scholarly journals Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 730 ◽  
Author(s):  
Sun ◽  
Wang ◽  
Ma ◽  
Li ◽  
Liu
Keyword(s):  
Somatic Embryogenesis ◽  
Upland Cotton ◽  
Expression Profiles ◽  
Gene Families ◽  
Early Response ◽  
Auxin Signaling ◽  
Evolutionary Divergence ◽  
Genome Wide ◽  
A Genome ◽  
Early Response Genes

Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.

scholarly journals Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

2019 ◽  
Author(s):  
Zheng Liu ◽  
Xiao-Xia Ge ◽  
Xiao-Meng Wu ◽  
Wen-Wu Guo
Keyword(s):  
Somatic Embryogenesis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
In Vitro Regeneration ◽  
Gene Families ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionary Features

Abstract Background In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few of B3 transcription factors are reported to regulate embryogenesis, little is known about the possible roles of B3 superfamily during SE especially in citrus. Results In this study, a total of 72 (CsB3) and 69 (CgB3) putative B3 superfamily members were identified in the sweet orange (Citrus sinensis) and pummelo (C. grandis) genomes, respectively, each comprised four gene families and 14 phylogenetic classes. The B3 genes were unevenly distributed over citrus chromosomes and other non-anchored scaffolds. Genome duplication analysis indicated that the segmental and tandem duplication events have significantly contributed to the expansion of the citrus B3 superfamily. The evolutionary relationships among the B3 family members and their putative functions were deduced based on the results of phylogenetic analysis. Furthermore, transcriptomic analysis showed that citrus B3 genes have differential expression levels in various tissues, suggesting distinct biological roles of different members. Expression analysis revealed that the B3 superfamily members showed four types of expression profiles during SE in citrus and may play functional roles during SE, especially at late SE stages. Of them, CsARF19 is specifically expressed in sweet orange and at markedly higher levels in the embryogenic callus (EC), implying its possible involvement in EC initiation. Conclusions This study provides a genome-wide analysis of citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, which contributes to a better understanding of the B3 genes in citrus and their association with SE.

scholarly journals Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

2020 ◽  
Author(s):  
Zheng Liu ◽  
Xiao-Xia Ge ◽  
Xiao-Meng Wu ◽  
Qiang Xu ◽  
Ross G. Atkinson ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionary Features ◽  
Duplication Events

Abstract Background: In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogenesis, little is known about the B3 superfamily in citrus, and which members might be involved in SE.Results: Genome-wide sequence analysis identified 72 (CsB3) and 69 (CgB3) putative B3 superfamily members in the genomes of sweet orange (Citrus sinensis, polyembryonic) and pummelo (C. grandis, monoembryonic), respectively. Genome duplication analysis indicated that segmental and tandem duplication events contributed to the expansion of the B3 superfamily in citrus, and that the B3 superfamily evolved under the effect of purifying selection. Phylogenetic relationships were well supported by conserved gene structure and motifs outside the B3 domain, which allowed possible functions to be inferred by comparison with homologous genes from Arabidopsis. Expression analysis identified 23 B3 superfamily members that were expressed during SE in citrus and 17 that may play functional roles at late SE stages. Eight B3 genes were identified that were specific to the genome of polyembryonic sweet orange compared to monoembryonic pummelo. Of these eight B3 genes, CsARF19 was found to be specifically expressed at higher levels in embryogenic callus (EC), implying its possible involvement in EC initiation. Conclusions: This study provides a genome-wide analysis of the citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, and identifies specific family members that may be associated with SE.

scholarly journals Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

2020 ◽  
Author(s):  
Muhammad Zulfiqar Ahmad ◽  
Xiangsheng Zeng ◽  
Qiang Dong ◽  
Sehrish Manan ◽  
Huanan Jin ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Expression Profiles ◽  
Plant Defence ◽  
Constitutive Expression ◽  
Gene Families ◽  
Strong Positive Selection ◽  
Genome Wide ◽  
A Genome ◽  
Bahd Acyltransferase

