Genetica最新文献_第3页

Comparative assessment of genotyping-by-sequencing and whole-exome sequencing for estimating genetic diversity and geographic structure in small sample sizes: insights from wild jaguar populations. 基因分型测序和全外显子组测序在估算小样本量遗传多样性和地理结构方面的比较评估：野生美洲虎种群的启示。

IF 1.3 4区生物学

Genetica Pub Date : 2024-12-01 Epub Date: 2024-09-26 DOI: 10.1007/s10709-024-00212-5

Gustavo P Lorenzana, Henrique V Figueiró, Luiz L Coutinho, Priscilla M S Villela, Eduardo Eizirik

{"title":"Comparative assessment of genotyping-by-sequencing and whole-exome sequencing for estimating genetic diversity and geographic structure in small sample sizes: insights from wild jaguar populations.","authors":"Gustavo P Lorenzana, Henrique V Figueiró, Luiz L Coutinho, Priscilla M S Villela, Eduardo Eizirik","doi":"10.1007/s10709-024-00212-5","DOIUrl":"10.1007/s10709-024-00212-5","url":null,"abstract":"Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"133-144"},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Genome-wide identification and data mining reveals major-latex protein (MLP) from the PR-10 protein family played defense-related roles against phytopathogenic challenges in cassava (Manihot esculenta Crantz). 通过全基因组鉴定和数据挖掘发现，PR-10 蛋白家族中的主要乳胶蛋白（MLP）在木薯（Manihot esculenta Crantz）的植物病原挑战中发挥着防御作用。

IF 1.3 4区生物学

Genetica Pub Date : 2024-12-01 Epub Date: 2024-08-31 DOI: 10.1007/s10709-024-00211-6

Unchera Viboonjun, Rawit Longsaward

{"title":"Genome-wide identification and data mining reveals major-latex protein (MLP) from the PR-10 protein family played defense-related roles against phytopathogenic challenges in cassava (Manihot esculenta Crantz).","authors":"Unchera Viboonjun, Rawit Longsaward","doi":"10.1007/s10709-024-00211-6","DOIUrl":"10.1007/s10709-024-00211-6","url":null,"abstract":"Despite being identified in previous articles, the pathogenesis-related 10 (PR-10) protein remains relatively overlooked and has yet to be fully characterized in numerous plant species. This research employs a comprehensive data mining approach to in silico characterize PR-10 proteins in cassava, a vital crop plant globally. In this study, the focus was on in silico identified 53 cassava PR-10 proteins, which can be categorized into two main subgroups: 34 major latex proteins (MLPs) and 13 major allergen proteins, Pru ar 1, based on their phylogenetic relationship. The genome collinearity analysis with the rubber tree showed a possible evolutionary relationship of the PR-10 gene between these two Euphorbiaceae species, specifically on their chromosome 15. Notably, MLP423 and other MLP proteins were identified in various previously published cassava transcriptome datasets in response to biotic treatments from diverse phytopathogens, including anthracnose fungus, viruses, and bacterial blight. Ligand prediction and molecular docking of three MLP423 proteins have revealed potential interaction with cytokinin and abscisic acid hormones. Their expressions and predicted binding affinities are discussed here, highlighting their role as contributors to cassava's defense network against key diseases.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"145-158"},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Phylogenetic exploration, codon usage bias, and genomic divergence in Hydrocotyle: a comparative plastome study across different geographical locations. Hydrocotyle的系统发育探索、密码子使用偏差和基因组分歧：跨不同地理位置的质粒体比较研究。

IF 1.3 4区生物学

Genetica Pub Date : 2024-12-01 Epub Date: 2024-09-26 DOI: 10.1007/s10709-024-00213-4

