aBIOTECH最新文献_第10页

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":null,"pages":null},"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

Advances in plastid transformation for metabolic engineering in higher plants 高等植物质体转化代谢工程研究进展

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-10-01 DOI: 10.1007/s42994-022-00083-4

Sheng Yang, Yi Deng, Shengchun Li

{"title":"Advances in plastid transformation for metabolic engineering in higher plants","authors":"Sheng Yang, Yi Deng, Shengchun Li","doi":"10.1007/s42994-022-00083-4","DOIUrl":"10.1007/s42994-022-00083-4","url":null,"abstract":"<div>The plastid (chloroplast) genome of higher plants is an appealing target for metabolic engineering via genetic transformation. Although the bacterial-type plastid genome is small compared with the nuclear genome, it can accommodate large quantities of foreign genes that precisely integrate through homologous recombination. Engineering complex metabolic pathways in plants often requires simultaneous and concerted expression of multiple transgenes, the possibility of stacking several transgenes in synthetic operons makes the transplastomic approach amazing. The potential for extraordinarily high-level transgene expression, absence of epigenetic gene silencing and transgene containment due to the exclusion of plastids from pollen transmission in most angiosperm species further add to the attractiveness of plastid transformation technology. This minireview describes recent advances in expanding the toolboxes for plastid genome engineering, and highlights selected high-value metabolites produced using transplastomic plants, including artemisinin, astaxanthin and paclitaxel.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590572/pdf/42994_2022_Article_83.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10506680","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

Fundamental and practical approaches for single-cell ATAC-seq analysis 单细胞ATAC-seq分析的基本和实用方法

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-09-27 DOI: 10.1007/s42994-022-00082-5

Peiyu Shi, Yage Nie, Jiawen Yang, Weixing Zhang, Zhongjie Tang, Jin Xu

{"title":"Fundamental and practical approaches for single-cell ATAC-seq analysis","authors":"Peiyu Shi, Yage Nie, Jiawen Yang, Weixing Zhang, Zhongjie Tang, Jin Xu","doi":"10.1007/s42994-022-00082-5","DOIUrl":"10.1007/s42994-022-00082-5","url":null,"abstract":"<div>Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With the rapid development of single-cell technology, open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches. The application of scATAC-seq has become as popular as that of scRNA-seq. However, owing to the nature of scATAC-seq data, which are sparse and noisy, processing the data requires different methodologies and empirical experience. This review presents a practical guide for processing scATAC-seq data, from quality evaluation to downstream analysis, for various applications. In addition to the epigenomic profiling from scATAC-seq, we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage. We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2022-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590475/pdf/42994_2022_Article_82.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10506674","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

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":null,"pages":null},"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

Construction of homozygous diploid potato through maternal haploid induction 通过母体单倍体诱导构建纯合二倍体马铃薯

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-09-15 DOI: 10.1007/s42994-022-00080-7

Jinzhe Zhang, Jian Yin, Jiayi Luo, Die Tang, Xijian Zhu, Jie Wang, Zhihong Liu, Pei Wang, Yu Zhong, Chenxu Liu, Canhui Li, Shaojiang Chen, Sanwen Huang

{"title":"Construction of homozygous diploid potato through maternal haploid induction","authors":"Jinzhe Zhang, Jian Yin, Jiayi Luo, Die Tang, Xijian Zhu, Jie Wang, Zhihong Liu, Pei Wang, Yu Zhong, Chenxu Liu, Canhui Li, Shaojiang Chen, Sanwen Huang","doi":"10.1007/s42994-022-00080-7","DOIUrl":"10.1007/s42994-022-00080-7","url":null,"abstract":"<div>Reinventing the tetraploid potato into a seed-propagated, diploid, hybrid potato would significantly accelerate potato breeding. In this regard, the development of highly homozygous inbred lines is a prerequisite for breeding hybrid potatoes, but self-incompatibility and inbreeding depression present challenges for developing pure inbred lines. To resolve this impediment, we developed a doubled haploid (DH) technology, based on mutagenesis of the potato DOMAIN OF UNKNOWN FUNCTION 679 membrane protein (StDMP) gene. Here, we show that a deficiency in StDMP allows the generation of maternal haploids for generating diploid potato lines. An exercisable protocol, involving hybridization, fluorescent marker screening, molecular and flow cytometric identification, and doubling with colchicine generates nearly 100% homozygous diploid potato lines. This dmp-triggered haploid induction (HI) system greatly shortens the breeding process and offers a robust method for generating diploid potato inbred lines with high purity.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2022-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00080-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9446913","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: 6

