Plant Biotechnology最新文献

Near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom. 番茄（Solanum lycopersicum）栽培品种Micro-Tom的近全基因组组装。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0522a

Kenta Shirasawa, Tohru Ariizumi

{"title":"Near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom.","authors":"Kenta Shirasawa, Tohru Ariizumi","doi":"10.5511/plantbiotechnology.24.0522a","DOIUrl":"10.5511/plantbiotechnology.24.0522a","url":null,"abstract":"We present a near-complete genome assembly of tomato (Solanum lycopersicum) cultivar Micro-Tom, which has been recognized as a model cultivar for fruit research. The genome DNA of Micro-Tom, provided by the National BioResource Project (NBRP) Tomato of Japan, was sequenced to obtain 72 Gb of high-fidelity long reads. These reads were assembled into 140 contigs, spanning 832.8 Mb, with an N50 length of 39.6 Mb. The contigs were aligned against the tomato reference genome sequence SL4.0 to establish a chromosome-level assembly. The genome assembly of Micro-Tom contained 98.5% complete BUSCOs and a total of 31,429 genes. Comparative genome structure analysis revealed that Micro-Tom possesses a cluster of ribosomal DNA genes spanning a 15 Mb stretch at the short arm of chromosome 2. This region was not found in the genome assemblies of previously sequenced tomato cultivars, possibly because of the inability of previous technologies to sequence such repetitive DNA. In conclusion, the near-complete genome assembly of Micro-Tom reported in this study would advance the genomics and genetics research on tomato and facilitate the breeding of improved tomato cultivars.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"41 4","pages":"367-374"},"PeriodicalIF":1.4,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of a minimal strong translation enhancer within the 5'-untranslated region of OsMac3 mRNA. 在OsMac3 mRNA的5'-非翻译区鉴定一个最小的强翻译增强子。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0909a

Hiromi Aoki-Mutsuro, Ryoko Tamukai, Miho Fukui, Mai Wajiki, Tomohiro Imamura, Lyubov A Ryabova, Mikhail V Schepetilnikov, Hiroshi Teramura, Hiroaki Kusano, Hiroaki Shimada

{"title":"Identification of a minimal strong translation enhancer within the 5'-untranslated region of OsMac3 mRNA.","authors":"Hiromi Aoki-Mutsuro, Ryoko Tamukai, Miho Fukui, Mai Wajiki, Tomohiro Imamura, Lyubov A Ryabova, Mikhail V Schepetilnikov, Hiroshi Teramura, Hiroaki Kusano, Hiroaki Shimada","doi":"10.5511/plantbiotechnology.24.0909a","DOIUrl":"10.5511/plantbiotechnology.24.0909a","url":null,"abstract":"The long 5' untranslated region (5'UTR) exhibits enhancer activity in translation of rice OsMac3 mRNA. In this report, we describe elements of OsMac3 5'UTR that may be responsible for its enhancer activity, including a long uORF and several secondary structure elements. OsMac3 5'UTR can be dissected into three stem-loop structures SL1, small SL and SL2, where the uORF starts within SL1 and ends within SL2. As expected, uORF inhibits translation of downstream ORF since deletion of the uORF AUG or the SL1 stem-loop increases translation by approximately two-fold. Thus, the 158 nt 3' region of the 5'UTR lacking SL1 together with the AUG uORF, which has significant enhancer activity, was named dMac3. We investigated two critical regions within dMac3 mRNA that influence its translation: SL2, which destabilization potentially decreases translation activity, and another 13 nt located downstream of SL2. We further confirmed that dMac3 promotes mRNA translation initiation in an in vitro translation system and during transient expression in either cultured cells or Nicotiana benthamiana leaves. Thus, the dMac3 5'UTR is a useful tool for efficient protein production in various in vitro and in vivo translation systems.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"41 4","pages":"437-446"},"PeriodicalIF":1.4,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improvement of genome editing efficiency by Cas9 codon optimization in Japanese cedar (Cryptomeria japonica D. Don). 通过优化 Cas9 密码子提高日本雪松（Cryptomeria japonica D. Don）的基因组编辑效率。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0709a

Yoshihiko Nanasato, Harunori Kawabe, Saneyoshi Ueno, Ken-Ichi Konagaya, Masaki Endo, Toru Taniguchi