Bimal K Chetri, Alok Senapati, Rahul G Shelke, Sudip Mitra, Latha Rangan

{"title":"Phylogenetic exploration, codon usage bias, and genomic divergence in Hydrocotyle: a comparative plastome study across different geographical locations.","authors":"Bimal K Chetri, Alok Senapati, Rahul G Shelke, Sudip Mitra, Latha Rangan","doi":"10.1007/s10709-024-00213-4","DOIUrl":"10.1007/s10709-024-00213-4","url":null,"abstract":"Hydrocotyle himalaica from Bhutan, a perennial herb that thrives from 1500 to 2600 m, possesses both ecological importance and medicinal properties. The plastome analysis revealed a length of 153,383 bp, showing variation from conspecific taxa in China. Its standard structure comprises two IR regions (18,336 bp IRa and 18,336 bp IRb), an LSC region of 97,944 bp, and an SSC region of 18,767 bp, with a GC content of 37.63%. Non-coding regions showed higher mutation susceptibility, with Pi values from 0.006 to 0.107. An AT-rich codon bias was consistent across all 18 Hydrocotyle species. Nucleotide composition and GC% in coding sequences differed among the species. The codon preference in Hydrocotyle is shaped by multiple factors, with natural selection being the primary influence, as indicated by the ENC-plot, PR2-plot, and Neutrality-plot. Codon usage patterns varied, with RSCU values from 0 to 2.23. Codons ending in A or U had RSCU > 1, while those ending in C or G had RSCU < 1. GC2 content surpassed GC3 and GC1 in most genes. The phylogenetic analysis placed H. himalaica, sourced from Kanglung, Bhutan, within the monophyly of the Hydrocotyloideae subfamily. However, the species showed weaker bootstrap support (BS < 50) with H. javanica and H. hookeri subsp., a deviation from a prior report on the same species from Jiangkou, Guizhou, China. This analysis highlighted the genomic characteristics and evolutionary relationships of H. himalaica from Bhutan, underscoring the need for a comprehensive phylogenetic, ecological, and botanical characterization to confirm intra-specific variation within Hydrocotyle species.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"199-209"},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Identifying hub genes and key functional modules in leaf tissue of Populus species based on WGCNA. 基于 WGCNA 确定杨树叶组织中的枢纽基因和关键功能模块。

IF 1.3 4区生物学

Genetica Pub Date : 2024-11-27 DOI: 10.1007/s10709-024-00222-3

Huanping Zhang, Tongming Yin

{"title":"Identifying hub genes and key functional modules in leaf tissue of Populus species based on WGCNA.","authors":"Huanping Zhang, Tongming Yin","doi":"10.1007/s10709-024-00222-3","DOIUrl":"https://doi.org/10.1007/s10709-024-00222-3","url":null,"abstract":"As one of the most important parts of plants, the genetic mechanisms of photosynthesis or the response of leaf to a single abiotic and biotic stress have been well studied. However, few researches have involved in the integration of data analysis from system level in leaf tissue under multiple abiotic stresses by utilizing biological networks. In this study, the weighted gene co-expression network analysis (WGCNA) strategy was used to integrate multiple data in leaf tissue of Populus species under different sample treatments. The gene co-expression networks were constructed and functional modules were identified by selecting the suitable soft threshold power β in the procedure of WGCNA. The identified hub genes and gene modules were annotated by agriGO, NetAffx Analysis Center, The Plant Genome Integrative Explorer (PlantGenIE) and other annotation tools. The annotation results have displayed that the highly correlated modules and hub genes are involved in the important biological processes or pathways related to module traits. The efficiency of the WGCNA strategy can generate comprehensive understanding of gene module-traits associations in leaf tissue, which will provide novel insight into the genetic mechanism of Populus species.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"5"},"PeriodicalIF":1.3,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142734777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Hidden diversity revealed by DNA barcoding of paralichthyidae fish along the caribbean and brazilian coast. 通过对加勒比和巴西沿岸的副鱼科鱼类进行 DNA 条形编码揭示隐藏的多样性。

IF 1.3 4区生物学

Genetica Pub Date : 2024-11-26 DOI: 10.1007/s10709-024-00221-4

Leandro A Argôlo, Robson T C Ramos, Jamille A Bitencourt, José Henrique Galdino, Iracilda Sampaio, Paulo R A M Affonso

