Genome最新文献

筛选
英文 中文
Genes influencing deposition of melanin in breast muscle of the Xuefeng black bone chicken based on bioinformatic analysis. 影响雪峰黑骨鸡胸肌黑色素沉积的基因生物信息学分析
IF 3.1 3区 生物学
Genome Pub Date : 2023-08-01 DOI: 10.1139/gen-2022-0090
Mingming Xu, Shengguo Tang, Xu Liu, Yuying Deng, Changqing He, Songchang Guo, Xiangyong Qu
{"title":"Genes influencing deposition of melanin in breast muscle of the Xuefeng black bone chicken based on bioinformatic analysis.","authors":"Mingming Xu,&nbsp;Shengguo Tang,&nbsp;Xu Liu,&nbsp;Yuying Deng,&nbsp;Changqing He,&nbsp;Songchang Guo,&nbsp;Xiangyong Qu","doi":"10.1139/gen-2022-0090","DOIUrl":"https://doi.org/10.1139/gen-2022-0090","url":null,"abstract":"<p><p>The Xuefeng black bone chicken (XFBC) represents an important poultry genetic resource. However, the darkness in breast muscle is heterogeneous. The molecular genetic mechanisms underlying melanogenesis of breast muscle in XFBC remains unclear. This study used RNA-seq to compare the difference in transcriptome between hyperpigmentation and hypopigmentation of breast muscle. Six cDNA libraries were constructed for hyperpigmentation and hypopigmentation groups in XFBC. We identified 395 differently expressed genes (DEGs) between hyperpigmentation and hypopigmentation group (<i>P</i> < 0.05, |log<sub>2</sub>FC|≥1). Gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated several differentially enriched biological functions and pathways involved in melanogenesis of the breast muscle. Gene set enrichment analysis (GSEA) GO analysis identified two significant gene sets, including the pathways of pigment metabolic process and transmembrane receptor protein tyrosine kinase activity. GSEA-KEGG analysis identified the process of tyrosine metabolism and several genes related with melanogenesis in breast muscle of the XFBC. The protein-protein interaction network was constructed and eight genes were clustered in the module. We identified nine hub genes, including <i>TYR, TYRP1, DCT, GPR143, MLANA, SLC24A5, GPNMB, MLPH</i>, and <i>EDNRB2</i>. Taken together, the DEGs and hub genes identified in the study provide a solid basis for the study of the genetic regulatory mechanisms involved the melanogenesis in the breast muscle of the XFBC.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 8","pages":"212-223"},"PeriodicalIF":3.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9913590","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: 1
Broad histone H4 monomethylation marks expressed genes involved in translation. 广泛的组蛋白H4单甲基化标记表达参与翻译的基因。
IF 3.1 3区 生物学
Genome Pub Date : 2023-08-01 Epub Date: 2023-05-08 DOI: 10.1139/gen-2023-0011
Narges Fatemiyan, James R Davie
{"title":"Broad histone H4 monomethylation marks expressed genes involved in translation.","authors":"Narges Fatemiyan,&nbsp;James R Davie","doi":"10.1139/gen-2023-0011","DOIUrl":"10.1139/gen-2023-0011","url":null,"abstract":"<p><p>H4K20me1 (histone H4 monomethylated at lysine 20) generally has a broad distribution along genes and has been reported to be associated with expressed and repressed genes. In contrast, H3K4me3 (histone H3 trimethylated at lysine 4) is positioned as a narrow peak at the 5' end of most expressed genes in vertebrate cells. A small population of genes involved in cell identity has H3K4me3 distributed throughout the gene body. In this report, we show that H4K20me1 is associated with expressed genes in estrogen receptor-positive breast cancer MCF7 cells and erythroleukemic K562 cells. Further, we identified the genes with the broadest H4K20me1 domains in these two cell types. The broad H4K20me1 domain marked gene bodies of expressed genes, but not the promoter or enhancer regions. The most significant GO term (biological processes) of these genes was cytoplasmic translation. There was little overlap between the genes marked with the broad H4K20me1 domain and those marked with H3K4me3. H4K20me1 and H3K79me2 distributions along expressed gene bodies were similar, suggesting a relationship between the enzymes catalyzing these histone modifications.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 8","pages":"224-234"},"PeriodicalIF":3.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9891857","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: 1