{"title":"Improvement of genome editing efficiency by Cas9 codon optimization in Japanese cedar (Cryptomeria japonica D. Don).","authors":"Yoshihiko Nanasato, Harunori Kawabe, Saneyoshi Ueno, Ken-Ichi Konagaya, Masaki Endo, Toru Taniguchi","doi":"10.5511/plantbiotechnology.24.0709a","DOIUrl":"10.5511/plantbiotechnology.24.0709a","url":null,"abstract":"Japanese cedar or sugi (Cryptomeria japonica D. Don) is among the most important plantation conifers in Japan, occupying 12% of the total land area in the country. We have successfully established a CRISPR/Cas9-based genome editing system in C. japonica. However, in practical use, we encountered problems of low efficiency when generating biallelic mutations, i.e., target gene knockouts. As part of our efforts to improve efficiency, we codon-optimized the Cas9 gene, evaluated by the genome editing efficiency of CjChl I, a gene encoding a chlorophyll biosynthesis enzyme. As a result, our codon-optimized SpCas9, named CjSpCas9, performed the highest genome editing efficiency of two targets (t4, t1+t2). Specifically, the biallelic disruption efficiency of the CjChl I with CjSpCas9 was 1.8-fold higher than that of the SpCas9 gene optimized for Arabidopsis thaliana (AtSpCas9) and 2.0-fold higher than that of the SpCas9 gene optimized for Orysa sativa (OsSpCas9) for t4, respectively. For t1+t2, the efficiency was 4.9-fold higher than that of AtSpCas9 and 1.4-fold higher than that of OsSpCas9, respectively. Our western blotting analysis proved that the Cas9 protein accumulation increased upon codon frequency optimization. We concluded that the observed efficiency improvement was due to the increased Cas9 protein quantity. The efficient genome editing system we report here would accelerate molecular breeding in conifers.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"41 4","pages":"335-344"},"PeriodicalIF":1.4,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TALE-based C-to-T base editor for multiple homologous genes with flexible precision. 基于tale的多同源基因C-to-T碱基编辑器，精度灵活。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0510a

Ayako Hosoda, Issei Nakazato, Miki Okuno, Takehiko Itoh, Hideki Takanashi, Nobuhiro Tsutsumi, Shin-Ichi Arimura

引用次数: 0

CmWOX2 modulates somatic embryogenesis in Chinese chestnut (Castanea mollissima Blume). CmWOX2调控板栗（Castanea mollissima Blume）体细胞胚胎发生。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0527a

Zhilin Sun, Bing Liu, Yuzhen Tian, Xiaowei Li, Yuyuan Long, Qingrong Zhang, TingTing Xiao, Qingqin Cao

{"title":"CmWOX2 modulates somatic embryogenesis in Chinese chestnut (Castanea mollissima Blume).","authors":"Zhilin Sun, Bing Liu, Yuzhen Tian, Xiaowei Li, Yuyuan Long, Qingrong Zhang, TingTing Xiao, Qingqin Cao","doi":"10.5511/plantbiotechnology.24.0527a","DOIUrl":"10.5511/plantbiotechnology.24.0527a","url":null,"abstract":"Chinese chestnut (Castanea mollissima Blume) is distinguished by its remarkable nut quality and robustness against disease and environmental stressor. However, its somatic embryogenesis process is notably slow, presenting a significant bottleneck in its cultivation. This study focuses on the WUSCHEL (WUS)-related homeobox 2 gene (WOX2), a member of WOX transcription factors gene family, known for its critical role in the somatic embryo development of Arabidopsis. We have identified and explored the function of a WOX2 homolog in Chinese chestnut, termed CmWOX2, in the context of somatic embryogenesis. Our analysis revealed seven WUS gene family members in the species, with CmWOX2 being uniquely upregulated in callus. Our experiments demonstrated that suppression of CmWOX2 expression diminishes somatic embryo production, whereas its overexpression enlarges the embryonic callus diameter. Notably, CmWOX2 expression levels are threefold higher in varieties with high embryogenic competence, such as 'Jingshuhong' and 'Huaihuang', compared to those with lower competence, including 'Jiujiazhong' and 'Shandonghongli'. These findings underscored the pivotal role of CmWOX2 in the initial stages of Chinese chestnut somatic embryogenesis, highlighting its potential as a target for enhancing somatic embryogenesis in this species.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"41 4","pages":"375-385"},"PeriodicalIF":1.4,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rhizobium rhizogenes-mediated hairy-root transformation of daughter plants from the model strawberry Fragaria vesca's stolons. 根瘤菌介导的模式草莓花椒匍匐茎子代毛根转化。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0925a

