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Identification of bHLH transcription factors and screening of anthocyanin-related genes in Lagerstroemia indica. 鉴定 Lagerstroemia indica 中的 bHLH 转录因子并筛选花青素相关基因。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-12-01 Epub Date: 2024-10-04 DOI: 10.1007/s10709-024-00215-2
Mengxin Yu, Mingzhu Bai, Mengmeng Chen, Guozhe Zhang, Yu Zhao, Qingqing Ma, Liyuan Yang, Cuihua Gu
{"title":"Identification of bHLH transcription factors and screening of anthocyanin-related genes in Lagerstroemia indica.","authors":"Mengxin Yu, Mingzhu Bai, Mengmeng Chen, Guozhe Zhang, Yu Zhao, Qingqing Ma, Liyuan Yang, Cuihua Gu","doi":"10.1007/s10709-024-00215-2","DOIUrl":"10.1007/s10709-024-00215-2","url":null,"abstract":"<p><p>The basic helix-loop-helix (bHLH) family is one of the three major transcription factor families that play important transcriptional regulatory roles in plant growth and development. One of the most crucial elements in defining Lagerstroemia indica's decorative qualities is flower color. However, the function of the bHLH transcription factor family in L. indica anthocyanin glycoside synthesis has not been clarified. Using the transcriptome data of flower color, 79 LibHLH genes were found in this study. Phylogenetic analysis showed that the LibHLH genes can be divided into 16 subfamilies, and most of the genes in the same subfamily have similar conserved motifs. The total anthocyanin glycoside content of L. indica 'Zihua Guifei' petals was determined during three developmental stages of the petals' growth. The results showed that the total anthocyanin glycoside content grew gradually with growth and development, and that it accumulated most during the full bloom stage. By using gene expression analysis, protein interaction network analysis, and bioinformatics, it was possible to determine which member of the III f family, LibHLH29, is important for the synthesis of anthocyanin glycosides in L. indica. Its expression was confirmed by qRT-PCR, and the results were essentially compatible with the transcriptome data. It was more prominent in the light-colored bloom stage the color-transition stage of L. indica 'Zihua Guifei'. It can be further investigated as a major candidate gene for regulating anthocyanin glycoside synthesis in L. indica, thus laying the foundation for an in-depth study of the interactions among transcription factors.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373609","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
Systematic analysis of the ARF gene family in Fagopyrum dibotrys and its potential roles in stress tolerance. 对 Fagopyrum dibotrys 的 ARF 基因家族及其在抗逆性中的潜在作用进行系统分析。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-12-01 Epub Date: 2024-10-04 DOI: 10.1007/s10709-024-00214-3
Ying Liu, Nan Ma, Ziyong Gao, Yangguang Hua, Yu Cao, Dengpan Yin, Qiaojun Jia, Dekai Wang
{"title":"Systematic analysis of the ARF gene family in Fagopyrum dibotrys and its potential roles in stress tolerance.","authors":"Ying Liu, Nan Ma, Ziyong Gao, Yangguang Hua, Yu Cao, Dengpan Yin, Qiaojun Jia, Dekai Wang","doi":"10.1007/s10709-024-00214-3","DOIUrl":"10.1007/s10709-024-00214-3","url":null,"abstract":"<p><p>The auxin response factor (ARF) is a plant-specific transcription factor that regulates the expression of auxin response genes by binding directly to their promoters. They play an important role in the regulation of plant growth and development, as well as in the response to biotic and abiotic stresses. However, the identification and functional analysis of ARFs in Fagopyrum dibotrys are still unclear. In this study, a total of 26 FdARF genes were identified using bioinformatic methods. Their chromosomal location, gene structure, physical and chemical properties of their encoded protein, subcellular location, phylogenetic tree, conserved motifs and cis-acting elements in FdARF promoters were analyzed. The results showed that 26 FdARF genes were unevenly distributed on 8 chromosomes, with the largest distribution on chromosome 4 and the least distribution on chromosome 3. Most FdARF proteins are located in the nucleus, except for the proteins FdARF7 and FdARF21 located to the cytoplasm and nucleus, while FdARF14, FdARF16, and FdARF25 proteins are located outside the chloroplast and nucleus. According to phylogenetic analysis, 26 FdARF genes were divided into 6 subgroups. Duplication analysis indicates that the expansion of the FdARF gene family was derived from segmental duplication rather than tandem duplication. The prediction based on cis-elements of the promoter showed that 26 FdARF genes were rich in multiple stress response elements, suggesting that FdARFs may be involved in the response to abiotic stress. Expression profiling analysis showed that most of the FdARF genes were expressed in the roots, stems, leaves, and tubers of F. dibotrys, but their expression exhibits a certain degree of tissue specificity. qRT-PCR analysis revealed that most members of the FdARF gene were up- or down-regulated in response to abiotic stress. The results of this study expand our understanding of the functional role of FdARFs in response to abiotic stress and lay a theoretical foundation for further exploration of other functions of FdARF genes.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373610","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
A "poly-matter network" conception of biological inheritance. 生物遗传的 "多物质网络 "概念。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-12-01 Epub Date: 2024-10-19 DOI: 10.1007/s10709-024-00216-1
Günter A Müller, Timo D Müller
