-11029-z","url":null,"abstract":"<p><strong>Background: </strong>Crossbreeding beef bulls with dairy cows can improve the economic value and fitness of calves not entering dairy production owing to increased meat yield and heterosis. However, outcrossing might reduce the dosage of alleles that confer local adaptation or result in a higher risk of dystocia due to increased calf size. Given the clear phenotypic differences between beef breeds, the varying phylogenetic distances between beef and dairy breeds, and the genomic variations within breeds, the attainable economic and fitness gains of calves will strongly depend on the selection of sires for crossing. Thus, the aim of this study was to assess genome complementarity between Angus (AAN), Limousin (LIM), or Simmental (SIM) beef bulls and Brown Swiss (BSW) dairy cows by quantifying genomic inbreeding reduction in F1 crosses and identifying genes potentially under BSW-specific selection that might be affected by outcrossing.</p><p><strong>Results: </strong>Low-pass sequencing data from 181 cows, 34 bulls, and 301 of their F1 progeny, and body weight and carcass composition measurements of 248 F1s were obtained. The high genomic inbreeding levels detected in the BSW cows were substantially reduced in the crossbreds, with only minor differences between the sire breeds. In the BSW cows, 585 candidate genes under selection were identified, overrepresenting genes associated with milk, meat and carcass, and production traits. Only a few genes were strongly differentiated at nonsynonymous variants between the BSW and beef breeds, including four tightly clustered genes (FAM184B, NCAPG, DCAF16, and LCORL) nearly fixed for alternate alleles in the BSW cows but mostly heterozygous or homozygous for the reference alleles in the AAN and LIM bulls. The alternate allele dosage at these genes significantly correlated with reduced carcass weight and protein mass in F1s.</p><p><strong>Conclusion: </strong>Some of the few genes that were highly divergent between the BSW and beef breeds at nonsynonymous variants were likely under strong selection for reduced carcass weight in the BSW breed, potentially due to trade-offs between beef and dairy productions. As alleles with opposing effects still segregate in beef cattle, marker-assisted selection of mating pairs may be used to modulate the desired phenotypes and simultaneously decrease genomic inbreeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1118"},"PeriodicalIF":3.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1186/s12864-024-11049-9
Zhijun Yu, Tingwei Pei, Xinyue Shi, Chuks F Nwanade, Ziyan Bing, Ziwen Gao, Jianglei Meng, Lu Li, Jingze Liu
Background: DNA methylation is an epigenetic modification that plays an important role in animal and plant development. Among the diverse types of DNA methylation modifications, methylation of cytosines catalyzed by DNA cytosine methyltransferases (DNMTs) is the most common. Recently, we characterized DNA methyltransferase genes including HlDnmt1 and HlDnmt from the Asian longhorned tick, Haemaphysalis longicornis. However, the dynamic expression and functions of these DNMTs at different developmental stages and feeding statuses of the important vector tick H. longicornis remain unknown.
Results: The expression levels of HlDnmt1 and HlDnmt were significantly different at the four developmental stages: eggs, larvae, nymphs, and adults, with the highest expression levels observed in the larval stage. HlDnmt1 and HlDnmt showed different expression trends in the midguts, ovary, Malpighian tubules, and salivary glands of engorged adults, with the highest expression of HlDnmt1 observed in the ovary and the lowest in the midguts; HlDnmt expression was the highest in the midguts and the lowest in the Malpighian tubules. After RNA interference, the relative expression of HlDnmt1 and HlDnmt in H. longicornis decreased significantly, resulting in a significant decrease in the biting rate of H. longicornis. RNA-seq revealed that the differentially expressed genes were mainly enriched in the biological processes of peptide biosynthesis and the cell components of ribosomes. Molecular functions were mainly concentrated on oxidoreductase activity, ribosome structure composition, serine-type endopeptidase activity, molecular function regulators, and endopeptidase inhibitor activity. KEGG enrichment analysis showed that the differentially expressed genes were mainly enriched in autophagy and lysosome pathways, amino sugar and nucleotide sugar metabolism, glyceride metabolism, ribosomes, and other pathways.