Genomics-based taxonomy to clarify cannabis classification. 以基因组学为基础的分类学阐明大麻的分类。
IF 3.1 3区 生物学
Genome Pub Date : 2023-08-01 DOI: 10.1139/gen-2023-0005
Éliana Lapierre, Adrian S Monthony, Davoud Torkamaneh
{"title":"Genomics-based taxonomy to clarify cannabis classification.","authors":"Éliana Lapierre,&nbsp;Adrian S Monthony,&nbsp;Davoud Torkamaneh","doi":"10.1139/gen-2023-0005","DOIUrl":"https://doi.org/10.1139/gen-2023-0005","url":null,"abstract":"<p><p>In the 18th century, Carolus Linnaeus created a formalized system of classification of living organisms based on their anatomic relationships, which we know as taxonomic nomenclature. Historically, the genus <i>Cannabis</i> has been described three ways under this system: <i>Cannabis sativa</i> by C. Linnaeus in 1753, <i>Cannabis indica</i> by J.B. Lamarck in 1785, and <i>Cannabis ruderalis</i> by D.E. Janischewsky in 1924, with these taxonomic classifications having been derived from physical, morphological, chemical, and geographical data. Today, this confusing taxonomy has led to an ongoing debate about whether the genus <i>Cannabis</i> consists of a single species or multiple distinct species or subspecies. Recently, genome sequencing and bioinformatics have provided greater resolution of taxonomic assignments at the species level. As a result, some previously discussed classification frameworks have been brought into question. The aim of this review is to provide a historical context for the confusion surrounding the taxonomy of the genus <i>Cannabis</i> and highlight recent research on genomics-based taxonomical approaches to clarify the question of <i>Cannabis</i> taxonomy. We suggest that the latest evidence shifts away from the previous multiple species framework and points towards the genus <i>Cannabis</i> consisting of a highly diverse monotypic species.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 8","pages":"202-211"},"PeriodicalIF":3.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9955007","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: 3
High-density linkage maps detail sex-specific regions of suppressed recombination near fusions of polymorphic chromosomes in purebred and hybrid North American Atlantic salmon (Salmo salar L.). 高密度连锁图谱详细描述了纯种和杂交北美大西洋鲑鱼(Salmo salar L.)多态性染色体融合附近抑制重组的性别特异性区域。
IF 3.1 3区 生物学
Genome Pub Date : 2023-07-01 DOI: 10.1139/gen-2022-0065
Melissa Lm MacLeod-Bigley, Elizabeth G Boulding
{"title":"High-density linkage maps detail sex-specific regions of suppressed recombination near fusions of polymorphic chromosomes in purebred and hybrid North American Atlantic salmon (<i>Salmo salar</i> L.).","authors":"Melissa Lm MacLeod-Bigley,&nbsp;Elizabeth G Boulding","doi":"10.1139/gen-2022-0065","DOIUrl":"https://doi.org/10.1139/gen-2022-0065","url":null,"abstract":"<p><p>The North American (NA) Atlantic salmon typically has 27 pairs of chromosomes, whereas the European (EU) subspecies typically has 29. We investigated within-family recombination within three previously identified chromosome rearrangements (<i>Ssa</i>01p/23, <i>Ssa</i>08/29, and <i>Ssa</i>26/28) in NA Atlantic salmon by creating high-density linkage maps using a custom 50K SNP chip developed for the Saint John River aquaculture strain. Linkage maps created for individual purebred and EU hybrid parents in 10 full-sibling families