{"title":"Hidden diversity revealed by DNA barcoding of paralichthyidae fish along the caribbean and brazilian coast.","authors":"Leandro A Argôlo, Robson T C Ramos, Jamille A Bitencourt, José Henrique Galdino, Iracilda Sampaio, Paulo R A M Affonso","doi":"10.1007/s10709-024-00221-4","DOIUrl":"10.1007/s10709-024-00221-4","url":null,"abstract":"DNA barcoding based on COI sequences has been highly informative for the taxonomic assessment of many fish species due to its high rate of species identification. Accordingly, numerous studies have employed this method to encompass species checklists of different areas, assessment of cryptic diversity, biodiversity monitoring, and other applications. Furthermore, most of the success of COI DNA barcoding relies on a comprehensive database (BOLD Systems) that holds sequences and detailed records of millions of species and applies a system (BIN) that clusters short DNA barcodes to generate OTUs. Besides COI, the 16S rDNA has proven to be suitable for the molecular identification of several taxa, and the combination of both markers could be advantageous in investigating species composition in the Neotropics. The family Paralichthyidae comprises over 60 flatfish species. Most of them inhabit tropical areas and remain understudied. Here, we evaluated the diversity of Paralichthyidae species along the Brazilian coast through COI and 16S DNA barcodes. Combining our dataset with BOLD (COI) and GenBank (16S) public records, we conducted tree-based and genetic distance analyses along with BIN-based and species delimitation methods. Our results were consistent for both markers, and we identified eight species of paralichthyids among our samples with high confidence. Interestingly, our analyses indicate several cases where public records assigned to the same species might be sequences from multiple species. Therefore, we provide new records and occurrences and explore important issues regarding misidentification and putative cryptic diversity for several species.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"4"},"PeriodicalIF":1.3,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Mitogenomics providing new insights into the phylogenetic structure of subfamily Panchaetothripinae (Thripidae: Terebrantia). 有丝分裂基因组学为 Panchaetothripinae 亚科（蓟马科：Terebrantia）的系统发育结构提供了新的见解。

IF 1.3 4区生物学

Genetica Pub Date : 2024-11-25 DOI: 10.1007/s10709-024-00218-z

Abhishek Ghosh, Kaomud Tyagi, Dhriti Banerjee, Vikas Kumar

{"title":"Mitogenomics providing new insights into the phylogenetic structure of subfamily Panchaetothripinae (Thripidae: Terebrantia).","authors":"Abhishek Ghosh, Kaomud Tyagi, Dhriti Banerjee, Vikas Kumar","doi":"10.1007/s10709-024-00218-z","DOIUrl":"https://doi.org/10.1007/s10709-024-00218-z","url":null,"abstract":"Complete mitochondrial genome of two species of subfamily Panchaetothripinae, Astrothrips tumiceps (16,467 bp) and Monilothrips kempi (14,773 bp) are generated by Next-Generation Sequencing Method. In this study, the detailed annotation of these mitogenomes as well as comparative analyses are carried out to explore the codon usage, gene composition, and phylogenetic relationship of subfamilies of family Thripidae. Moreover, the gene rearrangement of subfamily Panchaetothripinae of family Thripidae is also studied. Both the mitogenomes featured by 37 genes including 13 PCGs, 22 tRNAs, 2 rRNAs and with single putative control region with a positive AT-skew and negative GC-skew. trnS1 without DHU arm in both species, trnV without DHU arm in M. kempi, and trnE without TΨC loop in As. tumiceps. Further, codon based comparative analysis depicted the existence of natural selection pressure on all the PCGs in all the subfamilies of family Thripidae. The phylogenetic analyses, using the Bayesian inference (BI) and Maximum likelihood (ML) supported the monophyly of two suborders and family Phlaeothripidae. The family Thripidae is recovered as paraphyletic and subfamily Panchaetothripinae is in sister relationship with family Aeolothripidae and Stenurothripidae rather than the other subfamilies of family Thripidae. The gene order of the order Thysanoptera is highly rearranged, while few members of the subfamily Panchaetothripinae showed similar gene order to family Stenurothripidae. Therefore, this study suggests that the phylogenetic relationship between the subfamily Panchaetothripinae and other families is uncertain, necessitating a whole genome-based study to clarify the position of Panchaetothripinae within the suborder Terebrantia.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"3"},"PeriodicalIF":1.3,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Glutathione S-transferase TcGSTu1 contributes to defense against eucalyptol in Tribolium castaneum. 谷胱甘肽 S 转移酶 TcGSTu1 有助于蓖麻毛虫抵御桉叶油醇。