Conclusions: HlDnmt1 and HlDnmt played an important role during development and feeding of H. longicornis, and their functions were potentially associated with lysosome pathways. These results provide basic knowledge for understanding the epigenetic regulation of the development of the tick H. longicornis, which sheds light on control strategies for ticks and tick-borne diseases.
背景:DNA 甲基化是一种表观遗传修饰,在动物和植物发育过程中发挥着重要作用。在各种类型的 DNA 甲基化修饰中,由 DNA 胞嘧啶甲基转移酶(DNMTs)催化的胞嘧啶甲基化最为常见。最近,我们鉴定了亚洲长角蜱(Haemaphysalis longicornis)的 DNA 甲基转移酶基因,包括 HlDnmt1 和 HlDnmt。然而,这些 DNMTs 在长角蜱这种重要媒介蜱的不同发育阶段和摄食状态下的动态表达和功能仍然未知:结果:HlDnmt1和HlDnmt在卵、幼虫、若虫和成虫四个发育阶段的表达水平有显著差异,其中幼虫阶段的表达水平最高。HlDnmt1和HlDnmt在吞食成虫的中肠、卵巢、马氏管和唾液腺中表现出不同的表达趋势,其中HlDnmt1在卵巢中的表达量最高,在中肠中的表达量最低;HlDnmt在中肠中的表达量最高,在马氏管中的表达量最低。经过RNA干扰后,长角雉体内HlDnmt1和HlDnmt的相对表达量显著下降,导致长角雉的咬食率显著下降。RNA-seq 发现,差异表达的基因主要富集在多肽生物合成和核糖体细胞组分的生物过程中。分子功能主要集中在氧化还原酶活性、核糖体结构组成、丝氨酸型内肽酶活性、分子功能调节因子和内肽酶抑制剂活性等方面。KEGG富集分析表明,差异表达基因主要富集在自噬和溶酶体通路、氨基糖和核苷酸糖代谢、甘油酯代谢、核糖体等通路:结论:HlDnmt1和HlDnmt在龙虾的发育和摄食过程中发挥了重要作用,其功能可能与溶酶体途径有关。这些结果为了解长角蜱发育的表观遗传调控提供了基础知识,为蜱和蜱传疾病的控制策略提供了启示。
{"title":"The functions of DNA methyltransferases during the feeding and development of Haemaphysalis longicornis are potentially associated with lysosome pathways.","authors":"Zhijun Yu, Tingwei Pei, Xinyue Shi, Chuks F Nwanade, Ziyan Bing, Ziwen Gao, Jianglei Meng, Lu Li, Jingze Liu","doi":"10.1186/s12864-024-11049-9","DOIUrl":"10.1186/s12864-024-11049-9","url":null,"abstract":"<p><strong>Background: </strong>DNA methylation is an epigenetic modification that plays an important role in animal and plant development. Among the diverse types of DNA methylation modifications, methylation of cytosines catalyzed by DNA cytosine methyltransferases (DNMTs) is the most common. Recently, we characterized DNA methyltransferase genes including HlDnmt1 and HlDnmt from the Asian longhorned tick, Haemaphysalis longicornis. However, the dynamic expression and functions of these DNMTs at different developmental stages and feeding statuses of the important vector tick H. longicornis remain unknown.</p><p><strong>Results: </strong>The expression levels of HlDnmt1 and HlDnmt were significantly different at the four developmental stages: eggs, larvae, nymphs, and adults, with the highest expression levels observed in the larval stage. HlDnmt1 and HlDnmt showed different expression trends in the midguts, ovary, Malpighian tubules, and salivary glands of engorged adults, with the highest expression of HlDnmt1 observed in the ovary and the lowest in the midguts; HlDnmt expression was the highest in the midguts and the lowest in the Malpighian tubules. After RNA interference, the relative expression of HlDnmt1 and HlDnmt in H. longicornis decreased significantly, resulting in a significant decrease in the biting rate of H. longicornis. RNA-seq revealed that the differentially expressed genes were mainly enriched in the biological processes of peptide biosynthesis and the cell components of ribosomes. Molecular functions were mainly concentrated on oxidoreductase activity, ribosome structure composition, serine-type endopeptidase activity, molecular function regulators, and endopeptidase inhibitor activity. KEGG enrichment analysis showed that the differentially expressed genes were mainly enriched in autophagy and lysosome pathways, amino sugar and nucleotide sugar metabolism, glyceride metabolism, ribosomes, and other pathways.