Shigeru Hanano, Koichiro Otake, Shusei Sato

{"title":"Rhizobium rhizogenes-mediated hairy-root transformation of daughter plants from the model strawberry Fragaria vesca's stolons.","authors":"Shigeru Hanano, Koichiro Otake, Shusei Sato","doi":"10.5511/plantbiotechnology.24.0925a","DOIUrl":"10.5511/plantbiotechnology.24.0925a","url":null,"abstract":"Strawberry, a member of the Fragaria genus within the Rosaceae family, is one of the most cherished fruits worldwide. This perennial herbaceous plant also serves as a model for studying the Rosaceae family. Despite the complex polyploidy of strawberries, extensive efforts in traditional breeding over the years have resulted in improvements in yield, fruit size and shape, berry quality, and various other aspects of strawberry production. However, in addition to these conventional methods, advanced genetic technologies such as genetic modification and gene editing in intricate polyploidy varieties of strawberry are also required. Here, we present the Rhizobium rhizogenes-mediated hairy-root transformation of daughter plants from the model strawberry Fragaria vesca's stolons (also called runners), which exhibit diploid genomes. As a case study, new daughter plants were cut from the stolons, infected with R. rhizogenes harboring the mVENUS gene under Cauliflower mosaic virus 35S promoter, and then transferred on vermiculite-filled pots. After a couple of months of growth, fluorescence was observed in a few adventurous roots of the daughter plants. The hairy root transformation of daughter plants isolated from its vegetative propagation circumvents the need for seed production or callus formation and subsequent plant regeneration, which are often problematic for maintaining preferred genetic traits in complex ploidy levels. This method, which excludes genetic modification of the above-ground parts, especially the edible fruits, will open new avenues for strawberry breeding, particularly in the areas of plant nutrient absorption and fostering growth through interactions with microorganisms.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"41 4","pages":"453-458"},"PeriodicalIF":1.4,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Applications of the wheat germ cell-free protein synthesis system in plant biochemical studies. 小麦无生殖细胞蛋白合成系统在植物生化研究中的应用。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0501a

Keiichirou Nemoto

{"title":"Applications of the wheat germ cell-free protein synthesis system in plant biochemical studies.","authors":"Keiichirou Nemoto","doi":"10.5511/plantbiotechnology.24.0501a","DOIUrl":"10.5511/plantbiotechnology.24.0501a","url":null,"abstract":"The development of cell-free protein synthesis technology has made it possible to easily and quickly synthesize recombinant proteins. Among cell-free protein synthesis systems, wheat germ cell-free protein synthesis using eukaryotic ribosomes is an efficient approach to synthesize proteins with diverse and complex structures and functions. However, to date, cell-free protein synthesis systems, including wheat germ cell-free systems, have not been widely used in plant research, and little is known about their applications. Here, I first introduce a basic overview of the cell-free protein synthesis system of wheat germ. Next, I will focus on our previous research examples on plants and present the applications in which the wheat germ cell-free system is used. We provide protein expression and protein function screening methods at the semi-genomic level and also introduce new approaches to enhance study of chemical biology by adapting the cell-free system of wheat germ. With this review, I would like to highlight the potential of the wheat germ cell-free system and position it as a widely used tool for the previously difficult task of recombinant protein preparation and functional analysis.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"41 4","pages":"325-334"},"PeriodicalIF":1.4,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Soluble sugars make a greater contribution than cell wall components to the variability of freezing tolerance in wheat cultivars. 可溶性糖比细胞壁成分对小麦抗冻性变异的贡献更大。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0801a

Sushan Chowhan, Takuma Kikuchi, Momoka Ohashi, Tatsuya Kutsuno, Hiroto Handa, Toshihisa Kotake, Daisuke Takahashi

