scholarly journals Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley (Hordeum vulgare L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Tingting Li ◽  
Wenqiu Pan ◽  
Yiyuan Yuan ◽  
Ying Liu ◽  
Yihan Li ◽  
...  
Keyword(s):  
Hordeum Vulgare ◽  
Abiotic Stresses ◽  
Metal Ion ◽  
Profile Analysis ◽  
Purifying Selection ◽  
Hordeum Vulgare L ◽  
Functional Studies ◽  
Expression Profile Analysis ◽  
Intron Structure ◽  
Comprehensive Search

Plant mitochondrial transcription termination factor (mTERF) family regulates organellar gene expression (OGE) and is functionally characterized in diverse species. However, limited data are available about its functions in the agriculturally important cereal barley (Hordeum vulgare L.). In this study, we identified 60 mTERFs in the barley genome (HvmTERFs) through a comprehensive search against the most updated barley reference genome, Morex V2. Then, phylogenetic analysis categorized these genes into nine subfamilies, with approximately half of the HvmTERFs belonging to subfamily IX. Members within the same subfamily generally possessed conserved motif composition and exon-intron structure. Both segmental and tandem duplication contributed to the expansion of HvmTERFs, and the duplicated gene pairs were subjected to strong purifying selection. Expression analysis suggested that many HvmTERFs may play important roles in barley development (e.g., seedlings, leaves, and developing inflorescences) and abiotic stresses (e.g., cold, salt, and metal ion), and HvmTERF21 and HvmTERF23 were significant induced by various abiotic stresses and/or phytohormone treatment. Finally, the nucleotide diversity was decreased by only 4.5% for HvmTERFs during the process of barley domestication. Collectively, this is the first report to characterize HvmTERFs, which will not only provide important insights into further evolutionary studies but also contribute to a better understanding of the potential functions of HvmTERFs and ultimately will be useful in future gene functional studies.

scholarly journals Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6832 ◽  
Author(s):  
Jie Li ◽  
Xinhao Liu
Keyword(s):  
Hordeum Vulgare ◽  
Gene Family ◽  
Profile Analysis ◽  
Hordeum Vulgare L ◽  
Biotic Stresses ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Response To Stress ◽  
Hsp20 Gene Family ◽  
Shock Proteins

In plants, heat shock proteins (Hsps) play important roles in response to diverse stresses. Hsp20 is the major family of Hsps, but their role remains poorly understood in barley (Hordeum vulgare L.). To reveal the mechanisms of barley Hsp20s (HvHsp20s) response to stress conditions, we performed a comprehensive genome-wide analysis of the HvHsp20 gene family using bioinformatics-based methods. In total, 38 putative HvHsp20s were identified in barley and grouped into four subfamilies (C, CP, PX, and MT) based on predicted subcellular localization and their phylogenetic relationships. A sequence analysis indicated that most HvHsp20 genes have no intron or one with a relatively short length. In addition, the same group of HvHsp20 proteins in the phylogenetic tree shared similar gene structure and motifs, indicating that they were highly conserved and might have similar function. Based on RNA-seq data analysis, we showed that the transcript levels of HvHsp20 genes could be induced largely by abiotic and biotic stresses such as heat, salt, and powdery mildew. Three HvHsp20 genes, HORVU7Hr1G036540, HORVU7Hr1G036470, and HORVU3Hr1G007500, were up-regulated under biotic and abiotic stresses, suggesting their potential roles in mediating the response of barley plants to environment stresses. These results provide valuable information for further understanding the complex mechanisms of HvHsp20 gene family in barley.

scholarly journals Genome-wide identification and evolution of HECT genes in wheat

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10457
Author(s):  
Xianwen Meng ◽  
Ting Yang ◽  
Jing Liu ◽  
Mingde Zhao ◽  
Jiuli Wang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Profile Analysis ◽  
Purifying Selection ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Ubiquitin Proteasome ◽  
Proteasome Pathway

Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

scholarly journals Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9131
Author(s):  
Jie Cui ◽  
Xinyan Li ◽  
Junliang Li ◽  
Congyu Wang ◽  
Dayou Cheng ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Salinity Stress ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Plant Growth And Development ◽  
Auxin Response ◽  
Expression Profile Analysis ◽  
Sequence Identification ◽  
Genome Wide ◽  
Intron Structure

Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet’s growth, development and responses to salinity stress.

scholarly journals Effects of multiple abiotic stresses on lipids and sterols profile in barley leaves (Hordeum vulgare L.)