Coculture engineering for efficient production of vanillyl alcohol in Escherichia coli 大肠杆菌高效生产香草醇的共培养工程

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-09-05 DOI: 10.1007/s42994-022-00079-0

Meichen Yang, Hao Meng, Xianglai Li, Jia Wang, Xiaolin Shen, Xinxiao Sun, Qipeng Yuan

{"title":"Coculture engineering for efficient production of vanillyl alcohol in Escherichia coli","authors":"Meichen Yang, Hao Meng, Xianglai Li, Jia Wang, Xiaolin Shen, Xinxiao Sun, Qipeng Yuan","doi":"10.1007/s42994-022-00079-0","DOIUrl":"10.1007/s42994-022-00079-0","url":null,"abstract":"<div>Vanillyl alcohol is a precursor of vanillin, which is one of the most widely used flavor compounds. Currently, vanillyl alcohol biosynthesis still encounters the problem of low efficiency. In this study, coculture engineering was adopted to improve production efficiency of vanillyl alcohol in E. coli. First, two pathways were compared for biosynthesis of the immediate precursor 3, 4-dihydroxybenzyl alcohol in monocultures, and the 3-dehydroshikimate-derived pathway showed higher efficiency than the 4-hydroxybenzoate-derived pathway. To enhance the efficiency of the last methylation step, two strategies were used, and strengthening S-adenosylmethionine (SAM) regeneration showed positive effect while strengthening SAM biosynthesis showed negative effect. Then, the optimized pathway was assembled in a single cell. However, the biosynthetic efficiency was still low, and was not significantly improved by modular optimization of pathway genes. Thus, coculturing engineering strategy was adopted. At the optimal inoculation ratio, the titer reached 328.9 mg/L. Further, gene aroE was knocked out to reduce cell growth and improve 3,4-DHBA biosynthesis of the upstream strain. As a result, the titer was improved to 559.4 mg/L in shake flasks and to 3.89 g/L in fed-batch fermentation. These are the highest reported titers of vanillyl alcohol so far. This work provides an effective strategy for sustainable production of vanillyl alcohol.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2022-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00079-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50454349","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

Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection 隐性根结线虫感染下大豆全转录组N6-甲基腺苷（m6A）甲基化

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-08-18 DOI: 10.1007/s42994-022-00077-2

Xue Han, Qianqian Shi, Ziyi He, Wenwen Song, Qingshan Chen, Zhaoming Qi

{"title":"Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection","authors":"Xue Han, Qianqian Shi, Ziyi He, Wenwen Song, Qingshan Chen, Zhaoming Qi","doi":"10.1007/s42994-022-00077-2","DOIUrl":"10.1007/s42994-022-00077-2","url":null,"abstract":"<div>N6-methyladenosine (m6A) is a reversible epigenetic modification of mRNA and other RNAs that plays a significant role in regulating gene expression and biological processes. However, m6A abundance, dynamics, and transcriptional regulatory mechanisms remain unexplored in the context of soybean resistance to Meloidogyne incognita. In this study, we performed a comparative analysis of transcriptome-wide m6A and metabolome profiles of soybean root tissues with and without M. incognita infection. Global m6A hypermethylation was widely induced in response to M. incognita infection and was enriched around the 3′ end of coding sequences and in 3′ UTR regions. There were 2069 significantly modified m6A sites, 594 differentially expressed genes, and 103 differentially accumulated metabolites between infected and uninfected roots, including coumestrol, psoralidin, and 2-hydroxyethylphosphonate. Among 101 m6A-modified DEGs, 34 genes were hypomethylated and upregulated, and 39 genes were hypermethylated and downregulated, indicating a highly negative correlation between m6A methylation and gene transcript abundance. A number of these m6A-modified DEGs, including WRKY70, ERF60, POD47 and LRR receptor-like serine/threonine-protein kinases, were involved in plant defense responses. Our study provides new insights into the critical role of m6A modification in early soybean responses to M. incognita.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2022-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00077-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50491781","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

