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 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.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

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 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 Unravelling complex molecular mechanisms in pine with genome-wide association analysis and gene co-expression networks

2021 ◽  
Author(s):  
Stephanie Karenina Bajay ◽  
Alexandre Hild Aono ◽  
Matias Kirst ◽  
Anete Pereira de Souza
Keyword(s):  
Loblolly Pine ◽  
Molecular Mechanisms ◽  
Mixed Model ◽  
Genome Wide Association Study ◽  
Gene Families ◽  
Pinus Elliottii ◽  
Genome Wide Association ◽  
Integrated Analysis ◽  
Genome Wide ◽  
A Genome

Loblolly pine (LP), a long-lived tree species, is one of the most economically important forest trees in the world. Genetic improvement programmes for pine trees have focused on survival, early and rapid growth, resistance to diseases and pests, and stem shape. Most of these traits are quantitative and presumably influenced by the action of an unknown network of genes, interacting through complex molecular mechanisms. The extremely large size and high complexity of the Pinus genome have led to challenges in its characterization, sequencing and computational analysis. In this study, we present the first comprehensive integrated analysis of LP involving a genome-wide association study (GWAS) with gene co-expression networks to provide an improved characterization of the gene space and to identify patterns of selection among orthologous gene families. We used populations with full-sib progenies tested at seven sites of the Cooperative Forest Genetics Research Program in the 2nd cycle of Florida LP selection. A total of 1,999 individuals were phenotyped and genotyped using capture probes targeting putative genes based on an elite germplasm transcriptome from LP. A total of 31,589 SNPs were applied to perform a GWAS through a multilocus mixed model. For genome annotation and the construction of gene co-expression networks, three transcriptomes were assembled based on data from different pine species (Pinus taeda, Pinus elliottii and Pinus radiata). With the results obtained, we could select putative genes associated with the target traits and assess the cascade of related molecular mechanisms within co-expression networks. These results advance our understanding of the genetics influencing wood traits and reveal candidate genes for future functional studies and increase our understanding of quantitative genetics and the genomics of complex phenotypic variations in LP. Although the use of GWAS results coupled with genomics data sources did not allow a wide functional assessment of the molecular reactions associated with the traits used, the incorporation of transcriptomics enabled not only gene characterization but also the identification of relevant gene relationships.

scholarly journals Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuxia Li ◽  
Lei Zhang ◽  
Panpan Zhu ◽  
Qinghe Cao ◽  
Jian Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Sweet Potato ◽  
Gene Structure ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Functional Evaluation ◽  
Ipomoea Trifida ◽  
Wild Ancestor ◽  
Genome Wide ◽  
A Genome

Abstract Background WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried out a genome-wide analysis of WRKYs in Ipomoea trifida (H.B.K.) G. Don., the wild ancestor of sweet potato. Results A total of 83 WRKY genes encoding 96 proteins were identified in I. trifida, and their gene distribution, duplication, structure, phylogeny and expression patterns were studied. ItfWRKYs were distributed on 15 chromosomes of I. trifida. Gene duplication analysis showed that segmental duplication played an important role in the WRKY gene family expansion in I. trifida. Gene structure analysis showed that the intron-exon model of the ItfWRKY gene was highly conserved. Meanwhile, the ItfWRKYs were divided into five groups (I, IIa + IIb, IIc, IId + IIe and III) on the basis of the phylogenetic analysis on I. trifida and Arabidopsis thaliana WRKY proteins. In addition, gene expression profiles confirmed by quantitative polymerase chain reaction showed that ItfWRKYs were highly up-regulated or down-regulated under salt, drought, cold and heat stress conditions, implying that these genes play important roles in response and adaptation to abiotic stresses. Conclusions In summary, genome-wide identification, gene structure, phylogeny and expression analysis of WRKY gene in I. trifida provide basic information for further functional studies of ItfWRKYs and for the molecular breeding of sweet potato.

scholarly journals Characterization of auxin transporter AUX, PIN and PILS gene families in pineapple and evaluation of expression profiles during reproductive development and under abiotic stresses

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11410
Author(s):  
Heming Zhao ◽  
Yan Maokai ◽  
Han Cheng ◽  
Mingliang Guo ◽  
Yanhui Liu ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Expression Profiles ◽  
Lateral Roots ◽  
Expression Patterns ◽  
Gene Families ◽  
Transporter Gene ◽  
Specific Expression ◽  
Protein Motifs ◽  
A Genome ◽  
Auxin Transporter