averaged 14 337 SNPs per cross, covering 43 033 SNPs from the 50K SNP chip. Chromosomal translocation <i>Ssa</i>01p/23 was fixed except in one hybrid female map. In contrast, fusion <i>Ssa</i>08/29 was present in maps in 4 out of 10 females and 8 out of 10 males, whereas fusion <i>Ssa</i>26/28 was present in maps in 6 out of 10 females and 8 out of 10 males. The orientation of <i>Ssa</i>08/29 differed from the previous map; the short arm of the metacentric <i>Ssa</i>08 was fused to the centromere of the acrocentric <i>Ssa</i>29. We detected large regions of recombination suppression in female maps at the fusion of <i>Ssa</i>08 to <i>Ssa</i>29. This suppression may reduce the impacts of aneuploidy resulting from pairing of fused and unfused chromosomes, thereby allowing the persistence of chromosomal polymorphisms in this population.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 7","pages":"175-192"},"PeriodicalIF":3.1,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9730770","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
Cytogenetic characterization and karyotype evolution in six Macroptilium species (Leguminosae). 6种豆科植物的细胞遗传学特征及核型进化。
IF 3.1 3区 生物学
Genome Pub Date : 2023-07-01 DOI: 10.1139/gen-2022-0101
Daniela de Barros, Claudio Montenegro, Michelle Gomes, Maria Eduarda Ferraz, Silvia Teresinha Sfoggia Miotto, Andrea Pedrosa-Harand
{"title":"Cytogenetic characterization and karyotype evolution in six <i>Macroptilium</i> species (Leguminosae).","authors":"Daniela de Barros,&nbsp;Claudio Montenegro,&nbsp;Michelle Gomes,&nbsp;Maria Eduarda Ferraz,&nbsp;Silvia Teresinha Sfoggia Miotto,&nbsp;Andrea Pedrosa-Harand","doi":"10.1139/gen-2022-0101","DOIUrl":"https://doi.org/10.1139/gen-2022-0101","url":null,"abstract":"<p><p><i>Macroptilium</i> (Benth.) Urb. is a neotropical legume genus from the subtribe Phaseolinae. The investigated species present a stable chromosome number (2<i>n</i> = 22), but differ in their karyotype formulae, suggesting the presence of chromosome rearrangements. In this work, we comparatively analysed the karyotypes of six species (<i>Macroptilium atropurpureum, Macroptilium bracteatum, Macroptilium erythroloma, Macroptilium gracile, Macroptilium lathyroides</i>, and <i>Macroptilium martii</i>) from the two main clades that form the genus. Heterochromatin distribution was investigated with chromomycin A<sub>3</sub> (CMA)/4',6-diamidino-2-phenylindole (DAPI) staining and fluorescent in situ hybridization was used to localize the 5S and 35S ribosomal DNA (rDNA) sites. Single copy bacterial artificial chromosomes (BACs) previously mapped in the related genera <i>Phaseolus</i> L. and <i>Vigna</i> Savi were used to establish chromosome orthologies and to investigate possible rearrangements among species. CMA<sup>+</sup>/DAPI<sup>-</sup> bands were observed, mostly associated with rDNA sites. Additional weak, pericentromeric bands were observed on several chromosomes. Although karyotypes were similar, species could be differentiated mainly by the number and position of the 5S and 35S rDNA sites. BAC markers demonstrated conserved synteny of the main rDNA sites on orthologous chromosomes 6 and 10, as previously observed for <i>Phaseolus</i> and <i>Vigna</i>. The karyotypes of the six species could be differentiated, shedding light on its karyotype evolution.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 7","pages":"165-174"},"PeriodicalIF":3.1,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9731304","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
Patterns of genome size evolution versus fraction of repetitive elements in statu nascendi species: the case of the willistoni subgroup of Drosophila (Diptera, Drosophilidae). 新生物种基因组大小进化模式与重复元件的比例:以果蝇的willistoni亚群为例(双翅目,果蝇科)。
IF 3.1 3区 生物学
Genome Pub Date : 2023-07-01 DOI: 10.1139/gen-2022-0073