Current overview on the genetic basis of key genes involved in soybean domestication 大豆驯化关键基因的遗传基础研究进展

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-07-02 DOI: 10.1007/s42994-022-00074-5

Sijia Lu, Chao Fang, Jun Abe, Fanjiang Kong, Baohui Liu

{"title":"Current overview on the genetic basis of key genes involved in soybean domestication","authors":"Sijia Lu, Chao Fang, Jun Abe, Fanjiang Kong, Baohui Liu","doi":"10.1007/s42994-022-00074-5","DOIUrl":"10.1007/s42994-022-00074-5","url":null,"abstract":"<div>Modern crops were created through the domestication and genetic introgression of wild relatives and adaptive differentiation in new environments. Identifying the domestication-related genes and unveiling their molecular diversity provide clues for understanding how the domesticated variants were selected by ancient people, elucidating how and where these crops were domesticated. Molecular genetics and genomics have explored some domestication-related genes in soybean (Glycine max). Here, we summarize recent studies about the quantitative trait locus (QTL) and genes involved in the domestication traits, introduce the functions of these genes, clarify which alleles of domesticated genes were selected during domestication. A deeper understanding of soybean domestication could help to break the bottleneck of modern breeding by highlighting unused genetic diversity not selected in the original domestication process, as well as highlighting promising new avenues for the identification and research of important agronomic traits among different crop species.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2022-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590488/pdf/42994_2022_Article_74.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9549837","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

The application of CRISPR/Cas technologies to Brassica crops: current progress and future perspectives CRISPR/Cas技术在芸苔属作物中的应用现状与展望

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-07-02 DOI: 10.1007/s42994-022-00076-3

Jun Li, Xiaoxiao Yu, Chao Zhang, Na Li, Jianjun Zhao

{"title":"The application of CRISPR/Cas technologies to Brassica crops: current progress and future perspectives","authors":"Jun Li, Xiaoxiao Yu, Chao Zhang, Na Li, Jianjun Zhao","doi":"10.1007/s42994-022-00076-3","DOIUrl":"10.1007/s42994-022-00076-3","url":null,"abstract":"<div>Brassica species are a global source of nutrients and edible vegetable oil for humans. However, all commercially important Brassica crops underwent a whole-genome triplication event, hindering the development of functional genomics and breeding programs. Fortunately, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) technologies, by allowing multiplex and precise genome engineering, have become valuable genome-editing tools and opened up new avenues for biotechnology. Here, we review current progress in the use of CRISPR/Cas technologies with an emphasis on the latest breakthroughs in precise genome editing. We also summarize the application of CRISPR/Cas technologies to Brassica crops for trait improvements. Finally, we discuss the challenges and future directions of these technologies for comprehensive application in Brassica crops. Ongoing advancement in CRISPR/Cas technologies, in combination with other achievements, will play a significant role in the genetic improvement and molecular breeding of Brassica crops.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2022-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00076-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50440230","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: 8

Disruption of three polyamine uptake transporter genes in rice by CRISPR/Cas9 gene editing confers tolerance to herbicide paraquat CRISPR/Cas9基因编辑对水稻三个多胺摄取转运蛋白基因的破坏赋予其对除草剂百草枯的耐受性

IF 3.6 4区农林科学

aBIOTECH Pub Date : 2022-06-25 DOI: 10.1007/s42994-022-00075-4

Yu-Shu Lyu, Li-Miao Cao, Wen-Qian Huang, Jian-Xiang Liu, Hai-Ping Lu

引用次数: 10