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Epigenetic factors related to recalcitrance in plant biotechnology. 植物生物技术中与顽抗有关的表观遗传因素。
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0098
Mohsen Hesami, Marco Pepe, Ben Spitzer-Rimon, Milad Eskandari, Andrew Maxwell Phineas Jones
{"title":"Epigenetic factors related to recalcitrance in plant biotechnology.","authors":"Mohsen Hesami, Marco Pepe, Ben Spitzer-Rimon, Milad Eskandari, Andrew Maxwell Phineas Jones","doi":"10.1139/gen-2024-0098","DOIUrl":"10.1139/gen-2024-0098","url":null,"abstract":"<p><p>This review explores the challenges and potential solutions in plant micropropagation and biotechnology. While these techniques have proven successful for many species, certain plants or tissues are recalcitrant and do not respond as desired, limiting the application of these technologies due to unattainable or minimal in vitro regeneration rates. Indeed, traditional in vitro culture techniques may fail to induce organogenesis or somatic embryogenesis in some plants, leading to classification as in vitro recalcitrance. This paper focuses on recalcitrance to somatic embryogenesis due to its promise for regenerating juvenile propagules and applications in biotechnology. Specifically, this paper will focus on epigenetic factors that regulate recalcitrance as understanding them may help overcome these barriers. Transformation recalcitrance is also addressed, with strategies proposed to improve transformation frequency. The paper concludes with a review of CRISPR-mediated genome editing's potential in modifying somatic embryogenesis-related epigenetic status and strategies for addressing transformation recalcitrance.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-11"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The current regulatory status of biotechnologically bred crops in Canada and beyond. 目前在加拿大和其他国家的生物技术育种作物的监管状况。
IF 1.7 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0008
Stacy D Singer, Dominique Michaud
{"title":"The current regulatory status of biotechnologically bred crops in Canada and beyond.","authors":"Stacy D Singer, Dominique Michaud","doi":"10.1139/gen-2025-0008","DOIUrl":"https://doi.org/10.1139/gen-2025-0008","url":null,"abstract":"<p><p>Crop breeding, which relies on the presence and/or generation of alterations in DNA, has been essential to the development of agricultural production. Such breeding endeavours are carried out using a wide range of methods, which have diversified immensely over the years as our understanding of genetics has grown. While this expansion in our breeding \"toolbox\" has provided vast improvements in the specificity, pace and effectiveness of crop trait enhancement, apprehension surrounding the use of biotechnological breeding platforms in particular led countries to develop costly and lengthy regulatory processes for plants deemed to be \"genetically modified\" as a means of managing safety concerns and assuaging public unease. In this article, we discuss crop regulatory policies in Canada and beyond, in the context of transgenic crops, as well as those developed using newer biotechnological breeding platforms such as gene editing. We also examine the benefits of biotechnologically bred crops, and consider the broader socio-economic, ethical, and environmental impacts of overly restrictive regulatory frameworks, which could very feasibly limit the prospect of food security in the future.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-13"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144951669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic insights: integrating DNA barcoding with taxonomy in the study of Baccaurea (Phyllanthaceae). 遗传见解:整合DNA条形码与分类学在百兰科巴氏菌研究中的应用。
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0105
Lee Hong Tnah, Nuri Rasli Ahmad-Farhan, Alias Nur-Nabilah, Pei Sin Soo, Zakaria Hazwani-Humaira', Kevin Kit Siong Ng, Chai Ting Lee, Chin Hong Ng, Soon Leong Lee
