scholarly journals Genome-Wide Characterization and Evolutionary Analyses of Purple Acid Phosphatase (PAP) Gene Family with Their Expression Profiles in Response to Low Phosphorus Stresses in Moso Bamboo (Phyllostachys edulis)

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 326
Author(s):  
Mengyan Zhou ◽  
Wanting Chen ◽  
Mingzhen Zhao ◽  
Yachao Li ◽  
Ming Li ◽  
...  
Keyword(s):  
Acid Phosphatase ◽  
Gene Family ◽  
Secretory Pathway ◽  
Expression Profiles ◽  
Moso Bamboo ◽  
Purple Acid Phosphatase ◽  
Entire Genome ◽  
Specific Expression ◽  
Conserved Motifs ◽  
Low Phosphorus

Low phosphorus increases acid phosphatase activity and transfers soluble phosphorus from the underground to the above-ground, but also inhibits the growth and development of the Moso bamboo root system. Purple acid phosphatase (PAP), a kind of acid phosphatase, plays an important role in phosphorus (P) uptake and metabolism. In our study of the Moso bamboo PAP gene family, we identified 17 Moso bamboo PAP genes (PePAP) in the entire genome and further analyzed their physical and chemical properties and functions PePAP. According to the analysis of the phylogenetic tree, special domains and conserved motifs, these 17 genes can be divided into four categories. The gene structure and conserved motifs are relatively conservative, but the 17 sequences of the PePAP domain are diverse. The prediction of the subcellular location indicated that PePAPs are mainly located in the secretory pathway. We have studied the expression levels of these PePAP in different organs, such as the roots, stems and leaves of Moso bamboo, and the results show that the expression of most PePAP genes in roots and stems seems to be higher than that in leaves. In addition to tissue-specific expression analysis, we also studied the expression of PePAPs under low phosphorus stress. Under such conditions, the PePAP genes show an increase in expression in the roots, stem and leaves, and the extent of this change varies between genes. In summary, our results reveal the evolution of the PePAP gene in the Moso bamboo genome and provide a basis for understanding the molecular mechanism of the PePAP-mediated response of Moso bamboo to low phosphorus.

scholarly journals The BBX gene family in Moso bamboo (Phyllostachys edulis): identification, characterization and expression profiles

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruifang Ma ◽  
Jialu Chen ◽  
Bin Huang ◽  
Zhinuo Huang ◽  
Zhijun Zhang
Keyword(s):  
Gene Family ◽  
Target Genes ◽  
Zinc Finger Protein ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Moso Bamboo ◽  
Model Organisms ◽  
Phyllostachys Edulis ◽  
Sequence Alignments ◽  
Specific Expression

Abstract Background The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Although BBX genes have been characterized in many model organisms, genome-wide identification of the BBX family genes have not yet been reported in Moso bamboo (Phyllostachys edulis), and the biological functions of this family remain unknown. Result In the present study, we identified 27 BBX genes in the genome of Moso bamboo, and analysis of their conserved motifs and multiple sequence alignments revealed that they all shared highly similar structures. Additionally, phylogenetic and homology analyses indicated that PeBBX genes were divided into three clusters, with whole-genome duplication (WGD) events having facilitated the expansion of this gene family. Light-responsive and stress-related cis-elements were identified by analyzing cis-elements in the promoters of all PeBBX genes. Short time-series expression miner (STEM) analysis revealed that the PeBBX genes had spatiotemporal-specific expression patterns and were likely involved in the growth and development of bamboo shoots. We further explored the downstream target genes of PeBBXs, and GO/KEGG enrichment analysis predicted multiple functions of BBX target genes, including those encoding enzymes involved in plant photosynthesis, pyruvate metabolism and glycolysis/gluconeogenesis. Conclusions In conclusion, we analyzed the PeBBX genes at multiple different levels, which will contribute to further studies of the BBX family and provide valuable information for the functional validation of this family.

scholarly journals Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yuzhu Huo ◽  
Wangdan Xiong ◽  
Kunlong Su ◽  
Yu Li ◽  
Yawen Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Panicum Virgatum ◽  
Expression Profiles ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

scholarly journals Genome-wide identification, structural analysis and expression profiles of SRS gene family in quinoa