Polar auxin transport in plant is mediated by influx and efflux transporters, which are encoded by AUX/LAX, PIN and PILS genes, respectively. The auxin transporter gene families have been characterized in several species from monocots and eudicots. However, a genome-wide overview of auxin transporter gene families in pineapple is not yet available. In this study, we identified a total of threeAcAUX genes, 12 AcPIN genes, and seven AcPILS genes in the pineapple genome, which were variably located on 15 chromosomes. The exon-intron structure of these genes and properties of deduced proteins were relatively conserved within the same family. Most protein motifs were widespread in the AUX, PIN or PILS proteins, whereas a few motifs were absent in only one or two proteins. Analysis of the expression profiles of these genes elucidated that several genes exhibited either preferential or tissue-specific expression patterns in vegetative and/or reproductive tissues. AcAUX2 was specifically expressed in the early developmental ovules, while AcPIN1b and AcPILS2 were strongly expressed in stamens and ovules. AcPIN9b, AcPILS1, AcPILS6a, 6b and 6c were abundantly expressed in stamens. Furthermore, qRT-PCR results showed that several genes in these families were responsive to various abiotic stresses. Comparative analysis indicated that the genes with close evolutionary relationships among pineapple, rice and Arabidopsis exhibited similar expression patterns. Overexpression of the AcAUX1 in Arabidopsis rescued the phenotype in aux1-T, and resulted in increased lateral roots in WT. These results will provide new insights into auxin transporter genes of pineapple and facilitate our understanding of their roles in pineapple growth and development.

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 Polyamine and Ethylene pathways crosstalk revisited on a genome wide and gene function scale

2019 ◽  
Author(s):  
BLAISE PASCAL MUVUNYI ◽  
Fan Wu ◽  
Qi Yan ◽  
Gisele Kanzana ◽  
Yufei Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Tolerance ◽  
Abiotic Stresses ◽  
Primary Root ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Regulatory Elements ◽  
Pathway Gene ◽  
Genome Wide ◽  
A Genome

Abstract Background Polyamine and ethylene biosynthesis pathway genes are widely involved in the regulation of plant abiotic stresses. For their biosynthesis, both pathways require the same precursor, Synthase Adenosyl Methionine (SAM) enzyme. Whether they function as competitors or collaborators to regulate plant abiotic stress tolerance is still an elusive topic. Genome wide analysis of Cleistogenes songorica polyamine and ethylene pathway gene families was conducted to study their evolutionary relationship. And, using Arabidopsis plants transformed with a polyamine gene SAMDC2 from C. songorica, the expression of key genes from both pathways, and other previously well-studied stress responsive genes was investigated under salt or drought stress. Further, the ABA’s role on this interaction salt stress was also studied. Results 17 polyamine, 12 ethylene and 6 SAM biosynthesis related genes were identified at genome wide level in C. songorica. Phylogenetic analysis revealed close evolutionary similarities between gene families from both pathways. Also, analysis of cis regulatory elements indicated that SAM family genes promoters were rich into both ABA and ethylene related cis regulatory elements. Transcriptomic analysis, qRT-PCR validation, and confirmation using transgenic Arabidopsis showed that polyamine and ethylene key pathway genes can be concurrently expressed during abiotic stresses. Arabidopsis plants expressing a polyamine gene CsSAMDC2 driven by RD29A showed an improved drought and salt stress tolerance, and an increased expression of key polyamine and ethylene pathway genes. These plants maintained higher chlorophyll content and photosynthetic capacity. Morphological analysis of transgenic seedlings showed that leaves of these lines exhibited a more compact architecture following salt stress exposure. Application of ABA on transgenic lines under salt stress further improved the expression of polyamine and ethylene pathway genes. Further, lateral and primary root development were found improved during salt stress and ABA treatments. Interestingly, the expression of ethylene pathway genes was not reversed by exogenous ABA during salt stress treatment. Conclusion In silico and gene functional analysis assays revealed potential evolutionary and functional similarities between polyamine and ethylene pathway gene families. Such findings imply a synergetic interaction between polyamine and ethylene pathways, and the significant role of ABA on this crosstalk.

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