{"title":"Genetic insights: integrating DNA barcoding with taxonomy in the study of <i>Baccaurea</i> (Phyllanthaceae).","authors":"Lee Hong Tnah, Nuri Rasli Ahmad-Farhan, Alias Nur-Nabilah, Pei Sin Soo, Zakaria Hazwani-Humaira', Kevin Kit Siong Ng, Chai Ting Lee, Chin Hong Ng, Soon Leong Lee","doi":"10.1139/gen-2024-0105","DOIUrl":"https://doi.org/10.1139/gen-2024-0105","url":null,"abstract":"<p><p>Traditional taxonomic revisions based on macromorphological and leaf anatomical traits may have limitations in accurately distinguishing certain species within the genus. To improve taxonomic clarity, this study applied DNA barcoding to enhance the understanding of the taxonomy and phylogeny of <i>Baccaurea</i> Lour., a plant genus widely utilized for food, medicine, and building materials. DNA barcode regions, including <i>rbc</i>L, ITS2, and <i>trn</i>H-<i>psb</i>A, were used to analyze 64 samples representing 19 <i>Baccaurea</i> species. Using similarity Basic Local Alignment Search Tool and phylogenetic tree inference, we determined the discriminatory efficiencies of <i>rbc</i>L, ITS2, <i>trn</i>H<i>-ps</i>bA, and their combinations <i>rbc</i>L + ITS2 and <i>rbc</i>L + ITS2 + <i>trn</i>H-<i>psb</i>A as 21.1%, 89.5%, 87.5%, 89.5%, and 89.5%, respectively. The Neighbor-Joining tree revealed well-defined, monophyletic species clusters that largely align with phylogenetic positions based on macromorphological features. Notably, our results indicate that <i>Baccaurea parviflora</i> and the synonymized <i>Baccaurea scortechinii</i> are distinct species, recommending the re-establishment of <i>B. scortechinii</i> as a separate species. DNA barcoding is useful in delineating species boundaries, facilitating routine specimen identification, and flagging atypical samples for detailed examination.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-7"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparative and phylogenetic analysis of Platycarya longipes and related species based on the complete chloroplast genomes. 基于叶绿体全基因组的长形枣树及其近缘种的比较与系统发育分析。
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0126
Shuang Wang, Shuanggui Geng, Xiaoshuang Wang, Li Wang, Qiuying Li, Enrong Lu, Xiang Zhang, Zhongcheng Peng, Gaoyin Wu, Yingliang Liu
{"title":"Comparative and phylogenetic analysis of <i>Platycarya longipes</i> and related species based on the complete chloroplast genomes.","authors":"Shuang Wang, Shuanggui Geng, Xiaoshuang Wang, Li Wang, Qiuying Li, Enrong Lu, Xiang Zhang, Zhongcheng Peng, Gaoyin Wu, Yingliang Liu","doi":"10.1139/gen-2024-0126","DOIUrl":"https://doi.org/10.1139/gen-2024-0126","url":null,"abstract":"<p><p><i>Platycarya longipes</i> is a dominant tree species in karst forests. Due to limited genomic information, its exact phylogenetic position within the family Juglandaceae remains unclear. In this study, the complete chloroplast genome (cp genome) of <i>Platycarya longipes</i> was de novo assembled using Illumina reads. This circular cp genome was 158 592 bp in length, consisting of an 88 066 bp large single-copy region, an 18 524 bp small single-copy region, and a total of 26 001 bp derived from a pair of inverted repeats (IRa and IRb), with an average GC content of 36.15%. It accommodated a total of 113 genes, including 80 protein-coding genes, 29 tRNAs, and 4 rRNAs. Additionally, within the genome, 49 long repeats and 66 simple sequence repeats, which could be utilized as molecular markers, were identified. In comparison to the related <i>Platycarya strobilacea</i>, the K<sub>a</sub>/K<sub>s</sub> substitution rate values of <i>Platycarya</i> <i>longipes</i> exhibited significant divergence, supporting the differentiation between the species. The conserved gene order and structure of the <i>Platycarya longipes</i> cp genome compared to other Juglandaceae members. Phylogenetic analysis using maximum likelihood and Bayesian inference methods with Fagales genomes showed a close relationship between <i>Platycarya longipes</i> and <i>Platycarya strobilacea</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-12"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Whole genome sequencing and analysis of benzo(a)pyrene-degrading bacteria Bacillus cereus M72-4. 全基因组测序和苯并(a)芘降解细菌蜡样芽孢杆菌 M72-4 的分析。
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0114
