Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton

Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.

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

PeerJ ◽

10.7717/peerj.5816 ◽

2018 ◽

Vol 6 ◽

pp. e5816 ◽

Cited By ~ 4

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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Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.632509 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wei Zhao ◽

Yonghui Liu ◽

Lin Li ◽

Haijun Meng ◽

Ying Yang ◽

...

Keyword(s):

Transcription Factors ◽

Gene Family ◽

Developmental Stage ◽

Molecular Mechanisms ◽

Anthocyanin Biosynthesis ◽

Expression Profiles ◽

Juglans Regia ◽

Expression Patterns ◽

Regulatory Elements

Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut.

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Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

BMC Plant Biology ◽

10.1186/s12870-021-02872-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zihan Cheng ◽

Xuemei Zhang ◽

Wenjing Yao ◽

Kai Zhao ◽

Lin Liu ◽

...

Keyword(s):

Gene Family ◽

Higher Plants ◽

Abiotic Stress Tolerance ◽

Gene Families ◽

Regulatory Elements ◽

Late Embryogenesis Abundant ◽

Genome Wide ◽

Lea Gene ◽

Late Embryogenesis ◽

Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

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Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

International Journal of Molecular Sciences ◽

10.3390/ijms20133235 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3235 ◽

Cited By ~ 2

Author(s):

Yanguo Ke ◽

Farhat Abbas ◽

Yiwei Zhou ◽

Rangcai Yu ◽

Yuechong Yue ◽

...

Keyword(s):

Gene Family ◽

Developmental Stages ◽

Floral Scent ◽

Expression Profiles ◽

Expression Patterns ◽

Regulatory Elements ◽

Virus Induced Gene Silencing ◽

Cut Flowers ◽

Flower Opening ◽

Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

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Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

BMC Ecology and Evolution ◽

10.1186/s12862-021-01873-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhixuan Du ◽

Qitao Su ◽

Zheng Wu ◽

Zhou Huang ◽

Jianzhong Bao ◽

...

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Tandem Repeats ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Regulatory Elements ◽

Genome Wide ◽

Comprehensive Information ◽

Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

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Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽

10.3390/genes12121867 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1867

Author(s):

Yan Li ◽

Xiang Li ◽

Jiatong Wei ◽

Kewei Cai ◽

Hongzhi Zhang ◽

...

Keyword(s):

Transcription Factors ◽

Stress Response ◽

Cold Stress ◽

Gene Family ◽

Gene Families ◽

Regulatory Function ◽

Wrky Gene ◽

Wrky Transcription Factors ◽

Biotic Stresses ◽

Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

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Identifying Transcription Regulatory Elements in the Human and Mouse Genomes Using Tissue-specific Gene Expression Profiles

Journal of Integrative Bioinformatics ◽

10.1515/jib-2007-59 ◽

2007 ◽

Vol 4 (2) ◽

pp. 1-23

Author(s):

Amitava Karmaker ◽

Kihoon Yoon ◽

Mark Doderer ◽

Russell Kruzelock ◽

Stephen Kwek

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcription Factors ◽

Binding Sites ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Regulatory Elements ◽

Specific Gene ◽

Tissue Specific Gene ◽

Human And Mouse

Summary Revealing the complex interaction between trans- and cis-regulatory elements and identifying these potential binding sites are fundamental problems in understanding gene expression. The progresses in ChIP-chip technology facilitate identifying DNA sequences that are recognized by a specific transcription factor. However, protein-DNA binding is a necessary, but not sufficient, condition for transcription regulation. We need to demonstrate that their gene expression levels are correlated to further confirm regulatory relationship. Here, instead of using a linear correlation coefficient, we used a non-linear function that seems to better capture possible regulatory relationships. By analyzing tissue-specific gene expression profiles of human and mouse, we delineate a list of pairs of transcription factor and gene with highly correlated expression levels, which may have regulatory relationships. Using two closely-related species (human and mouse), we perform comparative genome analysis to cross-validate the quality of our prediction. Our findings are confirmed by matching publicly available TFBS databases (like TRANFAC and ConSite) and by reviewing biological literature. For example, according to our analysis, 80% and 85.71% of the targets genes associated with E2F5 and RELB transcription factors have the corresponding known binding sites. We also substantiated our results on some oncogenes with the biomedical literature. Moreover, we performed further analysis on them and found that BCR and DEK may be regulated by some common transcription factors. Similar results for BTG1, FCGR2B and LCK genes were also reported.