IF 1.3 4区生物学

Genetica Pub Date : 2024-11-23 DOI: 10.1007/s10709-024-00220-5

Shanshan Gao, Yizhuo Cao, Wenbo Miao, Dongyu Li, Can Zhou, Kunpeng Zhang

{"title":"Glutathione S-transferase TcGSTu1 contributes to defense against eucalyptol in Tribolium castaneum.","authors":"Shanshan Gao, Yizhuo Cao, Wenbo Miao, Dongyu Li, Can Zhou, Kunpeng Zhang","doi":"10.1007/s10709-024-00220-5","DOIUrl":"https://doi.org/10.1007/s10709-024-00220-5","url":null,"abstract":"Eucalyptol is one of the major insecticidal active ingredients in a variety of plant essential oils, and has good killing and avoidance effects on Tribolium castaneum. The presence of detoxifying enzymes glutathione S-transferase (GST) in T. castaneum makes it resistant to a variety of insecticides. However, whether GST is involved in regulating the sensitivity of eucalyptol by T. castaneum is not well understood. In our previous study, a glutathione S-transferase, TcGSTu1, was significantly up-regulated in RNA sequencing data when T. castaneum was exposed to eucalyptol. Therefore, in this study, the role of TcGSTu1 in the regulating the sensitivity of T. castaneum to eucalyptol was studied. The enzyme activities of GST and the transcription levels of TcGSTu1 were significantly increased following stimulation with eucalyptol. When using RNA interference technology knockdown TcGSTu1 heightens the sensitivity of T. castaneum to eucalyptol, demonstrating a link between TcGSTu1 and eucalyptol detoxification metabolism. Furthermore, TcGSTu1 is expressed in all developmental stages of T. castaneum, with higher expression levels observed particularly in the late egg stage. There was significant expression of TcGSTu1 in various tissues of different organisms, including larval head, fat body, and adult head. This observation indicated a possible connection between high TcGSTu1 expression and eucalyptol detoxification. The present findings suggest that TcGSTu1 may be involved in regulating the sensitivity and response of T. castaneum to treatment with eucalyptol, providing new research insight into pest control.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"2"},"PeriodicalIF":1.3,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Microsatellite based molecular characterization of Nattukuttai- a unique short statured Bos indicus cattle population of southern India. 基于微卫星的 Nattukuttai 分子特征研究--印度南部一个独特的短身材波士牛种群。

IF 1.3 4区生物学

Genetica Pub Date : 2024-11-15 DOI: 10.1007/s10709-024-00219-y

Ymberzal Koul, S M K Karthickeyan, P Hepsibha, C Jeevan, K Thilak Pon Jawahar, A Gopinathan

{"title":"Microsatellite based molecular characterization of Nattukuttai- a unique short statured Bos indicus cattle population of southern India.","authors":"Ymberzal Koul, S M K Karthickeyan, P Hepsibha, C Jeevan, K Thilak Pon Jawahar, A Gopinathan","doi":"10.1007/s10709-024-00219-y","DOIUrl":"10.1007/s10709-024-00219-y","url":null,"abstract":"Molecular characterization was conducted to characterise 'Nattukuttai', a native cattle population of the north-eastern agro-climatic zone of Tamil Nadu (India), using thirty microsatellite markers. The analyses revealed a high level of genetic diversity, with a total of 294 alleles observed across all the loci, averaging 9.8 alleles per locus. The allele sizes ranged from 83 bp to 302 bp, with frequencies ranging from 0.010 to 0.875. The microsatellite markers demonstrated high polymorphism, as indicated by an average polymorphic information content (PIC) of 0.763. Deviation from Hardy-Weinberg equilibrium was observed in a significant number of loci, indicating possible genetic influences such as selection or population structure. Bottleneck analysis suggested that the Nattukuttai population did not undergo any recent significant population contraction. Comparative analyses with three other cattle populations (Kangayam, Malai Madu, and Malnad Gidda) revealed varying genetic distances. Nattukuttai showed a distinct genetic profile, diverging from a common source that also gave rise to the Kangayam and Malai Madu clusters. Multivariate statistical analyses and phylogenetic reconstruction supported the genetic differentiation of Nattukuttai from the other populations, while Malai Madu and Kangayam were found to be genetically closer to each other. Overall, these findings provide insights into the genetic structure and relationships of the Nattukuttai cattle population, highlighting its distinct genetic identity and potential conservation significance.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"1"},"PeriodicalIF":1.3,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Identification and expression analysis of XIP gene family members in rice. 水稻中 XIP 基因家族成员的鉴定和表达分析

IF 1.3 4区生物学

Genetica Pub Date : 2024-06-01 Epub Date: 2024-05-14 DOI: 10.1007/s10709-024-00207-2

Manman Zhao, Zhiwei Liu, Jiangtao Gan, Chen Yang, Ai Lu, Qingqing Han, Haitao Yang, Yonghan Xu, Genlou Sun, Dechuan Wu

