scholarly journals Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Yong Zou ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Gene Structure ◽  
Abiotic Stresses ◽  
Growth And Development ◽  
Expression Profiles ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Evolutionary Features ◽  
Erf Family

Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

scholarly journals Identification and characterization of circular RNAs in Ganoderma lucidum

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Junjie Shao ◽  
Liqiang Wang ◽  
Xinyue Liu ◽  
Meng Yang ◽  
Haimei Chen ◽  
...  
Keyword(s):  
Ganoderma Lucidum ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Rna Seq ◽  
Polysaccharide Biosynthesis ◽  
Genome Wide ◽  
A Genome ◽  
Positive Correlations

Abstract Circular RNAs (circRNAs) play important roles in animals, plants, and fungi. However, no circRNAs have been reported in Ganoderma lucidum. Here, we carried out a genome-wide identification of the circRNAs in G.lucidum using RNA-Seq data, and analyzed their features. In total, 250 and 2193 circRNAs were identified from strand-specific RNA-seq data generated from the polyA(−) and polyA(−)/RNase R-treated libraries, respectively. Six of 131 (4.58%) predicted circRNAs were experimentally confirmed. Across three developmental stages, 731 exonic circRNAs (back spliced read counts ≥ 5) and their parent genes were further analyzed. CircRNAs were preferred originating from exons with flanking introns, and the lengths of the flanking intron were longer than those of the control introns. A total of 200 circRNAs were differentially expressed across the three developmental stages of G. lucidum. The expression profiles of 119 (16.3%) exonic circRNAs and their parent genes showed significant positive correlations (r ≥ 0.9, q < 0.01), whereas 226 (30.9%) exonic circRNAs and their parent genes exhibited significant negative correlations (r ≤ −0.9, q < 0.01), in which 53 parent genes are potentially involved in the transcriptional regulation, polysaccharide biosynthesis etc. Our results indicated that circRNAs are present in G. lucidum, with potentially important regulatory roles.

scholarly journals Genome-Wide Identification and Expression Analysis of MYB Transcription Factor Superfamily in Dendrobium catenatum

2021 ◽  
Vol 12 ◽  
Author(s):  
Tingting Zhang ◽  
Zheng Cui ◽  
Yuxin Li ◽  
Yuqian Kang ◽  
Xiqiang Song ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Molecular Breeding ◽  
Theoretical Foundation ◽  
Expression Profiles ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Genome Wide ◽  
Gene Structures ◽  
Myb Proteins ◽  
R2r3 Myb

Dendrobium catenatum is an important traditional Chinese medicine and naturally grows on tree trunks and cliffs, where it can encounter diverse environmental stimuli. MYB transcription factors are widely involved in response to abiotic stresses. However, the MYB gene family has not yet been systematically cataloged in D. catenatum. In this study, a total of 133 MYB proteins were identified in D. catenatum, including 32 MYB-related, 99 R2R3-MYB, 1 3R-MYB, and 1 4R-MYB proteins. Phylogenetic relationships, conserved motifs, gene structures, and expression profiles in response to abiotic stresses were then analyzed. Phylogenetic analysis revealed MYB proteins in D. catenatum could be divided into 14 subgroups, which was supported by the conserved motif compositions and gene structures. Differential DcMYB gene expression and specific responses were analyzed under drought, heat, cold, and salt stresses using RNA-seq and validated by qRT-PCR. Forty-two MYB genes were differentially screened following exposure to abiotic stresses. Five, 12, 11, and 14 genes were specifically expressed in response to drought, heat, cold, and salt stress, respectively. This study identified candidate MYB genes with possible roles in abiotic tolerance and established a theoretical foundation for molecular breeding of D. catenatum.

scholarly journals Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3747 ◽  
Author(s):  
Weilong Kong ◽  
Shaozong Yang ◽  
Yulu Wang ◽  
Mohammed Bendahmane ◽  
Xiaopeng Fu
Keyword(s):  
Sugar Beet ◽  
Beta Vulgaris ◽  
Growth And Development ◽  
Phylogenetic Analyses ◽  
Rna Seq ◽  
Reference Base ◽  
Genome Wide ◽  
Aquaporin Gene ◽  
Identification And Characterization

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.