{"title":"A \"poly-matter network\" conception of biological inheritance.","authors":"Günter A Müller, Timo D Müller","doi":"10.1007/s10709-024-00216-1","DOIUrl":"10.1007/s10709-024-00216-1","url":null,"abstract":"<p><p>Here we intend to shift the \"DNA- and information-centric\" conception of biological inheritance, with the accompanying exclusion of any non-DNA matter, to a \"poly-matter network\" framework which, in addition to DNA, considers the action of other cellular membranous constituents. These cellular structures, in particular organelles and plasma membranes, express \"landscapes\" of specific topologies at their surfaces, which may become altered in response to certain environmental factors. These so-called \"membranous environmental landscapes\" (MELs), which replicate by self-organization / autopoiesis rather than self-assembly, are transferred from donor to acceptor cells by various - vesicular and non-vesicular - mechanisms and exert novel features in the acceptor cells. The \"DNA-centric\" conception may be certainly explanatorily sufficient for the transfer of heritable phenotype variation to acceptor cells following the copying of DNA in donor cells and thereby for the phenomenon of biological inheritance of traits. However, it is not causally sufficient. With the observation of phenotype variation, as initially manifested during bacterial transformation, the impact of environmental factors, such as nutrition and stress, in the differential regulation of gene expression has been widely accepted and resulted in intense efforts to resolve the underlying epigenetic mechanisms. However, these are explained under a conceptual frame where the DNA (and associated proteins) are the only matter of inheritance. In contrast, it is our argumentation that inheritance can only be adequately understood as the transfer of DNA in concert with non-DNA matter in a \"poly-matter network\" conception. The adequate inclusion of the transfer of non-DNA matter is still a desideratum of future genetic research, which may pave the way for the experimental elucidation not only of how DNA and membrane matter act in concert to enable the inheritance of innate traits, but also whether they interact for that of acquired biological traits. Moreover, the \"poly-matter network\" conception may open new perspectives for an understanding of the pathogenesis of \"common complex\" diseases.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481366","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
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":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"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":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"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":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"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
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":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"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":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"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
A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus. 脆弱淡水鲑鱼(Thymallus ligericus)的多组织从头转录组组装和相对基因表达。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-06-01 Epub Date: 2024-06-18 DOI: 10.1007/s10709-024-00210-7
Giulia Secci-Petretto, Steven Weiss, André Gomes-Dos-Santos, Henri Persat, André M Machado, Inês Vasconcelos, L Filipe C Castro, Elsa Froufe
{"title":"A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus.","authors":"Giulia Secci-Petretto, Steven Weiss, André Gomes-Dos-Santos, Henri Persat, André M Machado, Inês Vasconcelos, L Filipe C Castro, Elsa Froufe","doi":"10.1007/s10709-024-00210-7","DOIUrl":"10.1007/s10709-024-00210-7","url":null,"abstract":"<p><p>Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11199216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141421935","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
Comparative genomic analysis reveals expansion of the DnaJ gene family in Lagerstroemia indica and its members response to salt stress. 比较基因组分析揭示了 Lagerstroemia indica 中 DnaJ 基因家族的扩展及其成员对盐胁迫的响应。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-06-01 Epub Date: 2024-05-10 DOI: 10.1007/s10709-024-00208-1
Jin Qin, Xiaoyu Hou, Huanzhe Wang, Tianyi Yuan, Hui Wei, Guoyuan Liu, Yanhong Chen, Bolin Lian, Fei Zhong, Jian Zhang, Chunmei Yu
{"title":"Comparative genomic analysis reveals expansion of the DnaJ gene family in Lagerstroemia indica and its members response to salt stress.","authors":"Jin Qin, Xiaoyu Hou, Huanzhe Wang, Tianyi Yuan, Hui Wei, Guoyuan Liu, Yanhong Chen, Bolin Lian, Fei Zhong, Jian Zhang, Chunmei Yu","doi":"10.1007/s10709-024-00208-1","DOIUrl":"10.1007/s10709-024-00208-1","url":null,"abstract":"<p><p>DnaJs/Hsp40s/JPDs are obligate co-chaperones of heat shock proteins (Hsp70), performing crucial biological functions within organisms. A comparative genome analysis of four genomes (Vitis vinifera, Eucalyptus grandis, Lagerstroemia indica, and Punica granatum) revealed that the DnaJ gene family in L. indica has undergone expansion, although not to the extent observed in P. granatum. Inter-genome collinearity analysis of four plants indicates that members belonging to Class A and B are more conserved during evolution. In L. indica, the expanded members primarily belong to Class-C. Tissue expression patterns and the biochemical characterization of LiDnaJs further suggested that DnaJs may be involved in numerous biological processes in L. indica. Transcriptome and qPCR analyses of salt stressed leaves identified at least ten LiDnaJs that responded to salt stress. In summary, we have elucidated the expansion mechanism of the LiDnaJs, which is attributed to a recent whole-genome triplication. This research laid the foundation for functional analysis of LiDnaJs and provides gene resources for breeding salt-tolerant varieties of L. indica.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900425","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}
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