2021 ◽  
Author(s):  
xiaolin zhu ◽  
baoqiang wang ◽  
xian wang ◽  
xiaohong wei
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Protein Interaction ◽  
Expression Profiles ◽  
Random Coil ◽  
Specific Expression ◽  
Tissue Specific ◽  
Response Elements ◽  
Tissue Specific Expression ◽  
Qrt Pcr

Abstract Based on the whole genome data information of quinoa, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (200 mmol/L), SA (200 umol/L) and low temperature (4℃) were detected by qRT-PCR. The results showed that a total of 10 SRS genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were 4 pairs of duplicated genes. The number of amino acids encoded ranged from 143 to 370, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil(Cc). Most of the CqSRS genes were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS gene was divided into three evolutionary groups, and the gene structure showed that the number of exons of CqSRS was between 2–5. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to SA, NaCl and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS family genes.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

scholarly journals Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum

2019 ◽  
Vol 20 (19) ◽  
pp. 4864 ◽  
Author(s):  
Liang Yang ◽  
Mingjun Miao ◽  
Hongjun Lyu ◽  
Xue Cao ◽  
Ju Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Ring Finger ◽  
Plant Evolution ◽  
Ring Domain ◽  
Tomato Genome ◽  
Specific Expression ◽  
Genome Wide ◽  
Ubiquitin Ligase Activity ◽  
Almost All

RING domain proteins generally have E3 ubiquitin ligase activity and are involved in degrading their substrate proteins. The roles of these proteins in growth, development, and responses to different abiotic stresses have been described well in various plant species, but little is available on tomatoes. Here, we identified 474 RING domains in 469 potential proteins encoded in the tomato genome. These RING genes were found to be located in 12 chromosomes and could be divided into 51 and 11 groups according to the conserved motifs outside the RING domain and phylogenetic analysis, respectively. Segmental duplication could be the major driver in the expansion of the tomato RING gene family. Further comparative syntenic analysis suggested that there have been functional divergences of RING genes during plant evolution and most of the RING genes in various species are under negative selection. Expression profiles derived from a transcriptomic analysis showed that most tomato RING genes exhibited tissue-specific expression patterning. Further RT–qPCR validation showed that almost all genes were upregulated by salt treatment, which was consistent with the microarray results. This study provides the first comprehensive understanding of the RING gene family in the tomato genome. Our results pave the way for further investigation of the classification, evolution, and potential functions of the RING domain genes in tomato.

scholarly journals Intron Retention: A Common Splicing Event within the Human Kallikrein Gene Family

2005 ◽  
Vol 51 (3) ◽  
pp. 506-515 ◽  
Author(s):  
Iacovos P Michael ◽  
Lisa Kurlender ◽  
Nader Memari ◽  
George M Yousef ◽  
Daisy Du ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Gene Family ◽  
Splice Variant ◽  
Hormonal Regulation ◽  
Splice Variants ◽  
Intron Retention ◽  
Expression Profiles ◽  
Catalytic Triad ◽  
Cancer Diagnostics ◽  
Specific Expression

Abstract Background: All human kallikrein (KLK) genes have at least one splice variant, some of which possess clinical utility in cancer diagnostics/prognostics. Given that introns <100 bp in length are retained in 95% of human genes and that splice variants of KLK3 and KLK4 retain intron III, we hypothesized that other proteins in this family, with a small intron III, may also retain it. Methods: Variant-specific reverse transcription-PCRs (RT-PCRs) for KLK1, KLK2, KLK5, and KLK15 were used to identify and clone the full coding sequence of intron III-containing splice variants. In addition, variant-specific RT-PCRs for the cloned KLK3 and KLK4 variants as well as for the “classical” forms of the six genes were used to determine their expression profiles in healthy tissues, their regulation by steroids, and their differential expression in prostate cancer. Results: KLK1, KLK2, KLK3, KLK4, KLK5, and KLK15 showed a common type of splice variant in which intron III is retained. Expression profiling of these splice variants revealed expression profiles similar to those of the classical mRNA forms, although the pattern of hormonal regulation was different. The KLK15 splice variant was up-regulated in 8 of 12 cancerous prostate tissues. All encoded variant proteins were predicted to be truncated and catalytically inactive because of a lack of the serine residue of the catalytic triad. Conclusions: The first six centromeric members of the KLK gene family have splice variants that retain intron III. Some variants show tissue-specific expression. The KLK15 splice variant appears to be a candidate biomarker for prostate cancer.