</p><p><strong>Conclusions: </strong>HlDnmt1 and HlDnmt played an important role during development and feeding of H. longicornis, and their functions were potentially associated with lysosome pathways. These results provide basic knowledge for understanding the epigenetic regulation of the development of the tick H. longicornis, which sheds light on control strategies for ticks and tick-borne diseases.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1109"},"PeriodicalIF":3.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1186/s12864-024-10952-5
Scott Ferguson, Yoav D Bar-Ness, Justin Borevitz, Ashley Jones
{"title":"Correction: A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world's tallest trees.","authors":"Scott Ferguson, Yoav D Bar-Ness, Justin Borevitz, Ashley Jones","doi":"10.1186/s12864-024-10952-5","DOIUrl":"10.1186/s12864-024-10952-5","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1107"},"PeriodicalIF":3.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1186/s12864-024-11032-4
Xumei Sun, Yu-Lei Chen, Fan Xin, Siyuan Zhang
Background: It has been reported that the most common post-transcriptional modification of eukaryotic RNA is N6-methyladenosine (m6A). Previous studies show m6A is a key regulator for viral infection and immune response. However, whether there is a pathogen stimulus-dependent m6A regulation in invertebrate shrimp has not been studied.
Results: In this study, we performed a transcriptome-wide profiling of mRNA m6A methylation in shrimp (Marsupenaeus japonicus) after white spot syndrome virus (WSSV) infection by methylated RNA immunoprecipitation sequencing (MeRIP-seq). A total of 15,436 m6A peaks were identified in the shrimp, distributed in 8,108 genes, mainly enriched in the CDS, 3' UTR region and near the stop codon. After WSSV infection, we identified 2,260 m6A peaks with significantly changes, of which 1,973 peaks were significantly up-regulated and 287 peaks were significantly down-regulated. 1,795 genes were identified as differentially methylated genes. GO and KEGG analysis showed that hyper-methylated genes or hypo-methylated genes were highly associated with innate immune process and related to metabolic pathways including HIF-1 signaling pathway, lysine degradation and Wnt signaling pathway. Combined analysis showed a positive correlation between m6A methylation levels and mRNA expression levels. In addition, computational predictions of protein-protein interaction indicated that genes with altered levels of m6A methylation and mRNA expression clustered in metabolism, DNA replication, and protein ubiquitination. ZC3H12A and HIF-1 were two hub genes in protein-protein interaction (PPI) network that involved in immune and metabolism processes, respectively.
Conclusion: Our study explored the m6A methylation pattern of mRNA in shrimp after WSSV infection, exhibited the first m6A map of shrimp at the stage of WSSV induced metabolic reprogramming. These findings may reveal the possible mechanisms of m6A-mediated innate immune response in invertebrates.
