IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2023-0099

Gurpreet S Kharey, Vince Palace, Lyle Whyte, Charles W Greer

{"title":"Pangenomic analysis of three putative hydrocarbon degrading genera Limnohabitans, Aquabacterium, and Novosphingobium collected from freshwater sources.","authors":"Gurpreet S Kharey, Vince Palace, Lyle Whyte, Charles W Greer","doi":"10.1139/gen-2023-0099","DOIUrl":"10.1139/gen-2023-0099","url":null,"abstract":"A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of three environmentally relevant genera, Limnohabitans, Aquabacterium, and Novosphingobium. These genera had been detected in hydrocarbon degrading cultures in previous research by our group. Using pangenomic tools we attempted to characterize the extent of hydrocarbon degradation potential within each pangenome and determine what ecological niche each genus occupies within hydrocarbon degradation. In total 46 Limnohabitans, 10 Aquabacterium, and 32 Novosphingobium freshwater genomes were collected from various databases and compiled into pangenomes. We found that each pangenome harbours downstream hydrocarbon degrading potential and unexpected genetic diversity within its core and accessory pangenomes possibly stemming from geographic and metagenomic data processing influences. This work was the first to explore pangenomes of these environmentally relevant genera.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016944","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

Note of appreciation. 表示感谢。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0172

引用次数: 0

Analysis of apoptosis levels and MMP7 gene expression in ovaries of postpartum female rabbits after long-term use of LHRH-A3. 长期使用LHRH-A3对产后雌兔卵巢细胞凋亡水平及MMP7基因表达的影响

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0146

Sen Wang, Fan Wang, Lei Wang, Zhiyuan Bao, Jiawei Cai, Bohao Zhao, Xinsheng Wu, Yang Chen

{"title":"Analysis of apoptosis levels and MMP7 gene expression in ovaries of postpartum female rabbits after long-term use of LHRH-A3.","authors":"Sen Wang, Fan Wang, Lei Wang, Zhiyuan Bao, Jiawei Cai, Bohao Zhao, Xinsheng Wu, Yang Chen","doi":"10.1139/gen-2024-0146","DOIUrl":"https://doi.org/10.1139/gen-2024-0146","url":null,"abstract":"Luteinizing hormone-releasing hormone A3 (LHRH-A3), a reproductive hormone analog, is widely used to stimulate ovulation in female rabbits. However, the long-term impact of sustained LHRH-A3 administration on the reproductive system, particularly ovarian health, remains unclear. In this study, we compared apoptosis levels in ovaries and molecular regulation between LHRH-A3-treated (A3 group) and untreated female rabbits (N group) after their 5th litter. Western blotting showed a significantly lower Bcl-2/Bax ratio in the A3 group compared with the N group (P < 0.01), indicating higher ovarian apoptosis. Ovarian tissues from four rabbits per group were divided into the A3 group and the N group, and RNA-seq technology was then utilized to conduct transcriptome analysis on these two groups. This analysis revealed 220 differentially expressed genes (DEGs), including BMP6, BMP15, CYP1A1, and other reproductive-related genes. KEGG analysis of these DEGs showed their involvement in processes such as the cell cycle, PI3K-Akt signaling pathway, and ovarian steroidogenesis. Subsequently, we selected the key gene Matrix metallopeptidase 7 (MMP7) for functional analysis using CCK8 and Annexin V-FITC/PI techniques. MMP7 was found to promote the proliferation of granulosa cells (GCs) and inhibit apoptosis (P < 0.01). In conclusion, LHRH-A3 treatment can modulate ovarian molecular regulation, with the key gene MMP7 involved in the proliferation and apoptosis of GCs.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-10"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143988490","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

Plant immune resilience to a changing climate: molecular insights and biotechnological roadmaps. 植物对气候变化的免疫复原力：分子见解和生物技术路线图。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-11-05 DOI: 10.1139/gen-2024-0088

Christian Danve M Castroverde, Chi Kuan, Jong Hum Kim

{"title":"Plant immune resilience to a changing climate: molecular insights and biotechnological roadmaps.","authors":"Christian Danve M Castroverde, Chi Kuan, Jong Hum Kim","doi":"10.1139/gen-2024-0088","DOIUrl":"10.1139/gen-2024-0088","url":null,"abstract":"Successful resistance to disease-causing pathogens is underpinned by properly regulated immune signalling and defence responses in plants. The plant immune system is controlled at multiple levels of gene and protein regulation-from chromatin-associated epigenetic processes to protein post-translational modifications. Optimal fine-tuning of plant immune signalling and responses is important to prevent plant disease development, which is being exacerbated by a globally changing climate. In this review, we focus on how changing climatic factors mechanistically intercept plant immunity at different levels of regulation (chromatin, transcriptional, post-transcriptional, translational, and post-translational). We specifically highlight recent studies that have provided molecular insights into critically important climate-sensitive nodes and mechanisms of the plant immune system. We then propose several potential future directions to build climate-resilient plant disease resistance using cutting-edge biotechnology. Overall, this conceptual understanding and promising biotechnological advances provide a foundational platform towards novel approaches to engineer plant immune resilience.","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":"142581766","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

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

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 Baccaurea (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":"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 Baccaurea Lour., a plant genus widely utilized for food, medicine, and building materials. DNA barcode regions, including rbcL, ITS2, and trnH-psbA, were used to analyze 64 samples representing 19 Baccaurea species. Using similarity Basic Local Alignment Search Tool and phylogenetic tree inference, we determined the discriminatory efficiencies of rbcL, ITS2, trnH-psbA, and their combinations rbcL + ITS2 and rbcL + ITS2 + trnH-psbA 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 Baccaurea parviflora and the synonymized Baccaurea scortechinii are distinct species, recommending the re-establishment of B. scortechinii as a separate species. DNA barcoding is useful in delineating species boundaries, facilitating routine specimen identification, and flagging atypical samples for detailed examination.","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 Platycarya longipes 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":"Platycarya longipes 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 Platycarya longipes 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 Platycarya strobilacea, the Ka/Ks substitution rate values of Platycarya longipes exhibited significant divergence, supporting the differentiation between the species. The conserved gene order and structure of the Platycarya longipes cp genome compared to other Juglandaceae members. Phylogenetic analysis using maximum likelihood and Bayesian inference methods with Fagales genomes showed a close relationship between Platycarya longipes and Platycarya strobilacea.","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 Bacillus cereus 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":"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. Bacillus cereus 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 Bacillus cereus M72-4, encoding genes dmpB and xylE, respectively. There are also monooxygenases and dehydrogenases. Therefore, it can be inferred that this strain mainly degrades benzo(a)pyrene through benzoate metabolic.","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 (Eleocharis, 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":"Eleocharis 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 Eleocharis 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 Eleocharis 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 Eleocharis maculosa, Eleocharis geniculata, Eleocharis parodii, Eleocharis elegans, and Eleocharis montana. 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 Eleocharis phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus Eleocharis. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.","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

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":"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 (Brassica napus 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.","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

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