aBIOTECH最新文献

TIR enzymatic functions: signaling molecules and receptor mechanisms TIR酶功能：信号分子和受体机制。

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2023-05-07 DOI: 10.1007/s42994-023-00104-w

Li Wan

引用次数: 0

Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development 染色质可达性景观揭示了小麦籽粒发育过程中亚基因组分化的调控网络。

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2023-02-10 DOI: 10.1007/s42994-023-00095-8

Hongcui Pei, Yushan Li, Yanhong Liu, Pan Liu, Jialin Zhang, Xueni Ren, Zefu Lu

{"title":"Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development","authors":"Hongcui Pei, Yushan Li, Yanhong Liu, Pan Liu, Jialin Zhang, Xueni Ren, Zefu Lu","doi":"10.1007/s42994-023-00095-8","DOIUrl":"10.1007/s42994-023-00095-8","url":null,"abstract":"<div>Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions, and the proportion of distal ACRs was increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed light on the improvement of wheat yields and qualities.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"4 1","pages":"8 - 19"},"PeriodicalIF":3.6,"publicationDate":"2023-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-023-00095-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Oryzalexin S biosynthesis: a cross-stitched disappearing pathway Oryzalexin S生物合成：一条交叉缝合的消失途径。

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2023-01-19 DOI: 10.1007/s42994-022-00092-3

Le Zhao, Richard Oyagbenro, Yiling Feng, Meimei Xu, Reuben J. Peters

{"title":"Oryzalexin S biosynthesis: a cross-stitched disappearing pathway","authors":"Le Zhao, Richard Oyagbenro, Yiling Feng, Meimei Xu, Reuben J. Peters","doi":"10.1007/s42994-022-00092-3","DOIUrl":"10.1007/s42994-022-00092-3","url":null,"abstract":"<div>Rice produces many diterpenoid phytoalexins and, reflecting the importance of these natural products in this important cereal crop plant, its genome contains three biosynthetic gene clusters (BGCs) for such metabolism. The chromosome 4 BGC (c4BGC) is largely associated with momilactone production, in part due to the presence of the initiating syn-copalyl diphosphate (CPP) synthase gene (OsCPS4). Oryzalexin S is also derived from syn-CPP. However, the relevant subsequently acting syn-stemarene synthase gene (OsKSL8) is not located in the c4BGC. Production of oryzalexin S further requires hydroxylation at carbons 2 and 19 (C2 and C19), presumably catalyzed by cytochrome P450 (CYP) monooxygenases. Here it is reported the closely related CYP99A2 and CYP99A3, whose genes are also found in the c4BGC catalyze the necessary C19-hydroxylation, while the closely related CYP71Z21 and CYP71Z22, whose genes are found in the recently reported chromosome 7 BGC (c7BGC), catalyze subsequent hydroxylation at C2α. Thus, oryzalexin S biosynthesis utilizes two distinct BGCs, in a pathway cross-stitched together by OsKSL8. Notably, in contrast to the widely conserved c4BGC, the c7BGC is subspecies (ssp.) specific, being prevalent in ssp. japonica and only rarely found in the other major ssp. indica. Moreover, while the closely related syn-stemodene synthase OsKSL11 was originally considered to be distinct from OsKSL8, it has now been reported to be a ssp. indica derived allele at the same genetic loci. Intriguingly, more detailed analysis indicates that OsKSL8(j) is being replaced by OsKSL11 (OsKSL8i), suggesting introgression from ssp. indica to (sub)tropical japonica, with concurrent disappearance of oryzalexin S production.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"4 1","pages":"1 - 7"},"PeriodicalIF":3.6,"publicationDate":"2023-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00092-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Recent advances in understanding of the epigenetic regulation of plant regeneration 植物再生的表观遗传学调控研究进展。

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2023-01-16 DOI: 10.1007/s42994-022-00093-2

Xuemei Liu, Kehui Zhu, Jun Xiao

引用次数: 2

Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways 整合多组学数据加速了植物初级和次级代谢途径的阐明。

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2023-01-11 DOI: 10.1007/s42994-022-00091-4