scholarly journals Identification and Characterization of the APX Gene Family and Its Expression Pattern under Phytohormone Treatment and Abiotic Stress in Populus trichocarpa

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 334
Author(s):  
Xue Leng ◽  
Hanzeng Wang ◽  
Shuang Zhang ◽  
Chunpu Qu ◽  
Chuanping Yang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Ammonium Concentration ◽  
Cis Elements ◽  
Specific Expression ◽  
Real Time Quantitative Pcr ◽  
Gene Structures

Ascorbate peroxidase (APX) is a member of class I of the heme-containing peroxidase family. The enzyme plays important roles in scavenging reactive oxygen species for protection against oxidative damage and maintaining normal plant growth and development, as well as in biotic stress responses. In this study, we identified 11 APX genes in the Populus trichocarpa genome using bioinformatic methods. Phylogenetic analysis revealed that the PtrAPX proteins were classifiable into three clades and the members of each clade shared similar gene structures and motifs. The PtrAPX genes were distributed on six chromosomes and four segmental-duplicated gene pairs were identified. Promoter cis-elements analysis showed that the majority of PtrAPX genes contained a variety of phytohormone- and abiotic stress-related cis-elements. Tissue-specific expression profiles indicated that the PtrAPX genes primarily function in roots and leaves. Real-time quantitative PCR (RT-qPCR) analysis indicated that PtrAPX transcription was induced in response to drought, salinity, high ammonium concentration, and exogenous abscisic acid treatment. These results provide important information on the phylogenetic relationships and functions of the APX gene family in P. trichocarpa.

scholarly journals Genome Identification of B-BOX Gene Family Members in Seven Rosacea Species and Their Expression Analysis in Response to Flower Induction in Malus domestica

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1763 ◽  
Author(s):  
Abdullah Shalmani ◽  
Sheng Fan ◽  
Peng Jia ◽  
Guofang Li ◽  
Izhar Muhammad ◽  
...  
Keyword(s):  
Gene Family ◽  
Malus Domestica ◽  
Growth And Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Structural Features ◽  
Flower Induction ◽  
Specific Expression ◽  
Flowering Induction

BBX proteins play important roles in regulating plant growth and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses. At present, the genomes of seven Rosacea fruit species have been fully sequenced. However, little is known about the BBX gene family and their evolutionary history in these Rosacea species. Therefore, in this study total, 212 BBX genes were investigated from seven Rosacea species (67 from Malus × domestica, 40 from Pyruscommunis, 22 from Rosa Chinesis, 20 from Prunuspersica, 21 from Fragariavesca, 22 from Prunusavium, and 20 from Rubusoccidentalis). The chemical properties, gene structures, and evolutionary relationships of the BBX genes were also studied. All the BBX genes were grouped into six subfamilies on the basis of their phylogenetic relationships and structural features. Analysis of gene structure, segmental and tandem duplication, gene phylogeny, and tissue-specific expression with the ArrayExpress database showed their diversification in function, quantity, and structure. The expression profiles of 19 MdBBX genes in different tissues were evaluated through qRT-PCR. These genes showed distinct transcription level among the tested tissues (bud, flower, fruit, stem, and leaf). Moreover, expression patterns of 19 MdBBX genes were examined during flowering induction time under flowering-related hormones and treatments (GA3, 6-BA, and sucrose). The expressions of the candidates BBX genes were affected and showed diverse expression profile. Furthermore, changes in response to these flowering-related hormones and treatment specifying their potential involvement in flowering induction. Based on these findings, BBX genes could be used as potential genetic markers for the growth and development of plants particularly in the area of functional analysis, and their involvement in flower induction in fruit plants.

scholarly journals Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Di Wu ◽  
Anqi Liu ◽  
Xiaoyu Qu ◽  
Jiayi Liang ◽  
Min Song
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Multigene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Specific Expression ◽  
Group I

Abstract Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

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