Henrique R M Antoniolli, Maríndia Deprá, Vera L S Valente
{"title":"Patterns of genome size evolution versus fraction of repetitive elements in <i>statu nascendi</i> species: the case of the <i>willistoni</i> subgroup of <i>Drosophila</i> (Diptera, Drosophilidae).","authors":"Henrique R M Antoniolli,&nbsp;Maríndia Deprá,&nbsp;Vera L S Valente","doi":"10.1139/gen-2022-0073","DOIUrl":"https://doi.org/10.1139/gen-2022-0073","url":null,"abstract":"<p><p>Genome size evolution is known to be related with transposable elements, yet such relation in incipient species remains poorly understood. For decades, the <i>willistoni</i> subgroup of <i>Drosophila</i> has been a model for evolutionary studies because of the different evolutionary stages and degrees of reproductive isolation its species present. Our main question here was how speciation influences genome size evolution and the fraction of repetitive elements, with a focus on transposable elements. We quantitatively compared the mobilome of four species and two subspecies belonging to this subgroup with their genome size, and performed comparative phylogenetic analyses. Our results showed that genome size and the fraction of repetitive elements evolved according to the evolutionary history of these species, but the content of transposable elements showed some discrepancies. Signals of recent transposition events were detected for different superfamilies. Their low genomic GC content suggests that in these species transposable element mobilization might be facilitated by relaxed natural selection. Additionally, a possible role of the superfamily DNA/<i>TcMar-Tigger</i> in the expansion of these genomes was also detected. We hypothesize that the undergoing process of speciation could be promoting the observed increase in the fraction of repetitive elements and, consequently, genome size.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 7","pages":"193-201"},"PeriodicalIF":3.1,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9733212","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: 1
Isolation, characterisation, and expression profiling of DXS and DXR genes in Atractylodes lancea. 苍术DXS和DXR基因的分离、鉴定及表达谱分析。
IF 3.1 3区 生物学
Genome Pub Date : 2023-06-01 DOI: 10.1139/gen-2022-0084
Rui Xu, Junxian Wu, Yazhong Zhang, Lu Jiang, Jinchen Yao, Liangping Zha, Jin Xie
{"title":"Isolation, characterisation, and expression profiling of <i>DXS</i> and <i>DXR</i> genes in <i>Atractylodes lancea</i>.","authors":"Rui Xu,&nbsp;Junxian Wu,&nbsp;Yazhong Zhang,&nbsp;Lu Jiang,&nbsp;Jinchen Yao,&nbsp;Liangping Zha,&nbsp;Jin Xie","doi":"10.1139/gen-2022-0084","DOIUrl":"https://doi.org/10.1139/gen-2022-0084","url":null,"abstract":"<p><p>1-Deoxy-d-xylulose-5-phosphate synthase and 1-deoxy-d-xylulose-5-phosphate reductoismerase are considered two key enzymes in the 2-<i>C</i>-methyl-d-erythritol-4-phosphate pathway of terpenoid biosynthesis and are related to the synthesis and accumulation of sesquiterpenoids. We cloned two <i>DXS</i> and <i>DXR</i> genes from <i>Atractylodes lancea</i> and analysed their expression in different tissues and in response to methyl jasmonate (MeJA). Subcellular localisation analysis revealed that the AlDXS and AlDXR1 proteins are located in the chloroplasts and cytoplasm, whereas AlDXR2 is only located in the chloroplasts. pET-AlDXS-28a and pGEX-AlDXR-4T-1 were expressed in <i>Escherichia coli</i> BL21(DE3) and BL21, respectively. Based on the abiotic stress analysis, the growth rate of the recombinant pGEX-AlDXR-4T-1 was higher than that of the control in HCl and NaOH. <i>AlDXS</i> exhibited the highest expression level in rhizomes of <i>A. lancea</i> from Hubei but was highest in leaves from Henan. In contrast, <i>AlDXR</i> showed maximum expression in the leaves of <i>A. lancea</i> from Hubei and Henan. Moreover, <i>DXS</i> and <i>DXR</i> gene expression, enzyme activities, and antioxidant enzyme activities oscillated in response to MeJA, with expression peaks appearing at different time points. Our findings indicated that the characterisation and function of <i>AlDXS</i> and <i>AlDXR</i> could be useful for further elucidating the functions of <i>DXR</i> and <i>DXR</i> genes in <i>A. lancea</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 6","pages":"150-164"},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9557221","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
Transposable elements in the transcriptome of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). 蚕豆毛虫(antiarsia gemmatalis h<e:1> bner)转录组的转座因子分析(鳞翅目:蚕豆科)。
IF 3.1 3区 生物学
Genome Pub Date : 2023-06-01 DOI: 10.1139/gen-2022-0066
Larissa Forim Pezenti, Jaqueline Fernanda Dionisio, Daniel Ricardo Sosa-Gómez, Rogério Fernandes de Souza, Renata da Rosa
{"title":"Transposable elements in the transcriptome of the velvetbean caterpillar <i>Anticarsia gemmatalis</i> Hübner, 1818 (Lepidoptera: Erebidae).","authors":"Larissa Forim Pezenti,&nbsp;Jaqueline Fernanda Dionisio,&nbsp;Daniel Ricardo Sosa-Gómez,&nbsp;Rogério Fernandes de Souza,&nbsp;Renata da Rosa","doi":"10.1139/gen-2022-0066","DOIUrl":"https://doi.org/10.1139/gen-2022-0066","url":null,"abstract":"<p><p>Transposable elements (TEs) are DNA sequences that possess the ability to move from one genomic location to another. These sequences contribute to a significant fraction of the genomes of most eukaryotes and can impact their architecture and regulation. In this paper, we present the first data related to the identification and characterization of TEs present in the transcriptome of <i>Anticarsia gemmatalis.</i> Approximately, 835 transcripts showed significant similarity to TEs and (or) characteristic domains. Retrotransposons accounted for 71.2% (595 sequences) of the identified elements, while DNA transposons were less abundant, with 240 annotations (28.8%). TEs were classified into 30 superfamilies, with <i>SINE3/5S</i> and <i>Gypsy</i> being the most abundant. Based on the sequences of TEs found in the transcriptome, we were able to locate conserved regions in the chromosomes of this species. The analysis of differential expression of TEs in susceptible and resistant strains, challenged and not challenged with <i>Bacillus thuringiensis</i> (<i>Bt</i>) from in silico analysis, indicated that exposure to <i>Bt</i> can regulate the transcription of mobile genetic elements in the velvetbean caterpillar. Thus, these data contribute significantly to the knowledge of the structure and composition of these elements in the genome of this species, and suggest the role of stress on their expression.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 6","pages":"116-130"},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9559328","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
Paenibacillus terrae NK3-4 regulates the transcription of growth-related and stress resistance-related genes in rice. 地芽孢杆菌NK3-4调控水稻生长相关和抗逆性相关基因的转录。
IF 3.1 3区 生物学
Genome Pub Date : 2023-06-01 DOI: 10.1139/gen-2022-0072
Wen Zhi Liu, Ze Yu Li, Cheng Liu, Xi Tao Yu, Wen Qing Yu, Peng Li