Abstract Background: Members of the BAHD acyltransferase (ACT) family play important roles in plant defence against biotic and abiotic stresses. Previous genome-wide studies explored different acyltransferase gene families, but not a single study was found so far on the overall genome-wide or positive selection analyses of the BAHD family genes in Glycine max . A better understanding of the functions that specific members of this family play in stress defence can lead to better breeding strategies for stress tolerance. Results: A total of 103 genes of the BAHD family (GmACT genes) were mined from the soybean genome, which could be grouped into four phylogenetic clades (I- IV). Clade III was further divided into two sub-clades (IIIA and IIIB). In each clade, the constituent part of the gene structures and motifs were relatively conserved. These 103 genes were distributed unequally on all 20 chromosomes, and 16 paralogous pairs were found within the family. Positive selection analysis revealed important amino acids under strong positive selection, which suggests that the evolution of this gene family modulated soybean domestication. Most of the expression of ACT genes in soybean was repressed with Al 3+ and fungal elicitor exposure, except for GmACT84 , which expression increased in these conditions 2- and 3-fold, respectively. The promoter region of GmACT84 contains the maximum number of stress-responsive elements among all GmACT genes and is especially enriched in MYB-related elements. Some GmACT genes showed expression specific under specific conditions, while others showed constitutive expression in all soybean tissues or conditions analysed. Conclusions: This study provided a genome-wide analysis of the BAHD gene family and assessed their expression profiles. We found evidence of a strong positive selection of GmACT genes. Our findings will help efforts of functional characterisation of ACT genes in soybean in order to discover their involvement in growth, development, and defence mechanisms.

scholarly journals Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhenming Yu ◽  
Guihua Zhang ◽  
Jaime A. Teixeira da Silva ◽  
Mingzhi Li ◽  
Conghui Zhao ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Dna Methyltransferase ◽  
Epigenetic Modification ◽  
Expression Profiles ◽  
Gene Families ◽  
Seedling Stage ◽  
Dendrobium Officinale ◽  
Integrated Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background DNA methylation is a conserved and important epigenetic modification involved in the regulation of numerous biological processes, including plant development, secondary metabolism, and response to stresses. However, no information is available regarding the identification of cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes in the orchid Dendrobium officinale. Results In this study, we performed a genome-wide analysis of DoC5-MTase and DodMTase gene families in D. officinale. Integrated analysis of conserved motifs, gene structures and phylogenetic analysis showed that eight DoC5-MTases were divided into four subfamilies (DoCMT, DoDNMT, DoDRM, DoMET) while three DodMTases were divided into two subfamilies (DoDML3, DoROS1). Multiple cis-acting elements, especially stress-responsive and hormone-responsive ones, were found in the promoter region of DoC5-MTase and DodMTase genes. Furthermore, we investigated the expression profiles of DoC5-MTase and DodMTase in 10 different tissues, as well as their transcript abundance under abiotic stresses (cold and drought) and at the seedling stage, in protocorm-like bodies, shoots, and plantlets. Interestingly, most DoC5-MTases were downregulated whereas DodMTases were upregulated by cold stress. At the seedling stage, DoC5-MTase expression decreased as growth proceeded, but DodMTase expression increased. Conclusions These results provide a basis for elucidating the role of DoC5-MTase and DodMTase in secondary metabolite production and responses to abiotic stresses in D. officinale.

scholarly journals Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

2019 ◽  
Author(s):  
Zheng Liu ◽  
Xiao-Xia Ge ◽  
Xiao-Meng Wu ◽  
Ross G. Atkinson ◽  
Wen-Wu Guo
Keyword(s):  
Somatic Embryogenesis ◽  
Sweet Orange ◽  
Expression Profiles ◽  
In Vitro Regeneration ◽  
Purifying Selection ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionary Features

