scholarly journals Genome-Wide Identification of Hsp90 Gene Family in Perennial Ryegrass and Expression Analysis under Various Abiotic Stresses

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2509
Author(s):  
Charlotte Appiah ◽  
Zhong-Fu Yang ◽  
Jie He ◽  
Yang Wang ◽  
Jie Zhou ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gene Family ◽  
Expression Analysis ◽  
Perennial Ryegrass ◽  
Brachypodium Distachyon ◽  
Heat Shock Protein 90 ◽  
Orthologous Gene ◽  
Gene Pairs ◽  
Stress Studies

The heat shock protein 90 (Hsp90) is a protein produced in plants in response to stress. This study identified and analyzed Hsp90 gene family members in the perennial ryegrass genome. From the results, eight Hsp90 proteins were obtained and their MW, pI and number of amino acid bases varied. The amino acid bases ranged from 526 to 862. The CDS also ranged from 20 (LpHsp0-4) to 1 (LpHsp90-5). The least number of CDS regions was 1 (LpHsp90-5) with 528 kb amino acids, while the highest was 20 (LpHsp90-4) with 862 kb amino acids, which showed diversity among the protein sequences. The phylogenetic tree revealed that Hsp90 genes in Lolium perenne, Arabidopsis thaliana, Oryza sativa and Brachypodium distachyon could be divided into two groups with five paralogous gene pairs and three orthologous gene pairs. The expression analysis after perennial ryegrass was subjected to heat, salt, chromium (Cr), cadmium (Cd), polyethylene glycol (PEG) and abscisic acid (ABA) revealed that LpHsp90 genes were generally highly expressed under heat stress, but only two LpHsp90 proteins were expressed under Cr stresses. Additionally, the expression of the LpHsp90 proteins differed at each time point in all treatments. This study provides the basis for an understanding of the functions of LpHsp90 proteins in abiotic stress studies and in plant breeding.

scholarly journals A Mating-Induced Protein of Phytophthora infestans Is a Member of a Family of Elicitors with Divergent Structures and Stage-Specific Patterns of Expression

2003 ◽  
Vol 16 (10) ◽  
pp. 926-935 ◽  
Author(s):  
Anna-Liisa Fabritius ◽  
Howard S. Judelson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gene Family ◽  
Phytophthora Infestans ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
Terminal Domain ◽  
Defense Reactions ◽  
The Family ◽  
Microbe Interactions

Five members of an elicitor-like gene family from Phytophthora infestans were examined. The family was identified through the analysis of M81, a mating-induced gene. The predicted M81 product resembled a 42-kDa P. sojae glycoprotein known to elicit defense reactions in plants, including a host of P. infestans, potato. M81 was the most structurally and functionally divergent of the P. infestans genes compared with the P. sojae sequence. M81 lacked elicitor activity, had the lowest protein identity (47%), displayed mating-specific transcription, and had a novel C-terminal domain. The latter contained a 30-residue proline- and threonine-rich motif, which, remarkably, was tandemly repeated 24 to 36 times in different alleles. M81C, M81D, and M81E better resembled the P. sojae protein based on amino acid identity (63 to 75%) and conserved elicitor activity. M81C and M81D mRNA accumulated only during zoosporogenesis, while M81E expression was restricted to hyphae. M81B, an apparent pseudogene, was physically linked to M81. The protein products of each gene were predicted to be extracellular transglutaminases ranging in size from 436 to 1,607 amino acids. Genes with an elicitor, proline- and threonine-rich repeat, and both elicitor and repeat domains were widely distributed throughout Phytophthora infestans. These findings help explain the natural functions of elicitors in pathogen biology and plant-microbe interactions.

scholarly journals Genome-Wide Analysis of the Amino Acid Auxin Permease (AAAP) Gene Family and Identification of an AAAP Gene Associated with the Growth and Reproduction of the Brown Planthopper, Nilaparvata lugens (Stål)

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 746
Author(s):  
Lei Yue ◽  
Rui Pang ◽  
Hu Tian ◽  
Ziying Guan ◽  
Mingzhao Zhong ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gene Family ◽  
Brown Planthopper ◽  
Larval Growth ◽  
Family Members ◽  
Nilaparvata Lugens ◽  
Hatching Rate ◽  
Characteristic Analysis ◽  
Transporter Family

Amino acids play a vital role in several biological processes in organisms and are mainly acquired through diet by most insects. The amino acid auxin permease (AAAP) transporter family is an important amino acid transporter gene family in insects for the transportation of amino acids into and out of cells across the plasma membrane. Here, we identified 21 putative AAAP family members in the genome of the brown planthopper (BPH), Nilaparvata lugens, a devastating pest that feeds only on the phloem sap of rice plants. Molecular characteristic analysis indicated large variations in protein features and amino acid sequences among the predicted AAAP family members in BPH. Phylogenetic analysis clustered these AAAP transporters into three subgroups, with the members in the same group sharing a similar pattern of conserved motif distribution. Through ortholog gene recognition and spatiotemporal gene expression analysis, the AAAP gene NlAAAP07, which was predicted to regulate BPH larval growth and female fecundity, was identified. RNA interference (RNAi)-mediated suppression of NlAAAP07 significantly postponed the duration of 3rd instar nymphs developing into adults from 7.4 days to 9.0 days, and decreased the oviposition amount and egg hatching rate of females by 30.7% and 11.0%, respectively. Our results provide a foundation for further functional analysis of AAAP transporters in BPH.