{"title":"Soluble sugars make a greater contribution than cell wall components to the variability of freezing tolerance in wheat cultivars.","authors":"Sushan Chowhan, Takuma Kikuchi, Momoka Ohashi, Tatsuya Kutsuno, Hiroto Handa, Toshihisa Kotake, Daisuke Takahashi","doi":"10.5511/plantbiotechnology.24.0801a","DOIUrl":"10.5511/plantbiotechnology.24.0801a","url":null,"abstract":"Wheat, the second most produced cereal globally, is primarily cultivated in cooler regions. Unexpected freezing temperatures can severely impact wheat production. Wheat and other temperate plants have a cold acclimation mechanism that enhances freezing tolerance, but reduces growth under low, non-freezing temperatures. During cold acclimation, plants break down storage polysaccharides like starch and fructan to accumulate soluble sugars such as glucose and fructose. These soluble sugars aid freezing tolerance through osmotic adjustments, membrane stabilization, and freezing point depression. However, plant cell walls, composed of insoluble polysaccharides, are the first line of defense against extracellular freezing. We analyzed the contributions of soluble sugars, storage polysaccharides, and cell wall polysaccharides to freezing tolerance and growth under cold acclimation in wheat. The study involved two Japanese winter cultivars (Yumechikara and Norin-61) and one Japanese spring cultivar (Haruyokoi). While Yumechikara showed poor growth after four weeks of cold acclimation, it exhibited higher freezing tolerance than the other cultivars. Our analysis revealed that Yumechikara accumulated higher levels of glucose, fructose, starch, and fructan than Norin-61 and Haruyokoi, whereas no significant differences in cell wall composition among the cultivars were observed. Gene expression patterns related to soluble sugar metabolism supported these findings. Additionally, the distribution of sugar changes between leaves (source) and crown (sink) correlated with the relationship between growth and freezing tolerance. These results suggest that freezing tolerance in wheat involves a balance between sugar accumulation and growth regulation during cold acclimation.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"41 4","pages":"401-415"},"PeriodicalIF":1.4,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analysis and characteristics of coronaridine, an alkaloid found in Catharanthus roseus. 花楸属生物碱冠碱的分析与特征。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0717a

Hiroaki Kisaka, Sachise Karakawa, Tetsuya Miwa, Hiroto Hirano, Takashi Onuki, Mayu Iyo

引用次数: 0

Occurrence of caffeoylquinic acids in bamboo suspension cells cultured under light. 光培养竹悬浮细胞中咖啡酰奎宁酸的发生。

IF 1.4 4区生物学

Plant Biotechnology Pub Date : 2024-12-25 DOI: 10.5511/plantbiotechnology.24.0812a

Naoki Ube, Yasuo Kato, Taiji Nomura

{"title":"Occurrence of caffeoylquinic acids in bamboo suspension cells cultured under light.","authors":"Naoki Ube, Yasuo Kato, Taiji Nomura","doi":"10.5511/plantbiotechnology.24.0812a","DOIUrl":"10.5511/plantbiotechnology.24.0812a","url":null,"abstract":"Rational metabolic-flow switching is an effective strategy that we previously proposed to produce exogenous high-value natural products in cultured plant cells through redirecting a highly active inherent metabolic pathway to a pathway producing related exogenous compounds. In previous proof-of-concept studies, we demonstrated that bamboo (Phyllostachys nigra; Pn) cells are a suitable host for production of phenylpropanoid-derived compounds, in particular those derived from feruloyl- and p-coumaroyl-CoAs. To expand the utility of Pn cells for production of exogenous metabolites via the rational metabolic-flow switching strategy, it is important to evaluate the metabolic potential of Pn cells under diverse culture conditions. In this study, we examined highly active metabolic pathway(s) in Pn suspension cells cultured under light. The Pn suspension cells strongly accumulated two light-induced compounds. These compounds were isolated and identified as 3-O-caffeoylquinic acid (neochlorogenic acid) and its regioisomer 5-O-caffeoylquinic acid (chlorogenic acid). Through optimization of the culture conditions, production titers of 3-O-caffeoylquinic acid and 5-O-caffeoylquinic acid in the Pn suspension cells reached 121 and 77.9 mg l-1, respectively. These findings indicate that Pn cells are a suitable host for bioproduction of exogenous metabolites, in particular those derived from caffeoyl-CoA via the rational metabolic-flow switching strategy.","PeriodicalId":20411,"journal":{"name":"Plant Biotechnology","volume":"41 4","pages":"417-424"},"PeriodicalIF":1.4,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0