Abstract Background In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogenesis, little is known about the B3 superfamily in citrus, and which members might be involved in SE.Results Genome-wide sequence analysis identified 72 ( CsB3 ) and 69 ( CgB3 ) putative B3 superfamily members in the genomes of sweet orange ( Citrus sinensis , polyembryonic) and pummelo ( C. grandis , monoembryonic), respectively. Genome duplication analysis indicated that segmental and tandem duplication events contributed to the expansion of the B3 superfamily in citrus, and that the B3 superfamily evolved under the effect of purifying selection. Phylogenetic relationships were well supported by conserved gene structure and motifs outside the B3 domain, which allowed possible functions to be inferred by comparison with homologous genes from Arabidopsis . Expression analysis identified 23 B3 superfamily members that were expressed during SE in citrus and 17 that may play functional roles at late SE stages. Eight B3 genes were identified that were specific to the genome of polyembryonic sweet orange compared to monoembryonic pummelo. Of these eight, CsARF19 was found to be specifically expressed at higher levels in embryogenic callus (EC), implying its possible involvement in EC initiation.Conclusions This study provides a genome-wide analysis of the citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, and identifies specific family members that may be associated with SE.

scholarly journals Genome-wide identification of ZIP gene family members in wheat

2019 ◽  
Author(s):  
Song Li ◽  
ZiHui Liu ◽  
Linlin Guo ◽  
Hongjie Li ◽  
Xiaojun Nie ◽  
...  
Keyword(s):  
Essential Gene ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Reference Sequence ◽  
Protein Structure Analysis ◽  
Transporter Family ◽  
Genome Wide ◽  
A Genome ◽  
Zip Family

Abstract Background: The plant ZIP (Zn-regulated, iron-regulated transporter-like protein) transporter family is one of the most essential gene families regulating the uptake, transport and accumulation of microelements, which play important roles in plant growth, development and biofortification. Although the ZIP family has been systematically studied in many plant species, the significance of this family in wheat is not well understood at present. Results: Through a genome-wide search based on the latest wheat reference sequence (IWGSC_V1.1), 58 TaZIP genes were identified. Most of these genes were represented by two to three homoalleles, which were named TaZIP_-A, TaZIP_-B, TaZIP_-D, Protein structure analysis revealed that most TaZIP proteins contain more than six transmembrane (TM) domains and that the distance between TM-3 and TM-4 is variable. Furthermore, the TaZIP proteins clustered into four groups in a phylogenetic tree, and the proteins belonging to the same group shared similar exon-intron structures and conserved motifs. Expression pattern analysis revealed that most TaZIP genes were significantly highly expressed in root, and that nine TaZIP genes were up-regulated at the grain filling stage. When exposed to ZnSO4 and FeCl 3 solutions, TaZIP genes showed different expression patterns, and 16 TaZIP genes were identified as candidate high-affinity Zn transporter genes and 23 as low-affinity Zn transporter genes. Finally, using yeast complementation analysis three TaZIP genes were demonstrated to have the capacity to transport Zn and Fe.Conclusion: This study systematically analyzed the genomic organization, gene structures and expression profiles of TaZIPs. The findings not only provide candidates for further functional analysis, but also contribute to a better understanding of the regulatory roles of ZIPs in wheat.

scholarly journals Genome-wide gene expression changes in postpartum depression point towards an altered immune landscape

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Divya Mehta ◽  
Karen Grewen ◽  
Brenda Pearson ◽  
Shivangi Wani ◽  
Leanne Wallace ◽  
...  
Keyword(s):  
Gene Expression ◽  
Depressive Symptoms ◽  
Postpartum Depression ◽  
Expression Profiles ◽  
Depression Scale ◽  
Well Being ◽  
Health Concern ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Gene Expression