{"title":"<i>Paenibacillus terrae</i> NK3-4 regulates the transcription of growth-related and stress resistance-related genes in rice.","authors":"Wen Zhi Liu,&nbsp;Ze Yu Li,&nbsp;Cheng Liu,&nbsp;Xi Tao Yu,&nbsp;Wen Qing Yu,&nbsp;Peng Li","doi":"10.1139/gen-2022-0072","DOIUrl":"https://doi.org/10.1139/gen-2022-0072","url":null,"abstract":"<p><p><i>Paenibacillus terrae</i> NK3-4 is a plant growth-promoting rhizobacterium. In this study, the effects of NK3-4 on rice growth and gene transcription were determined. The results indicated that a seed soaking treatment and a pre-germination seed treatment using NK3-4 promoted rice growth, especially spraying rice seedlings with NK3-4 increased the root number and root length by 34.2% and 34.1%, respectively. Moreover, NK3-4 induced the differential transcription of genes annotated with gene ontology (GO) terms; the number of up-regulated genes was 4.38-times higher than the number of down-regulated genes. The NK3-4 treatment induced the differential transcription of genes in 1794 GO functional groups, with 1531 functional groups containing up-regulated genes. Specific growth-related genes up-regulated by NK3-4 are involved in biological processes, including responses to auxin, hormone biosynthesis, cellular component biogenesis, root system development, and other functions. Furthermore, stress resistance-related genes were up-regulated, some of which encode WRKYs, NPK1-related protein kinase, NPR1-like 4, CaM-like proteins, MYBs, ERFs, TIFYs, NACs, EL5s, PR1s, PR2, PR8, PODs, and PAD4. Considered together, these findings imply that NK3-4 may promote plant growth and enhance stress resistance by regulating gene expression, making it a potentially useful microbe for regulating rice growth and stress resistance.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 6","pages":"131-149"},"PeriodicalIF":3.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9562424","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
Identification and expression analysis of C2H2-zinc finger protein genes reveals their role in stress tolerance in Brassica napus. c2h2 -锌指蛋白基因的鉴定与表达分析揭示了c2h2 -锌指蛋白基因在甘蓝型油菜逆境抗性中的作用。
IF 3.1 3区 生物学
Genome Pub Date : 2023-05-01 DOI: 10.1139/gen-2022-0100
Kawalpreet Kaur, Swati Megha, Zhengping Wang, Nat N V Kav, Habibur Rahman
{"title":"Identification and expression analysis of C2H2-zinc finger protein genes reveals their role in stress tolerance in <i>Brassica napus</i>.","authors":"Kawalpreet Kaur,&nbsp;Swati Megha,&nbsp;Zhengping Wang,&nbsp;Nat N V Kav,&nbsp;Habibur Rahman","doi":"10.1139/gen-2022-0100","DOIUrl":"https://doi.org/10.1139/gen-2022-0100","url":null,"abstract":"<p><p>C2H2-zinc finger (C2H2-ZF) genes are involved in various biological processes in plants including stress response; however, they lack characterization in <i>Brassica napus</i>. We identified 267 C2H2-ZF genes in <i>B. napus</i> and deciphered their physiological properties, subcellular localization, structure, synteny, and phylogeny and investigated the expression of 20 genes in response to different stresses and phytohormone treatments. The 267 genes were distributed on 19 chromosomes; phylogenetic analysis categorized them into five clades. They varied from 0.41 to 9.2 kb in length, had stress-responsive <i>cis</i>-acting elements in promoter regions, and their protein length varied from 9 to 1366 amino acids. About 42% of the genes had one exon, and 88% genes had orthologs in <i>Arabidopsis thaliana</i>. About 97% of the genes were located in nucleus and 3% in cytoplasmic organelles. qRT-PCR analysis showed a different expression pattern of these genes in response to biotic stresses (<i>Plasmodiophora brassicae</i> and <i>Sclerotinia sclerotiorum</i>) and abiotic stresses (cold, drought, and salinity) and hormonal treatments. Differential expression of the same gene was observed under multiple stress conditions, and a few genes showed similar expression in response to more than one phytohormones. Our results suggest that the C2H2-ZF genes can be targeted for the improvement of stress tolerance in canola.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 5","pages":"91-107"},"PeriodicalIF":3.1,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9438684","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: 2
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信