{"title":"Transcriptome-wide identification and analysis reveals m6A regulation of metabolic reprogramming in shrimp (Marsupenaeus japonicus) under virus infection.","authors":"Xumei Sun, Yu-Lei Chen, Fan Xin, Siyuan Zhang","doi":"10.1186/s12864-024-11032-4","DOIUrl":"10.1186/s12864-024-11032-4","url":null,"abstract":"<p><strong>Background: </strong>It has been reported that the most common post-transcriptional modification of eukaryotic RNA is N6-methyladenosine (m6A). Previous studies show m6A is a key regulator for viral infection and immune response. However, whether there is a pathogen stimulus-dependent m6A regulation in invertebrate shrimp has not been studied.</p><p><strong>Results: </strong>In this study, we performed a transcriptome-wide profiling of mRNA m6A methylation in shrimp (Marsupenaeus japonicus) after white spot syndrome virus (WSSV) infection by methylated RNA immunoprecipitation sequencing (MeRIP-seq). A total of 15,436 m6A peaks were identified in the shrimp, distributed in 8,108 genes, mainly enriched in the CDS, 3' UTR region and near the stop codon. After WSSV infection, we identified 2,260 m6A peaks with significantly changes, of which 1,973 peaks were significantly up-regulated and 287 peaks were significantly down-regulated. 1,795 genes were identified as differentially methylated genes. GO and KEGG analysis showed that hyper-methylated genes or hypo-methylated genes were highly associated with innate immune process and related to metabolic pathways including HIF-1 signaling pathway, lysine degradation and Wnt signaling pathway. Combined analysis showed a positive correlation between m6A methylation levels and mRNA expression levels. In addition, computational predictions of protein-protein interaction indicated that genes with altered levels of m6A methylation and mRNA expression clustered in metabolism, DNA replication, and protein ubiquitination. ZC3H12A and HIF-1 were two hub genes in protein-protein interaction (PPI) network that involved in immune and metabolism processes, respectively.</p><p><strong>Conclusion: </strong>Our study explored the m6A methylation pattern of mRNA in shrimp after WSSV infection, exhibited the first m6A map of shrimp at the stage of WSSV induced metabolic reprogramming. These findings may reveal the possible mechanisms of m6A-mediated innate immune response in invertebrates.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1103"},"PeriodicalIF":3.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1186/s12864-024-11054-y
Jiageng Du, Weilong Li, Zhuo Wang, Zhiheng Chen, Chao Wang, Wei Lu, Aisheng Xiong, Guofei Tan, Yangxia Zheng, Mengyao Li
Drought, a prevalent abiotic stressor, significantly impacts plant yield and quality. Melatonin (MT), a potent and economical growth regulator, plays a pivotal role in augmenting crop resilience against stress. This study investigated the efficacy of exogenous MT on drought-stressed celery seedlings by comprehensively analyzing phenotypic, physiological, and molecular attributes. The results revealed that exogenous MT mitigated celery seedling damage under drought stress, lowered malondialdehyde (MDA) concentrations, elevated oxidase activities, osmolyte levels, chlorophyll content, and augmented light energy conversion efficiency. Transcriptomic analysis demonstrated that MT could regulate chlorophyll synthesis genes (AgPORA1 and AgDVR2), contributing to heightened photosynthetic potential and increased drought tolerance in celery. Moreover, MT was found to modulate glycolytic pathways, upregulate pyruvate synthesis genes (AgPEP1 and AgPK3), and downregulate degradation genes (AgPDC2 and AgPDHA2), thereby promoting pyruvate accumulation and enhancing peroxidase activity and drought tolerance. The RNA-seq and qRT-PCR analyses demonstrated similar results, showing the same general expression trends. The study elucidates the physiological and molecular mechanisms underlying MT's stress-alleviating effects in celery seedlings, offering insights into MT-based strategies in plant cultivation and breeding for arid environments.