Aofei Jin, Dilbar Tursun, Lirong Tan, Zhuonan Yang, Zhixian Duo, Yanan Qin, Rui Zhang
{"title":"Whole genome sequencing and analysis of benzo(a)pyrene-degrading bacteria <i>Bacillus cereus</i> M72-4.","authors":"Aofei Jin, Dilbar Tursun, Lirong Tan, Zhuonan Yang, Zhixian Duo, Yanan Qin, Rui Zhang","doi":"10.1139/gen-2024-0114","DOIUrl":"10.1139/gen-2024-0114","url":null,"abstract":"<p><p>Benzo(a)pyrene produced by food during high-temperature process enters the body through ingestion, which causes food safety issues to the human body. To alleviate the harm of foodborne benzo(a)pyrene to human health, a strain that can degrade benzo(a)pyrene was screened from Kefir, a traditional fermented product in Xinjiang. <i>Bacillus cereus</i> M72-4 is a Gram-positive bacteria sourced from Xinjiang traditional fermented product Kefir; under benzo(a)pyrene stress conditions, there was 69.39% degradation rate of 20 mg/L benzo(a)pyrene by strain M72-4 after incubation for 72 h. The whole genome of M72-4 was sequenced using PacBio sequencing technology in this study. The genome size was 5754 801 bp and a GC content was 35.24%; a total of 5719 coding genes were predicted bioinformatically. Through functional database annotation, it was found that the strain has a total of 219 genes involved in the transportation and metabolism of hydrocarbons, a total of 9 metabolic pathways related to the degradation and metabolism of exogenous substances, and a total of 67 coding genes. According to the Kyoto Encyclopedia of Genes and Genomes database annotation results, a key enzyme related to benzo(a)pyrene degradation, catechol 2,3-dioxygenase, was detected in the genome data of <i>Bacillus cereus</i> M72-4, encoding genes <i>dmpB</i> and <i>xylE</i>, respectively. There are also monooxygenases and dehydrogenases. Therefore, it can be inferred that this strain mainly degrades benzo(a)pyrene through benzoate metabolic.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-9"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (Eleocharis, Cyperaceae). 穗花杉(Eleocharis,茜草科)全中心染色体中 satDNA 分布的不同模式。
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 Epub Date: 2024-09-16 DOI: 10.1139/gen-2024-0089
Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Luís Laforga Vanzela
{"title":"Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (<i>Eleocharis</i>, Cyperaceae).","authors":"Thaíssa Boldieri de Souza, Letícia Maria Parteka, Yi-Tzu Kuo, Thiago Nascimento, Veit Schubert, Andrea Pedrosa-Harand, André Marques, Andreas Houben, André Luís Laforga Vanzela","doi":"10.1139/gen-2024-0089","DOIUrl":"10.1139/gen-2024-0089","url":null,"abstract":"<p><p><i>Eleocharis</i> R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. High intra- and interspecific variations in chromosome numbers and genome sizes are documented for different <i>Eleocharis</i> species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in this genus. In our study, we confirmed the holocentricity of <i>Eleocharis</i> chromosomes by immunostaining against the kinetochore protein KNL1 and the cell-cycle dependent posttranslational modifications histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in the newly sequenced species <i>Eleocharis maculosa, Eleocharis</i> <i>geniculata, Eleocharis parodii, Eleocharis elegans</i>, and <i>Eleocharis</i> <i>montana</i>. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was distributed irregularly along the chromatid length in a line-like manner. EmaSAT14 monomers were present in a few copies in few species across the <i>Eleocharis</i> phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus <i>Eleocharis</i>. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142284426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular characterization and chromosomal distribution of Tc1/mariner transposons in Boana species (Anura, Hylidae). Boana物种(无尾目,水螅科)Tc1/mariner转座子的分子特征和染色体分布
IF 2.3 3区 生物学
Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0004
Sebastião Venancio Neto, Matheus Azambuja, Viviane Demetrio Nascimento, Viviane Nogaroto, Marcelo Ricardo Vicari, Rafael Bueno Noleto