AbstractMaternal postpartum depression (PPD) is a significant public health concern due to the severe negative impact on maternal and child health and well-being. In this study, we aimed to identify genes associated with PPD. To do this, we investigated genome-wide gene expression profiles of pregnant women during their third trimester of pregnancy and tested the association of gene expression with perinatal depressive symptoms. A total of 137 women from a cohort from the University of North Carolina, USA were assessed. The main phenotypes analysed were Edinburgh Postnatal Depression Scale (EPDS) scores at 2 months postpartum and PPD (binary yes/no) based on an EPDS cutoff of 10. Illumina NextSeq500/550 transcriptomic sequencing from whole blood was analysed using the edgeR package. We identified 71 genes significantly associated with postpartum depression scores at 2 months, after correction for multiple testing at 5% FDR. These included several interesting candidates including TNFRSF17, previously reported to be significantly upregulated in women with PPD and MMP8, a matrix metalloproteinase gene, associated with depression in a genome-wide association study. Functional annotation of differentially expressed genes revealed an enrichment of immune response-related biological processes. Additional analysis of genes associated with changes in depressive symptoms from recruitment to 2 months postpartum identified 66 genes significant at an FDR of 5%. Of these genes, 33 genes were also associated with depressive symptoms at 2 months postpartum. Comparing the results with previous studies, we observed that 15.4% of genes associated with PPD in this study overlapped with 700 core maternal genes that showed significant gene expression changes across multiple brain regions (P = 7.9e-05) and 29–53% of the genes were also associated with estradiol changes in a pharmacological model of depression (P values range = 1.2e-4–2.1e-14). In conclusion, we identified novel genes and validated genes previously associated with oestrogen sensitivity in PPD. These results point towards the role of an altered immune transcriptomic landscape as a vulnerability factor for PPD.

scholarly journals Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11

2021 ◽  
Vol 22 (11) ◽  
pp. 5798
Author(s):  
Shoko Tokumoto ◽  
Yugo Miyata ◽  
Ruslan Deviatiiarov ◽  
Takahiro G. Yamada ◽  
Yusuke Hiki ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Desiccation Tolerance ◽  
Expression Profiles ◽  
Insect Cell Line ◽  
Gene Expression Profiles ◽  
Late Embryogenesis Abundant ◽  
Heat Shock Factor 1 ◽  
Genome Wide ◽  
A Genome

The Pv11, an insect cell line established from the midge Polypedilum vanderplanki, is capable of extreme hypometabolic desiccation tolerance, so-called anhydrobiosis. We previously discovered that heat shock factor 1 (HSF1) contributes to the acquisition of desiccation tolerance by Pv11 cells, but the mechanistic details have yet to be elucidated. Here, by analyzing the gene expression profiles of newly established HSF1-knockout and -rescue cell lines, we show that HSF1 has a genome-wide effect on gene regulation in Pv11. The HSF1-knockout cells exhibit a reduced desiccation survival rate, but this is completely restored in HSF1-rescue cells. By comparing mRNA profiles of the two cell lines, we reveal that HSF1 induces anhydrobiosis-related genes, especially genes encoding late embryogenesis abundant proteins and thioredoxins, but represses a group of genes involved in basal cellular processes, thus promoting an extreme hypometabolism state in the cell. In addition, HSF1 binding motifs are enriched in the promoters of anhydrobiosis-related genes and we demonstrate binding of HSF1 to these promoters by ChIP-qPCR. Thus, HSF1 directly regulates the transcription of anhydrobiosis-related genes and consequently plays a pivotal role in the induction of anhydrobiotic ability in Pv11 cells.

scholarly journals Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10617
Author(s):  
Jie Li ◽  
Xinhao Liu ◽  
Qingmei Wang ◽  
Junyan Sun ◽  
Dexian He
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Seed Formation ◽  
Aphid Infestation ◽  
Genome Wide ◽  
A Genome ◽  
Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

scholarly journals Genome-wide identification and analysis of the CNGC gene family in maize

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5816 ◽  
Author(s):  
Lidong Hao ◽  
Xiuli Qiao
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Gene Families ◽  
Regulatory Elements ◽  
Vital Role ◽  
Signal Pathways ◽  
Cis Acting ◽  
Genome Wide ◽  
Gramineous Plant ◽  
Gated Channel

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

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