{"title":"Effects of exogenous melatonin on drought stress in celery (Apium graveolens L.): unraveling the modulation of chlorophyll and glucose metabolism pathways.","authors":"Jiageng Du, Weilong Li, Zhuo Wang, Zhiheng Chen, Chao Wang, Wei Lu, Aisheng Xiong, Guofei Tan, Yangxia Zheng, Mengyao Li","doi":"10.1186/s12864-024-11054-y","DOIUrl":"10.1186/s12864-024-11054-y","url":null,"abstract":"<p><p>Drought, a prevalent abiotic stressor, significantly impacts plant yield and quality. Melatonin (MT), a potent and economical growth regulator, plays a pivotal role in augmenting crop resilience against stress. This study investigated the efficacy of exogenous MT on drought-stressed celery seedlings by comprehensively analyzing phenotypic, physiological, and molecular attributes. The results revealed that exogenous MT mitigated celery seedling damage under drought stress, lowered malondialdehyde (MDA) concentrations, elevated oxidase activities, osmolyte levels, chlorophyll content, and augmented light energy conversion efficiency. Transcriptomic analysis demonstrated that MT could regulate chlorophyll synthesis genes (AgPORA1 and AgDVR2), contributing to heightened photosynthetic potential and increased drought tolerance in celery. Moreover, MT was found to modulate glycolytic pathways, upregulate pyruvate synthesis genes (AgPEP1 and AgPK3), and downregulate degradation genes (AgPDC2 and AgPDHA2), thereby promoting pyruvate accumulation and enhancing peroxidase activity and drought tolerance. The RNA-seq and qRT-PCR analyses demonstrated similar results, showing the same general expression trends. The study elucidates the physiological and molecular mechanisms underlying MT's stress-alleviating effects in celery seedlings, offering insights into MT-based strategies in plant cultivation and breeding for arid environments.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1104"},"PeriodicalIF":3.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1186/s12864-024-11040-4
Amy L Toth, Christopher D R Wyatt, Rick E Masonbrink, Katherine S Geist, Ryan Fortune, Sarah B Scott, Emeline Favreau, Sandra M Rehan, Seirian Sumner, Mary M Gardiner, Frances S Sivakoff
Background: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.
Results: PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6 Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with ≥ 96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.
Conclusions: Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.
{"title":"New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens.","authors":"Amy L Toth, Christopher D R Wyatt, Rick E Masonbrink, Katherine S Geist, Ryan Fortune, Sarah B Scott, Emeline Favreau, Sandra M Rehan, Seirian Sumner, Mary M Gardiner, Frances S Sivakoff","doi":"10.1186/s12864-024-11040-4","DOIUrl":"10.1186/s12864-024-11040-4","url":null,"abstract":"<p><strong>Background: </strong>The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.</p><p><strong>Results: </strong>PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6 Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with ≥ 96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.</p><p><strong>Conclusions: </strong>Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1106"},"PeriodicalIF":3.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1186/s12864-024-11010-w
Wang Liangdeng, Yin Fengrui, Zhu Weifeng, Zhang Ming, Xiao Xufeng, Yao Yuekeng, Ge Fei, Wang Wenjing
Background: Pueraria is a widely cultivated medicinal and edible homologous plant in Asia, and its tuberous roots are commonly used in the food, nutraceutical, and pharmaceutical industries. "Gange No. 5" is a local variety of Pueraria montana var. thomsonii (Bentham) M.R. Almeida (PMT) in Jiangxi Province, China. After optimizing its cultivation technique, we shortened the cultivation cycle of this variety from two years to one year, suggesting that the regulatory mechanism of the endogenous hormone system during tuberous root expansion may have changed significantly. In this study, we focused on the molecular mechanisms of endogenous hormones in promoting tuberous root expansion during one-year cultivation of "Gange No. 5".