2019 ◽  
Vol 141 ◽  
pp. 215-224 ◽  
Author(s):  
Anetta Kuczyńska ◽  
Vladimiro Cardenia ◽  
Piotr Ogrodowicz ◽  
Michał Kempa ◽  
Maria Teresa Rodriguez-Estrada ◽  
...  
Keyword(s):  
Hordeum Vulgare ◽  
Abiotic Stresses ◽  
Hordeum Vulgare L ◽  
Barley Leaves

scholarly journals Expansion of Imaginal Disc Growth Factor Gene Family in Diptera Reflects the Evolution of Novel Functions

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 365 ◽  
Author(s):  
Martina Zurovcova ◽  
Vladimir Benes ◽  
Michal Zurovec ◽  
Lucie Kucerova
Keyword(s):  
Imaginal Disc ◽  
Purifying Selection ◽  
Growth Stimulation ◽  
Single Copy ◽  
Factor Gene ◽  
Multiple Functions ◽  
Functional Studies ◽  
Growth Factor Gene ◽  
Intron Structure

Imaginal disc growth factors (IDGFs) are a small protein family found in insects. They are related to chitinases and implicated in multiple functions, including cell growth stimulation, antimicrobial activity, insect hemolymph clotting, and maintenance of the extracellular matrix. A number of new IDGFs have been found in several insect species and their detailed phylogenetic analysis provides a good basis for further functional studies. To achieve this goal, we sequenced Idgf cDNAs from several lepidopteran and trichopteran species and supplemented our data with sequences retrieved from public databases. A comparison of Idgf genes in different species showed that Diptera typically contain several Idgf paralogs with a simple exon-intron structure (2–3 exons), whereas lepidopteran Idgfs appear as a single copy per genome and contain a higher number of exons (around 9). Our results show that, while lepidopteran Idgfs, having single orthologs, are characterized by low divergence and stronger purifying selection over most of the molecule, the duplicated Idgf genes in Diptera, Idgf1 and Idgf4, exhibit signs of positive selection. This characterization of IDGF evolution provides, to our knowledge, the first information on the changes that formed these important molecules.

scholarly journals Genome-wide identification and expression analysis of the invertase gene family in common wheat

2021 ◽  
Author(s):  
Chao Wang ◽  
Guanghao Wang ◽  
Xiaojian Qu ◽  
Xiangyu Zhang ◽  
pingchuan Deng ◽  
...  
Keyword(s):  
Gene Family ◽  
Segmental Duplication ◽  
Profile Analysis ◽  
Functional Characterization ◽  
Purifying Selection ◽  
Specific Expression ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Family Based ◽  
Yield Formation

Background: The degradation of sucrose plays an important role in the process of crop biomass allocation and yield formation. Invertase (INV) irreversibly catalyzes the conversion of sucrose into glucose and fructose, which doomed its' important role in plant development and stress tolerance. However, the functions of INV genes in wheat, one of the most important crops, were less studied due to the polyploidy. Results: Here, we systematically analyzed the INV gene family based on the latest published wheat reference genomic information. A total of 126 TaINV genes were identified and classified into three classes based on the phylogenetic relationship and their gene structure. Of which, 11 and 83 gene pairs were identified as tandem and segmental duplication genes respectively, while the Ka/Ks ratios of tandem and segmental duplication TaINV genes were less than 1. Expression profile analysis shows that 18 TaINV genes have tissue-specific expression, and 54 TaINV genes were involved in stress response. Furthermore, RNA-seq showed that 35 genes are differentially expressed in grain weight NILs N0910-81L/N0910-81S, in which 9 TaINVs were stably detected by qRT-PCR at three time-points, 4, 7 and 10 DPA. Four of them (TaCWI47, TaCWI48, TaCWI50 and TaVI27) different expressed between the NILs resided in 4 QTL segments (QTGW.nwafu-5DL.1, QTGW.nwafu-5DL.2, QTGW.nwafu-7AS.1 and QTGW.nwafu-7AS.2). These findings facilitate function investigations of the wheat INV gene family and provide new insights into the grain development mechanism in wheat. Conclusions: Our results showed that allopolyploid events were the main reason for the expansion of the TaINV gene family in hexaploid wheat, and duplication genes might undergo purifying selection. The expression profiling of TaINV genes implied that they are likely to play an important role in wheat growth and development and adaption to stressful environments. And TaCWI47, TaCWI48, TaCWI50 and TaVI27 may have more important roles in grain developments. Our study lay a base for further dissecting the functional characterization of TaINV family members.

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