{"title":"Identification and expression analysis of XIP gene family members in rice.","authors":"Manman Zhao, Zhiwei Liu, Jiangtao Gan, Chen Yang, Ai Lu, Qingqing Han, Haitao Yang, Yonghan Xu, Genlou Sun, Dechuan Wu","doi":"10.1007/s10709-024-00207-2","DOIUrl":"10.1007/s10709-024-00207-2","url":null,"abstract":"Xylanase inhibitor proteins (XIP) are widely distributed in the plant kingdom, and also exist in rice. However, a systematic bioinformatics analysis of this gene family in rice (OsXIP) has not been conducted to date. In this study, we identified 32 members of the OsXIP gene family and analyzed their physicochemical properties, chromosomal localization, gene structure, protein structure, expression profiles, and interaction networks. Our results indicated that OsXIP genes exhibit an uneven distribution across eight rice chromosomes. These genes generally feature a low number of introns or are intronless, all family members, except for OsXIP20, contain two highly conserved motifs, namely Motif 8 and Motif 9. In addition, it is worth noting that the promoter regions of OsXIP gene family members feature a widespread presence of abscisic acid response elements (ABRE) and gibberellin response elements (GARE-motif and TATC-box). Quantitative Real-time PCR (qRT-PCR) analysis unveiled that the expression of OsXIP genes exhibited higher levels in leaves and roots, with considerable variation in the expression of each gene in these tissues both prior to and following treatments with abscisic acid (ABA) and gibberellin (GA3). Protein interaction studies and microRNA (miRNA) target prediction showed that OsXIP engages with key elements within the hormone-responsive and drought signaling pathways. The qRT-PCR suggested osa-miR2927 as a potential key regulator in the rice responding to drought stress, functioning as tissue-specific and temporally regulation. This study provides a theoretical foundation for further analysis of the functions within the OsXIP gene family.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"83-100"},"PeriodicalIF":1.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Genome-wide identification and expression analysis of the universal stress protein (USP) gene family in Arabidopsis thaliana, Zea mays, and Oryza sativa. 拟南芥、玉米和大豆中通用应激蛋白（USP）基因家族的全基因组鉴定和表达分析。

IF 1.3 4区生物学

Genetica Pub Date : 2024-06-01 Epub Date: 2024-05-24 DOI: 10.1007/s10709-024-00209-0

Mingxia Fan, Song Gao, Yating Yang, Shuang Yang, He Wang, Lei Shi

{"title":"Genome-wide identification and expression analysis of the universal stress protein (USP) gene family in Arabidopsis thaliana, Zea mays, and Oryza sativa.","authors":"Mingxia Fan, Song Gao, Yating Yang, Shuang Yang, He Wang, Lei Shi","doi":"10.1007/s10709-024-00209-0","DOIUrl":"10.1007/s10709-024-00209-0","url":null,"abstract":"The Universal Stress Protein (USP) primarily participates in cellular responses to biotic and abiotic stressors, playing a pivotal role in plant growth, development, and Stress responses to adverse environmental conditions. Totals of 23, 26 and 26 USP genes were recognized in Arabidopsis thaliana, Zea mays, and Oryza sativa, respectively. According to USP genes physicochemical properties, proteins from USP I class were identified as hydrophilic proteins with high stability. Based on phylogenetic analysis, USP genes family were classified into nine groups, USP II were rich in motifs. Additionally, members of the same subgroup exhibited similar numbers of introns/exons, and shared conserved domains, indicating close evolutionary relationships. Motif analysis results demonstrated a high degree of conservation among USP genes. Chromosomal distribution suggested that USP genes might have undergone gene expansion through segmental duplication in Arabidopsis thaliana, Zea mays, and Oryza sativa. Most Ka/Ks ratios were found to be less than 1, suggesting that USP genes in Arabidopsis thaliana, Zea mays, and Oryza sativa have experienced purifying selection. Expression profile analysis revealed that USP genes primarily respond to drought stress in Oryza sativa, temperature, and drought stress in Zea mays, and cold stress in Arabidopsis thaliana. Gene collinearity analysis can reveal correlations between genes, aiding subsequent in-depth investigations. This study sheds new light on the evolution of USP genes in monocots and dicots and lays the foundation for a better understanding of the biological functions of the USP genes family.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"119-132"},"PeriodicalIF":1.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141094672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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