{"title":"Molecular characterization and chromosomal distribution of <i>Tc1/mariner</i> transposons in <i>Boana</i> species (Anura, Hylidae).","authors":"Sebastião Venancio Neto, Matheus Azambuja, Viviane Demetrio Nascimento, Viviane Nogaroto, Marcelo Ricardo Vicari, Rafael Bueno Noleto","doi":"10.1139/gen-2025-0004","DOIUrl":"10.1139/gen-2025-0004","url":null,"abstract":"<p><p>Transposable elements play an important role in determining the size and structure of eukaryotic genomes. Represented by several families, the <i>Tc1/mariner</i> superfamily is widely distributed in animal and plant genomes, and its structure has been characterized. <i>Boana</i> is a Neotropical genus of treefrogs, and despite the frequent 2<i>n</i> = 24 chromosomes found in its representatives, the karyotypic organization of the species cannot be considered conserved due to the scarcity of studies focusing on chromosomal mapping of repetitive DNA sequences. Here, <i>Tc1/mariner</i> elements were isolated and mapped on the chromosomes of three <i>Boana</i> species, followed by structural and phylogenetic analysis. The physical mapping revealed dispersed signals in euchromatin with small accumulations in some heterochromatic regions. All <i>Tc1</i>/<i>mariner</i> transposons isolated in this study presented high sequence integrity, suggesting that these elements had a recent invasion phase and are active in the host genomes of these frog species. <i>Boana albopuntata</i> and <i>Boana faber</i> presented a DD36E signature, while <i>Boana prasina</i> showed a new DD37E signature with a similar organizational structure and a close relationship with the known DD36E/<i>Incomer</i> family. These findings improve our understanding of the diversity of <i>Tc1</i>/<i>mariner</i> transposons and their role in the evolution of the hylid frog genome and karyotype.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-9"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analysis of the winter oilseed rape recombination landscape suggests maternal-paternal bias. 对冬季油菜基因重组情况的分析表明,母本与父本之间存在偏差。
IF 2.3 3区 生物学
Genome Pub Date : 2024-12-01 Epub Date: 2024-10-21 DOI: 10.1139/gen-2023-0110
Nayyer Abdollahi Sisi, Eva Herzog, Amine Abbadi, Rod J Snowdon, Agnieszka A Golicz
{"title":"Analysis of the winter oilseed rape recombination landscape suggests maternal-paternal bias.","authors":"Nayyer Abdollahi Sisi, Eva Herzog, Amine Abbadi, Rod J Snowdon, Agnieszka A Golicz","doi":"10.1139/gen-2023-0110","DOIUrl":"10.1139/gen-2023-0110","url":null,"abstract":"<p><p>Recombination, the reciprocal exchange of DNA between homologous chromosomes, is a mandatory step necessary for meiosis progression. Crossovers between homologous chromosomes generate new combinations of alleles and maintain genetic diversity. Due to genetic, epigenetic, and environmental factors, the recombination landscape is highly heterogeneous along the chromosomes and it also differs between populations and between sexes. Here, we investigated recombination characteristics across the 19 chromosomes of the model allopolyploid crop species oilseed rape (<i>Brassica napus</i> L.), using two unique multiparental populations derived from two genetically divergent founder pools, each of which comprised 50 genetically diverse founder accessions. A fully balanced, pairwise chain-crossing scheme was utilized to create each of the two populations. A total of 3213 individuals, spanning five successive generations, were genotyped using a 15K SNP array. We observed uneven distribution of recombination along chromosomes, with some genomic regions undergoing substantially more frequent recombination in both populations. In both populations, maternal recombination events were more frequent than paternal recombination. This study provides unique insight into the recombination landscape at chromosomal level and reveals a maternal-paternal bias for recombination number with implications for breeding.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"445-453"},"PeriodicalIF":2.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mapping of quantitative trait loci (QTL) in Brassica napus L. for tolerance to water stress. 绘制甘蓝型油菜对水分胁迫耐受性的数量性状位点(QTL)图。
IF 2.3 3区 生物学
Genome Pub Date : 2024-12-01 Epub Date: 2024-10-17 DOI: 10.1139/gen-2023-0127