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Genome-wide identification of small heat shock protein (HSP20) gene family in grape and expression profile during berry development

10.21203/rs.2.11373/v2 ◽

2019 ◽

Author(s):

Xiao-Ru Ji ◽

Yi-He Yu ◽

Pei-Yi Ni ◽

Guo-Hai Zhang ◽

Da-Long Guo

Keyword(s):

Heat Shock ◽

Heat Shock Protein ◽

Gene Family ◽

Expression Profiles ◽

Evolutionary Relationship ◽

Functional Differentiation ◽

Regulatory Elements ◽

Pcr Analysis ◽

Berry Development ◽

Hsp20 Gene Family

Abstract Background : Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well studied. Results : A total of 48 VvHsp20 genes were identified from the grape genome, which were divided into 11 subfamilies (CI, CII, CIII, CV, CVI, CVII, MI, MII, ER, CP and PX/Po) based on a phylogenetic analysis and subcellular localization. Further structural analysis showed that most of the VvHsp20 genes (93.8%) had no intron or only one intron, while genes that clustered together based on a phylogenetic tree had similar motifs and evolutionarily conserved structures. The HSP20s share a conservedα-crystalline domain (ACD) and the different components of the ACD domain suggest the functional diversity of VvHSP20s. In addition, the 48 VvHSP20 genes were distributed on 12 grape chromosomes and the majority of VvHSP20 genes were located at the proximal or distal ends of chromosomes. Chromosome mapping indicated that four groups of VvHSP20 genes were identified as tandem duplication genes. Phytohormone responsive, abiotic and biotic stress-responsive, and plant development-related cis-elements were identified from the cis-regulatory elements analysis of VvHSP20s. The expression profiles of VvHSP20s genes (VvHsp20-1, 11, 14, 17, 18, 19, 20, 24, 25, 28, 31, 39, 42, and 43) were largely similar between RNA-Seq and qRT-PCR analysis after hydrogen peroxide (H 2 O 2 ) treatment. The results showed that most VvHSP20s were down-regulated by H 2 O 2 treatment during fruit development. VvHSP20s genes were indeed found to be involved in the grape berry development and differences in their transcriptional levels may be the result of functional differentiation during evolution. Conclusions : Our results provide valuable information on the evolutionary relationship of genes in the VvHSP20 family, which is useful for future studies on the functional characteristics of VvHSP20 genes in grape.

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Genome-Wide Analysis Reveals the Potential Role of MYB Transcription Factors in Floral Scent Formation in Hedychium coronarium

Frontiers in Plant Science ◽

10.3389/fpls.2021.623742 ◽

2021 ◽

Vol 12 ◽

Author(s):

Farhat Abbas ◽

Yanguo Ke ◽

Yiwei Zhou ◽

Yunyi Yu ◽

Muhammad Waseem ◽

...

Keyword(s):

Transcription Factors ◽

Gene Family ◽

Floral Scent ◽

Expression Patterns ◽

Acid Methyl Ester ◽

Regulatory Elements ◽

Composition Analysis ◽

Myb Gene ◽

Hedychium Coronarium

The MYB gene family is one of the largest groups of transcription factors (TFs) playing diverse roles in several biological processes. Hedychium coronarium (white ginger lily) is a renowned ornamental plant both in tropical and subtropical regions due to its flower shape and strong floral scent mainly composed of terpenes and benzenoids. However, there is no information available regarding the role of the MYB gene family in H. coronarium. In the current study, the MYB gene family was identified and extensively analyzed. The identified 253 HcMYB genes were unevenly mapped on 17 chromosomes at a different density. Promoter sequence analysis showed numerous phytohormones related to cis-regulatory elements. The majority of HcMYB genes contain two to three introns and motif composition analysis showed their functional conservation. Phylogenetic analysis revealed that HcMYBs could be classified into 15 distinct clades, and the segmental duplication events played an essential role in the expansion of the HcMYB gene family. Tissue-specific expression patterns of HcMYB genes displayed spatial and temporal expression. Furthermore, seven HcMYB (HcMYB7/8/75/79/145/238/248) were selected for further investigation. Through RT-qPCR, the response of candidates HcMYB genes toward jasmonic acid methyl ester (MeJA), abscisic acid (ABA), ethylene, and auxin was examined. Yeast one-hybrid (Y1H) assays revealed that candidate genes directly bind to the promoter of bottom structural volatile synthesis genes (HcTPS1, HcTPS3, HcTPS10, and HcBSMT2). Moreover, yeast two-hybrid (Y2H) assay showed that HcMYB7/8/75/145/248 interact with HcJAZ1 protein. In HcMYB7/8/79/145/248-silenced flowers, the floral volatile contents were decreased and downregulated the expression of key structural genes, suggesting that these genes might play crucial roles in floral scent formation in H. coronarium by regulating the expression of floral scent biosynthesis genes. Collectively, these findings indicate that HcMYB genes might be involved in the regulatory mechanism of terpenoids and benzenoid biosynthesis in H. coronarium.

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