Feng Zhu, Weiwei Wen, Yunjiang Cheng, Saleh Alseekh, Alisdair R. Fernie

{"title":"Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways","authors":"Feng Zhu, Weiwei Wen, Yunjiang Cheng, Saleh Alseekh, Alisdair R. Fernie","doi":"10.1007/s42994-022-00091-4","DOIUrl":"10.1007/s42994-022-00091-4","url":null,"abstract":"<div>Plants are the most important sources of food for humans, as well as supplying many ingredients that are of great importance for human health. Developing an understanding of the functional components of plant metabolism has attracted considerable attention. The rapid development of liquid chromatography and gas chromatography, coupled with mass spectrometry, has allowed the detection and characterization of many thousands of metabolites of plant origin. Nowadays, elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding. Recently, the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways. Here, we review the recent research which integrates metabolomic with different omics methods, to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways. Finally, we discuss other novel methods that can accelerate the process of identification of metabolic pathways and, ultimately, identify metabolite function(s).</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"4 1","pages":"47 - 56"},"PeriodicalIF":3.6,"publicationDate":"2023-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00091-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9509473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Weed genomics: yielding insights into the genetics of weedy traits for crop improvement 杂草基因组学：为作物改良提供杂草性状遗传学见解。

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2023-01-09 DOI: 10.1007/s42994-022-00090-5

Yujie Huang, Dongya Wu, Zhaofeng Huang, Xiangyu Li, Aldo Merotto Jr, Lianyang Bai, Longjiang Fan

引用次数: 0

Genetic architecture and molecular regulation of sorghum domestication 高粱驯化的遗传结构和分子调控。

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-12-19 DOI: 10.1007/s42994-022-00089-y

Fengyong Ge, Peng Xie, Yaorong Wu, Qi Xie

{"title":"Genetic architecture and molecular regulation of sorghum domestication","authors":"Fengyong Ge, Peng Xie, Yaorong Wu, Qi Xie","doi":"10.1007/s42994-022-00089-y","DOIUrl":"10.1007/s42994-022-00089-y","url":null,"abstract":"<div>Over time, wild crops have been domesticated by humans, and the knowledge gained from parallel selection and convergent domestication-related studies in cereals has contributed to current techniques used in molecular plant breeding. Sorghum (Sorghum bicolor (L.) Moench) is the world’s fifth-most popular cereal crop and was one of the first crops cultivated by ancient farmers. In recent years, genetic and genomic studies have provided a better understanding of sorghum domestication and improvements. Here, we discuss the origin, diversification, and domestication processes of sorghum based on archeological discoveries and genomic analyses. This review also comprehensively summarized the genetic basis of key genes related to sorghum domestication and outlined their molecular mechanisms. It highlights that the absence of a domestication bottleneck in sorghum is the result of both evolution and human selection. Additionally, understanding beneficial alleles and their molecular interactions will allow us to quickly design new varieties by further de novo domestication.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"4 1","pages":"57 - 71"},"PeriodicalIF":3.6,"publicationDate":"2022-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00089-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9515725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

G2-LIKE CAROTENOID REGULATOR (SlGCR) is a positive regulator of lutein biosynthesis in tomato G2类胡萝卜素调节因子（SlGCR）是番茄叶黄素生物合成的正调节因子

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-11-29 DOI: 10.1007/s42994-022-00088-z