Samadhi B Jayarathna, Harmeet S Chawla, Mohammed M Mira, Robert W Duncan, Claudio Stasolla
{"title":"Mapping of quantitative trait loci (QTL) in <i>Brassica napus</i> L. for tolerance to water stress.","authors":"Samadhi B Jayarathna, Harmeet S Chawla, Mohammed M Mira, Robert W Duncan, Claudio Stasolla","doi":"10.1139/gen-2023-0127","DOIUrl":"10.1139/gen-2023-0127","url":null,"abstract":"<p><p><i>Brassica napus</i> L. plants are sensitive to water stress conditions throughout their life cycle from seed germination to seed setting. This study aims at identifying quantitative trait loci (QTL) linked to <i>B. napus</i> tolerance to water stress mimicked by applications of 10% polyethylene glycol-6000 (PEG-6000). Two doubled haploid populations, each consisting of 150 genotypes, were used for this research. Plants at the two true leaf stage of development were grown in the absence (control) or presence (stress) of PEG-6000 under controlled environmental conditions for 48 h, and the drought stress index was calculated for each genotype. All genotypes, along with their parents, were genotyped using the Brassica Infinium 90K SNP BeadChip Array. Inclusive composite interval mapping was used to identify QTL. Six QTL and 12 putative QTL associated with water stress tolerance were identified across six chromosomes (A2, A3, A4, A9, C3, and C7). Collectively, 2154 candidate genes for water stress tolerance were identified for all the identified QTL. Among them, 213 genes were identified as being directly associated with water stress (imposed by PEG-6000) tolerance based on nine functional annotations. These results can be incorporated into future breeding initiatives to select plant material with the ability to cope effectively with water stress.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"482-492"},"PeriodicalIF":2.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Heat shock responsive genes in Brassicaceae: genome-wide identification, phylogeny, and evolutionary associations within and between genera. 十字花科植物的热休克反应基因:全基因组鉴定、系统发育以及属内和属间的进化关联。
IF 2.3 3区 生物学
Genome Pub Date : 2024-12-01 Epub Date: 2024-10-16 DOI: 10.1139/gen-2024-0061
Aldrin Y Cantila, Sheng Chen, Kadambot H M Siddique, Wallace A Cowling
{"title":"Heat shock responsive genes in Brassicaceae: genome-wide identification, phylogeny, and evolutionary associations within and between genera.","authors":"Aldrin Y Cantila, Sheng Chen, Kadambot H M Siddique, Wallace A Cowling","doi":"10.1139/gen-2024-0061","DOIUrl":"10.1139/gen-2024-0061","url":null,"abstract":"<p><p>Heat stress affects the growth and development of Brassicaceae crops. Plant breeders aim to mitigate the effects of heat stress by selecting for heat stress tolerance, but the genes responsible for heat stress in Brassicaceae remain largely unknown. During heat stress, heat shock proteins (HSPs) function as molecular chaperones to aid in protein folding, and heat shock transcription factors (HSFs) serve as transcriptional regulators of HSP expression. We identified 5002 heat shock related genes, including HSPs and HSFs, across 32 genomes in Brassicaceae. Among these, 3347 genes were duplicated, with segmented duplication primarily contributing to their expansion. We identified 466 physical gene clusters, including 240 homogenous clusters and 226 heterogeneous clusters, shedding light on the organization of heat shock related genes. Notably, 37 genes were co-located with published thermotolerance quantitative trait loci, which supports their functional role in conferring heat stress tolerance. This study provides a comprehensive resource for the identification of functional Brassicaceae heat shock related genes, elucidates their clustering and duplication patterns and establishes the genomic foundation for future heat tolerance research. We hypothesise that genetic variants in HSP and HSF genes in certain species have potential for improving heat stress tolerance in Brassicaceae crops.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"464-481"},"PeriodicalIF":2.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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