Results: The mid-late expansion period (S4) is critical for the rapid swelling of "Gange No. 5" tuberous roots during annual cultivation. At S4, the number of cells increased dramatically and their volume enlarged rapidly in the tuberous roots, the fresh weight of a single root quickly increased, and the contents of multiple nutrients (total protein, total phenol, isoflavones) and medicinal components (puerarin, puerarin apigenin, and soy sapogenin) were at their peak values. We compared the transcriptomes and metabolomes of S1 (the pre-expansion period), S4, and S6 (the final expansion period), and screened 42 differentially accumulated hormone metabolites and 1,402 differentially expressed genes (DEGs) associated with hormone biosynthesis, metabolism, and signaling. Most Auxin, cytokinins (CKs), jasmonic acids (JAs), salicylic acid (SA), melatonin (MLT), and ethylene (ETH), reached their maximum levels at S1 and then gradually decreased; however, abscisic acid (ABA) appeared in S6, indicating that most of the endogenous hormones may play a key role in regulating the initiation of tuberous root expansion, while ABA mainly promotes tuberous root maturation. Notably, multiple key genes of the 'Tryptophan metabolism' pathway (ko00380) were significantly differentially expressed, and COBRA1, COBRA2, YUCCA10, IAA13, IAA16, IAA20, IAA27, VAN3, ACAA2, and ARF were also identified to be significantly correlated with the expansion of "Gange No. 5" tuberous roots.
Conclusions: Our study has revealed how endogenous hormone regulation affects the expansion of "Gange No. 5" tuberous roots. These findings offer a theoretical foundation for improving the yield of PMT tuberous roots.
{"title":"Transcriptomics integrated with targeted metabolomics reveals endogenous hormone changes in tuberous root expansion of Pueraria.","authors":"Wang Liangdeng, Yin Fengrui, Zhu Weifeng, Zhang Ming, Xiao Xufeng, Yao Yuekeng, Ge Fei, Wang Wenjing","doi":"10.1186/s12864-024-11010-w","DOIUrl":"10.1186/s12864-024-11010-w","url":null,"abstract":"<p><strong>Background: </strong>Pueraria is a widely cultivated medicinal and edible homologous plant in Asia, and its tuberous roots are commonly used in the food, nutraceutical, and pharmaceutical industries. \"Gange No. 5\" is a local variety of Pueraria montana var. thomsonii (Bentham) M.R. Almeida (PMT) in Jiangxi Province, China. After optimizing its cultivation technique, we shortened the cultivation cycle of this variety from two years to one year, suggesting that the regulatory mechanism of the endogenous hormone system during tuberous root expansion may have changed significantly. In this study, we focused on the molecular mechanisms of endogenous hormones in promoting tuberous root expansion during one-year cultivation of \"Gange No. 5\".</p><p><strong>Results: </strong>The mid-late expansion period (S4) is critical for the rapid swelling of \"Gange No. 5\" tuberous roots during annual cultivation. At S4, the number of cells increased dramatically and their volume enlarged rapidly in the tuberous roots, the fresh weight of a single root quickly increased, and the contents of multiple nutrients (total protein, total phenol, isoflavones) and medicinal components (puerarin, puerarin apigenin, and soy sapogenin) were at their peak values. We compared the transcriptomes and metabolomes of S1 (the pre-expansion period), S4, and S6 (the final expansion period), and screened 42 differentially accumulated hormone metabolites and 1,402 differentially expressed genes (DEGs) associated with hormone biosynthesis, metabolism, and signaling. Most Auxin, cytokinins (CKs), jasmonic acids (JAs), salicylic acid (SA), melatonin (MLT), and ethylene (ETH), reached their maximum levels at S1 and then gradually decreased; however, abscisic acid (ABA) appeared in S6, indicating that most of the endogenous hormones may play a key role in regulating the initiation of tuberous root expansion, while ABA mainly promotes tuberous root maturation. Notably, multiple key genes of the 'Tryptophan metabolism' pathway (ko00380) were significantly differentially expressed, and COBRA1, COBRA2, YUCCA10, IAA13, IAA16, IAA20, IAA27, VAN3, ACAA2, and ARF were also identified to be significantly correlated with the expansion of \"Gange No. 5\" tuberous roots.</p><p><strong>Conclusions: </strong>Our study has revealed how endogenous hormone regulation affects the expansion of \"Gange No. 5\" tuberous roots. These findings offer a theoretical foundation for improving the yield of PMT tuberous roots.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1112"},"PeriodicalIF":3.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Calcium-dependent protein kinases (CDPKs) phosphorylate downstream target proteins in response to signals transmitted by free calcium ions (Ca2+, one of the second messengers) and thus play important regulatory roles in many biological processes, such as plant growth, development, and stress response.