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 Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Luzhao Pan ◽  
Jiaqiu Zheng ◽  
Jia Liu ◽  
Jun Guo ◽  
Fawan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Pepper Plant ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Group I

Acetylserotonin methyltransferase (ASMT) in plant species, one of the most important enzymes in melatonin biosynthesis, plays a rate-limiting role in the melatonin production. In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. The results showed that at least 16 CaASMT genes were identified in the pepper genome. Phylogenetic analyses of all the CaASMTs were divided into three groups (group I, group II, and group III) with a high bootstrap value. Through the online MEME tool, six distinct motifs (motif 1 to motif 6) were identified. Chromosome location found that most CaASMT genes were mapped in the distal ends of the pepper chromosomes. In addition, RNA-seq analysis revealed that, during the vegetative and reproductive development, the difference in abundance and distinct expression patterns of these CaASMT genes suggests different functions. The qRT-PCR analysis showed that high abundance of CaASMT03, CaASMT04, and CaASMT06 occurred in mature green fruit and mature red fruit. Finally, using RNA-seq and qRT-PCR technology, we also found that several CaASMT genes were induced under abiotic stress conditions. The results will not only contribute to elucidate the evolutionary relationship of ASMT genes but also ascertain the biological function in pepper plant response to abiotic stresses.

scholarly journals Transcriptome-wide identification and characterization of WD40 genes, as well as their tissue-specific expression profiles and responses to heat stress in Dimocarpus longan Lour.

2021 ◽  
Vol 49 (1) ◽  
pp. 12191
Author(s):  
Wei ZHENG ◽  
Ziwei ZHANG ◽  
Xuefei YU ◽  
Tongtong XIE ◽  
Ning CHEN ◽  
...  
Keyword(s):  
Heat Stress ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Flavonoid Biosynthesis ◽  
Functional Verification ◽  
Specific Expression ◽  
Cis Acting ◽  
Qrt Pcr

The WD40 transcription factor (TF) family is widespread in plants and plays important roles in plant growth and development, transcriptional regulation, and tolerance to abiotic stresses. WD40 TFs have been identified and characterized in a diverse series of plant species. However, little information is available on WD40 genes from D. longan. In this study, a total of 45 DlWD40 genes were identified from D. longan RNA-Seq data, and further analysed by bioinformatics tools. Also, the expression patterns of DlWD40 genes in roots and leaves, as well as responses to heat stress, were evaluated using quantitative real-time PCR (qRT-PCR). We found that the 45 DlWD40 proteins, together with 80 WD40 proteins from Arabidopsis and Zea mays, could be categorized into six groups. Of these, the DlWD40-4 protein was highly homologous to Arabidopsis WDR5a, a protein participating in tolerance to abiotic stresses. Moreover, a total of 25 cis-acting elements, such as abiotic stress and flavonoid biosynthesis elements, were found in the promoters of DlWD40 genes. The DlWD40-33 gene is targeted by miR3627, which has been proposed to be involved in flavonoid biosynthesis. Using qRT-PCR, ten of the 45 DlWD40 genes were demonstrated to have diverse expression patterns between roots and leaves, and these ten DlWD40 genes could also respond to varying durations of a 38 °C heat stress in roots and leaves. The results reported here will provide a basis for the further functional verification of DlWD40 genes in D. longan.

scholarly journals Genome-Wide Survey and Identification of AP2/ERF Genes Involved in Shoot and Leaf Development in Liriodendron Chinense

2020 ◽  
Author(s):  
Yaxian Zong ◽  
Ziyuan Hao ◽  
Zhonghua Tu ◽  
Yufang Shen ◽  
Chengge Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Leaf Development ◽  
Early Stage ◽  
Expression Profiles ◽  
Leaf Primordium ◽  
Rna Seq ◽  
Response Factors ◽  
Genome Database ◽  
Genome Wide ◽  
Erf Family