Siyan Ren, Yong Yuan, Hsihua Wang, Yang Zhang

{"title":"G2-LIKE CAROTENOID REGULATOR (SlGCR) is a positive regulator of lutein biosynthesis in tomato","authors":"Siyan Ren, Yong Yuan, Hsihua Wang, Yang Zhang","doi":"10.1007/s42994-022-00088-z","DOIUrl":"10.1007/s42994-022-00088-z","url":null,"abstract":"<div>Lutein is an oxygen-containing carotenoid synthesized in plant chloroplasts and chromoplasts. It plays an indispensable role in promoting plant growth and maintaining eye health in humans. The rate-limiting step of lutein biosynthesis is catalyzed by the lycopene ε-cyclase enzyme (LCYE). Although great progress has been made in the identification of transcription factors involved in the lutein biosynthetic pathway, many systematic molecular mechanisms remain to be elucidated. Here, using co-expression analysis, we identified a gene, G2-LIKE CAROTENOID REGULATOR (SlGCR), encoding a GARP G2-like transcription factor, as the potential regulator of SlLCYE in tomato. Silencing of SlGCR reduced the expression of carotenoid biosynthetic genes and the accumulation of carotenoids in tomato leaves. By contrast, overexpression of SlGCR in tomato fruit significantly increased the expression of relevant genes and enhanced the accumulation of carotenoids. SlGCR can directly bind to the SlLCYE promoter and activate its expression. In addition, we also discovered that expression of SlGCR was negatively regulated by the master regulator SlRIN, thereby inhibiting lutein synthesis during tomato fruit ripening. Taken together, we identified SlGCR as a novel regulator involved in tomato lutein biosynthesis, elucidated the regulatory mechanism, and provided a potential tool for tomato lutein metabolic engineering.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 4","pages":"267 - 280"},"PeriodicalIF":3.6,"publicationDate":"2022-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00088-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9235746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants LncPheDB:一个全基因组lncRNA调控的植物表型数据库

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-10-05 DOI: 10.1007/s42994-022-00084-3

Danjing Lou, Fei Li, Jinyue Ge, Weiya Fan, Ziran Liu, Yanyan Wang, Jingfen Huang, Meng Xing, Wenlong Guo, Shizhuang Wang, Weihua Qiao, Zhenyun Han, Qian Qian, Qingwen Yang, Xiaoming Zheng

{"title":"LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants","authors":"Danjing Lou, Fei Li, Jinyue Ge, Weiya Fan, Ziran Liu, Yanyan Wang, Jingfen Huang, Meng Xing, Wenlong Guo, Shizhuang Wang, Weihua Qiao, Zhenyun Han, Qian Qian, Qingwen Yang, Xiaoming Zheng","doi":"10.1007/s42994-022-00084-3","DOIUrl":"10.1007/s42994-022-00084-3","url":null,"abstract":"<div>LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations, lncRNA-phenotype correlations, and the similar non-coding regions of the queried sequence in multiple species. LncPheDB sorted out a total of 203,391 lncRNA sequences, 2000 phenotypes, and 120,271 variants of nine species (Zea mays L., Gossypium barbadense L., Triticum aestivum L., Lycopersicon esculentum Mille, Oryza sativa L., Hordeum vulgare L., Sorghum bicolor L., Glycine max L., and Cucumis sativus L.). By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis, a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits. More importantly, to facilitate the study of the functions of lncRNAs, we analyzed the possible target genes of lncRNAs, constructed a blast tool for performing similar fragmentation studies in all species, linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-modal convenient data search engine. We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 3","pages":"169 - 177"},"PeriodicalIF":3.6,"publicationDate":"2022-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00084-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9462831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

The global integrative network: integration of signaling and metabolic pathways 全球整合网络：信号和代谢途径的整合

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-09-21 DOI: 10.1007/s42994-022-00078-1

Yuying Lin, Shen Yan, Xiao Chang, Xiaoquan Qi, Xu Chi

{"title":"The global integrative network: integration of signaling and metabolic pathways","authors":"Yuying Lin, Shen Yan, Xiao Chang, Xiaoquan Qi, Xu Chi","doi":"10.1007/s42994-022-00078-1","DOIUrl":"10.1007/s42994-022-00078-1","url":null,"abstract":"<div>The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis. However, current databases use distinct structures to present signaling and metabolic pathways, which leads to the chaos in the integrated networks. Moreover, for the metabolic pathways, the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes, which hinders the topological analysis of the integrated networks. Here, we propose a novel “meta-pathway” structure, which uses the uniformed structure to display the signaling and metabolic pathways, and resolves the difficulty in linking the metabolic enzymes to the reactions topologically. We compiled a comprehensive collection of global integrative networks (GINs) by merging the meta-pathways of 7077 species. We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species—human, mouse, Arabidopsis, and rice. Almost all of the nodes were assembled into one major network for each of the four species, which provided opportunities for robust crosstalk and topological analysis, and knowledge graph construction.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 4","pages":"281 - 291"},"PeriodicalIF":3.6,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00078-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9096669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1