Results: A bioinformatic analysis, as well as thorough evolutionary and expression investigations, were conducted to confirm previous reports of functional evidence for plant CDPKs. Using the Phytozome database's BLAST search engine and the HMM search tool in TBtools software, we discovered that CDPKs are well conserved from green algae to flowering angiosperms in various gene family sizes. Additional investigations of the obtained CDPKs revealed high conservation of domain and motif numbers, gene architectures, and patterns. However, this conservation differed among plant species. Phylogenetic analysis demonstrated that the CDPK gene family diverged from a common ancient gene. Similarly, investigations into plant interspecies evolutionary relationships revealed common ancestral plant species, suggesting speciation of plants and evolution based on plant adaptation and diversification. A search for the driving force of CDPK gene family expansion revealed that dispersed duplication events, among other duplication events, contributed largely to CDPK gene family expansion. Gene localization analysis in P. trichocarpa demonstrated that most CDPK genes are localized within several cell organelles and bind other kinases and proteins to perform their biological functions efficiently. Using RNA-seq data and qPCR analyses, we postulated that PtCDPKs play functional roles in abiotic stress responses by regulating cold, heat, drought and salt stress to varying extents.
Conclusion: The CDPK genes are well conserved in plants and are critical entities in abiotic stress regulation, and further exploration and manipulation of these genes in the future may provide solutions to some of the challenges in agriculture, forestry and food security.
{"title":"Genomic survey and evolution analysis of calcium-dependent protein kinases in plants and their stress-responsive patterns in populus.","authors":"Zhiying Mu, Mingyue Xu, Teja Manda, Liming Yang, Delight Hwarari, Fu-Yuan Zhu","doi":"10.1186/s12864-024-10962-3","DOIUrl":"10.1186/s12864-024-10962-3","url":null,"abstract":"<p><strong>Background: </strong>Calcium-dependent protein kinases (CDPKs) phosphorylate downstream target proteins in response to signals transmitted by free calcium ions (Ca<sup>2+</sup>, one of the second messengers) and thus play important regulatory roles in many biological processes, such as plant growth, development, and stress response.</p><p><strong>Results: </strong>A bioinformatic analysis, as well as thorough evolutionary and expression investigations, were conducted to confirm previous reports of functional evidence for plant CDPKs. Using the Phytozome database's BLAST search engine and the HMM search tool in TBtools software, we discovered that CDPKs are well conserved from green algae to flowering angiosperms in various gene family sizes. Additional investigations of the obtained CDPKs revealed high conservation of domain and motif numbers, gene architectures, and patterns. However, this conservation differed among plant species. Phylogenetic analysis demonstrated that the CDPK gene family diverged from a common ancient gene. Similarly, investigations into plant interspecies evolutionary relationships revealed common ancestral plant species, suggesting speciation of plants and evolution based on plant adaptation and diversification. A search for the driving force of CDPK gene family expansion revealed that dispersed duplication events, among other duplication events, contributed largely to CDPK gene family expansion. Gene localization analysis in P. trichocarpa demonstrated that most CDPK genes are localized within several cell organelles and bind other kinases and proteins to perform their biological functions efficiently. Using RNA-seq data and qPCR analyses, we postulated that PtCDPKs play functional roles in abiotic stress responses by regulating cold, heat, drought and salt stress to varying extents.</p><p><strong>Conclusion: </strong>The CDPK genes are well conserved in plants and are critical entities in abiotic stress regulation, and further exploration and manipulation of these genes in the future may provide solutions to some of the challenges in agriculture, forestry and food security.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1108"},"PeriodicalIF":3.5,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}