Abstract Background: Liriodendron chinense is a distinctive ornamental tree species due to its unique-shaped leaves and tulip-like flowers. The discovery of genes involved in leaf development and morphogenesis is critical for uncovering the underlying genetic basis of these traits. Genes in the AP2/ERF family were recognized as plant-specific transcription factors contributing to plant growth, hormone-induced development, ethylene response factors and stress responses. Results: In this study, we identified 104 putative AP2/ERF genes in the recently released Liriodendron genome database and RNA-seq dataset. Accordingly, all 104 genes were grouped into four subfamilies, including the AP2, ERF, RAV and Soloist subfamilies. This classification was further supported by the results of gene structure and conserved motif analyses. Moreover, based on the expression profiles of various tissues and organs, we discovered three LcAP2 genes as well as two VIII group genes that were significantly enriched in a shoot-specific manner by applying expression pattern and category enrichment analyses. Of these five genes, the relative expression levels of LcERF 94, LcERF 96 and LcERF 98 in the RT-qPCR assay were highly consistent with the RNA-seq results. Furthermore, we illustrated by dissection of Liriodendron shoots and subsequent qPCR assays that LcERF 94, LcERF 96 and LcERF 98 were expressed extensively in the early stage of leaf primordium development but rarely in tender leaves. In addition, these three genes displayed nuclear subcellular localizations through transient transformation of tobacco epidermal cells. Conclusions: Taken together, we identified all the AP2/ERF family members at the genome-wide level and provided candidates that might participate in the development and morphogenesis of the leaf primordium in L. chinense.

scholarly journals Identification and in Silico Characterization of GT Factors Involved in Phytohormone and Abiotic Stresses Responses in Brachypodium distachyon

2019 ◽  
Vol 20 (17) ◽  
pp. 4115
Author(s):  
Feng Wen ◽  
Liangwei Xu ◽  
Yuebin Xie ◽  
Liang Liao ◽  
Tongjian Li ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Expression Profiles ◽  
Brachypodium Distachyon ◽  
Plant Stress ◽  
Functional Domain ◽  
Syntenic Relationship ◽  
Genome Wide ◽  
Regulation Network ◽  
In Silico Characterization

GT factors play critical roles in plant growth and development and in response to various environmental stimuli. Considering the new functions of GT factors on the regulation of plant stress tolerance and seeing as few studies on Brachypodium distachyon were available, we identified GT genes in B. distachyon, and the gene characterizations and phylogenies were systematically analyzed. Thirty-one members of BdGT genes were distributed on all five chromosomes with different densities. All the BdGTs could be divided into five subfamilies, including GT-1, GT-2, GTγ, SH4, and SIP1, based upon their sequence homology. BdGTs exhibited considerably divergent structures among each subfamily according to gene structure and conserved functional domain analysis, but the members within the same subfamily were relatively structure-conserved. Synteny results indicated that a large number of syntenic relationship events existed between rice and B. distachyon. Expression profiles indicated that the expression levels of most of BdGT genes were changed under abiotic stresses and hormone treatments. Moreover, the co-expression network exhibited a complex regulatory network between BdGTs and BdWRKYs as well as that between BdGTs and BdMAPK cascade gene. Results showed that GT factors might play multiple functions in responding to multiple environmental stresses in B. distachyon and participate in both the positive and negative regulation of WRKY- or MAPK-mediated stress response processes. The genome-wide analysis of BdGTs and the co-regulation network under multiple stresses provide valuable information for the further investigation of the functions of BdGTs in response to environment stresses.

scholarly journals Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification of GmDUF4228–70 in Response to Drought and Salt Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhi-Xin Leng ◽  
Ying Liu ◽  
Zhan-Yu Chen ◽  
Jun Guo ◽  
Jun Chen ◽  
...  
Keyword(s):  
Salt Stress ◽  
Drought Stress ◽  
Transgenic Plants ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Marker Genes ◽  
Rna Seq ◽  
Functional Identification ◽  
Qrt Pcr ◽  
Drought And Salt Stresses