scholarly journals Genome-wide identification and expression analysis of the JAZ gene family in turnip

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kai Jia ◽  
Cunyao Yan ◽  
Jing Zhang ◽  
Yunxia Cheng ◽  
Wenwen Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Specific Protein ◽  
Gene Pairs ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structure And Expression

AbstractJAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.

scholarly journals Amino acid transporter (AAT) gene family in foxtail millet (Setaria italica L.): widespread family expansion, functional differentiation, roles in quality formation and response to abiotic stresses

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yang Yang ◽  
Yongmao Chai ◽  
Jiayi Liu ◽  
Jie Zheng ◽  
Zhangchen Zhao ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Foxtail Millet ◽  
Functional Differentiation ◽  
Setaria Italica ◽  
Evolutionary Features ◽  
Sequence Characteristics ◽  
Quality Formation

Abstract Background Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria and abiotic stress by modulating the transmembrane transfer of amino acids. In this study, we performed a genome-wide screening to analyze the AAT genes in foxtail millet (Setaria italica L.), especially those associated with quality formation and abiotic stresses response. Results A total number of 94 AAT genes were identified and divided into 12 subfamilies by their sequence characteristics and phylogenetic relationship. A large number (58/94, 62%) of AAT genes in foxtail millet were expanded via gene duplication, involving 13 tandem and 12 segmental duplication events. Tandemly duplicated genes had a significant impact on their functional differentiation via sequence variation, structural variation and expression variation. Further comparison in multiple species showed that in addition to paralogous genes, the expression variations of the orthologous AAT genes also contributed to their functional differentiation. The transcriptomic comparison of two millet cultivars verified the direct contribution of the AAT genes such as SiAAP1, SiAAP8, and SiAUX2 in the formation of grain quality. In addition, the qRT-PCR analysis suggested that several AAT genes continuously responded to diverse abiotic stresses, such as SiATLb1, SiANT1. Finally, combined with the previous studies and analysis on sequence characteristics and expression patterns of AAT genes, the possible functions of the foxtail millet AAT genes were predicted. Conclusion This study for the first time reported the evolutionary features, functional differentiation, roles in the quality formation and response to abiotic stresses of foxtail millet AAT gene family, thus providing a framework for further functional analysis of SiAAT genes, and also contributing to the applications of AAT genes in improving the quality and resistance to abiotic stresses of foxtail millet, and other cereal crops.

scholarly journals Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1848
Author(s):  
Meimei Hu ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Patterns ◽  
Protein Structures ◽  
Evolutionary Process ◽  
Orthologous Gene ◽  
Evolutionary Relationships ◽  
Protein Motifs ◽  
Gene Pairs ◽  
Gene Structures

SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

Identification, characterization, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon

2018 ◽  
Vol 18 (6) ◽  
pp. 709-724 ◽  
Author(s):  
Xiaojian Zhou ◽  
Xiaozhu Wu ◽  
Tongjian Li ◽  
Mingliang Jia ◽  
Xinshen Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Brachypodium Distachyon ◽  
Auxin Response Factor ◽  
Response Factor ◽  
Auxin Response

scholarly journals Amino Acid Transporter (AAT) Gene Family in Foxtail Millet (Setaria Italica L.): Widespread Family Expansion, Functional Differentiation, Roles in Quality Formation and Response to Abiotic Stresses

2020 ◽  
Author(s):  
Yang Yang ◽  
Yongmao Chai ◽  
Jiayi Liu ◽  
Jie Zheng ◽  
Zhangchen Zhao ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Foxtail Millet ◽  
Functional Differentiation ◽  
Setaria Italica ◽  
Evolutionary Features ◽  
Sequence Characteristics ◽  
Quality Formation

Abstract Background: Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacteria and abiotic stress by modulating the transmembrane transfer of amino acids. In this study, we performed a genome-wide screening to analyze the AAT genes in foxtail millet (Setaria italica L.), especially those associated with quality formation and abiotic stresses response.Results: A total number of 94 AAT genes were identified and divided into 12 subfamilies by their sequence characteristics and phylogenetic relationship. A large number (58/94, 62%) of AAT genes in foxtail millet were expanded via gene duplication, involving 13 tandem and 12 segmental duplication events. Tandemly duplicated genes had a significant impact on their functional differentiation via sequence variation, structural variation and expression variation. Further comparison in multiple species showed that in addition to paralogous genes, the expression variations of the orthologous AAT genes also contributed to their functional differentiation. The transcriptomic comparison of two millet cultivars verified the direct contribution of the AAT genes such as SiAAP1, SiAAP8, and SiAUX2 in the formation of grain quality. In addition, the qRT-PCR analysis suggested that several AAT genes continuously responded to diverse abiotic stresses, such as SiATLb1, SiANT1. Finally, combined with the previous studies and analysis on sequence characteristics and expression patterns of AAT genes, the possible functions of the foxtail millet AAT genes were predicted.Conclusion: This study for the first time reported the evolutionary features, functional differentiation, roles in the quality formation and response to abiotic stresses of foxtail millet AAT gene family, thus providing a framework for further functional analysis of SiAAT genes, and also contributing to the applications of AAT genes in improving the quality and resistance to abiotic stresses of foxtail millet, and other cereal crops.

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