Domain of unknown function 4228 (DUF4228) proteins are a class of proteins widely found in plants, playing an important role in response to abiotic stresses. However, studies on the DUF4228 family in soybean (Glycine max L.) are sparse. In this study, we identified a total of 81 DUF4228 genes in soybean genome, named systematically based on their chromosome distributions. Results showed that these genes were unevenly distributed on the 20 chromosomes of soybean. The predicted soybean DUF4228 proteins were identified in three groups (Groups I–III) based on a maximum likelihood phylogenetic tree. Genetic structure analysis showed that most of the GmDUF4228 genes contained no introns. Expression profiling showed that GmDUF4228 genes were widely expressed in different organs and tissues in soybean. RNA-seq data were used to characterize the expression profiles of GmDUF4228 genes under the treatments of drought and salt stresses, with nine genes showing significant up-regulation under both drought and salt stress further functionally verified by promoter (cis-acting elements) analysis and quantitative real-time PCR (qRT-PCR). Due to its upregulation under drought and salt stresses based on both RNA-seq and qRT-PCR analyses, GmDUF4228-70 was selected for further functional analysis in transgenic plants. Under drought stress, the degree of leaf curling and wilting of the GmDUF4228-70-overexpressing (GmDUF4228-70-OE) line was lower than that of the empty vector (EV) line. GmDUF4228-70-OE lines also showed increased proline content, relative water content (RWC), and chlorophyll content, and decreased contents of malondialdehyde (MDA), H2O2, and O2–. Under salt stress, the changes in phenotypic and physiological indicators of transgenic plants were the same as those under drought stress. In addition, overexpression of the GmDUF4228-70 gene promoted the expression of marker genes under both drought and salt stresses. Taken together, the results indicated that GmDUF4228 genes play important roles in response to abiotic stresses in soybean.

scholarly journals Genome-Wide Identification and Expression Analysis of AP2/EREBP Transcription Factors in Litchi (Litchi chinensis Sonn.)

2021 ◽  
Author(s):  
Jia-li Men ◽  
Fang Li ◽  
Jin-hua Sun ◽  
Guo Wang ◽  
Huan-ling Li ◽  
...  
Keyword(s):  
Tandem Duplication ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Orthologous Gene ◽  
Gene Interaction ◽  
Rna Seq ◽  
Plant Organ ◽  
Ethylene Response ◽  
Genome Wide ◽  
Evolutionary Features

AbstractAPETALA2/ethylene response element binding proteins (AP2/EREBP) are a vital type of TF involved in plant organ development and embryogenesis. In this study we identified 202 Litchi AP2/EREBP TFs from the litchi genome. They were classified into four subfamilies by phylogenetic clustering, including AP2s (20), ERFs (112), DREBs (64), and RAVs (6). Analysis of conserved domains, motifs, gene structure, and genome localization were carried out to investigate the evolutionary features of litchi AP2/EREBPs. Over 35% of DREBs and ERFs involved in the expansion of litchi AP2/EREBPs resulted from tandem duplication. The majority of genomic organizations were conservative, except those of the AP2 subfamily, which had no intron and contained less conservative motif numbers. The expression profiles of litchi AP2/EREBPs in ten tissues were investigated using RNA-Seq data and fifty-nine showed tissue-specific expressions. Their expression patterns were confirmed by qRT-PCR with eight tissues-specificity genes. Six genes related to embryogenesis were identified using the map of orthologous gene interaction between Arabidopsis and litchi. This paper is a comprehensive report on the characteristics of the litchi AP2/EREBP gene superfamily. It will serve to further explore the regulatory mechanisms of AP2/EREBP TFs in the litchi somatic embryogenesis and provide information for litchi molecular breeding.

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