scholarly journals Analysis of the oligopeptide transporter gene family in Ganoderma lucidum: structure, phylogeny, and expression patterns

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 293-302 ◽  
Author(s):  
Quanju Xiang ◽  
Keyu Shen ◽  
Xiumei Yu ◽  
Ke Zhao ◽  
Yunfu Gu ◽  
...  
Keyword(s):  
Ganoderma Lucidum ◽  
Metabolic Regulation ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Genome Database ◽  
Functional Conservation ◽  
Functional Development ◽  
Expression Profile Analysis ◽  
Starting Point ◽  
Extracellular Environment

Oligopeptide transporters (OPTs) are believed to transport broad ranges of substrates across the plasma membrane from the extracellular environment into the cell and are thought to contribute to various biological processes. In the present study, 13 putative OPTs (Gl-OPT1 to Gl-OPT13) were identified through extensive search of Ganoderma lucidum genome database. Phylogenetic analysis with OPTs from other fungi and plants indicates that these genes can be further divided into five groups. Motif compositions of OPT members are highly conserved in each group, indicative of functional conservation. Expression profile analysis of the 13 Gl-OPT genes indicated that, with the exception of Gl-OPT7–Gl-OPT9, for which no transcripts were detected, all paralogues were differentially expressed, suggesting their potential involvement in stress response and functional development of fungi. Overall, the analyses in this study provide a starting point for elucidating the functions of OPT in G. lucidum, and for understanding the complexities of metabolic regulation.

scholarly journals Functional conservation and divergence of five AP1/FUL-like genes in Marigold (Tagetes erecta)

2020 ◽  
Author(s):  
Chunling Zhang ◽  
Yalin Sun ◽  
Ludan Wei ◽  
Wenjing Wang ◽  
Hang Li ◽  
...  
Keyword(s):  
Profile Analysis ◽  
Floral Organ ◽  
Tagetes Erecta ◽  
Functional Conservation ◽  
Floral Buds ◽  
Expression Profile Analysis ◽  
Petal Identity ◽  
Organ Identity ◽  
Insight Into

Abstract Background: Members of AP1/FUL subfamily genes play an essential role in the regulation of floral meristem transition, floral organ identity, and fruit ripping. At present, there have been insufficient studies to explain the function of the AP1/FUL-like subfamily genes in Asteraceae. Results: Here, we cloned two euAP1 clade genes TeAP1-1 and TeAP1-2, and three euFUL clade genes TeFUL1, TeFUL2, and TeFUL3 from marigold (Tagetes erecta). Expression profile analysis demonstrated that TeAP1-1 and TeAP1-2 were mainly expressed in receptacles, sepals, petals, and ovules. TeFUL1 and TeFUL3 were expressed in floral buds, stems and leaves as well as in productive tissues, while TeFUL2 was mainly expressed in floral buds and vegetative tissues. Transgenic Arabidopsis lines showed that overexpression TeAP1-2 or TeFUL2 resulted in early flowering, implying that these two genes might regulate the floral transition. Yeast two-hybrid analysis indicated that TeAP1/FUL proteins only interacted with TeSEP proteins to form heterodimers, and that TeFUL2 could also form a homodimer.Conclusion: In general, TeAP1-1 and TeAP1-2 might play a conserved role in regulating sepal and petal identity, just like the role of MADS-box class A genes, while TeFUL genes might display divergent functions. This study provides an insight into molecular mechanism of AP1/FUL-like genes in Asteraceae species.

scholarly journals Genome-wide characterization, evolution and expression profiling of UDP-glycosyltransferase family in pomelo (Citrus grandis) fruit

2020 ◽  
Author(s):  
Boping Wu ◽  
Xiaohong Liu ◽  
Kai Xu ◽  
Bo Zhang
Keyword(s):  
Secondary Metabolites ◽  
Profile Analysis ◽  
Intron Insertion ◽  
Genome Database ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Major Species ◽  
Screening And Identification ◽  
Available Information

Abstract Background: Pomelo is one of the three major species of citrus. The fruit accumulates a variety of abundant secondary metabolites that affect the flavor. UDP-glycosyltransferases (UGTs) are involved in the glycosylation of secondary metabolites. Results: In the present study, we performed a genome-wide analysis of pomelo UGT family, a total of 145 UGTs was identified based on the conserved plant secondary product glycosyltransferase (PSPG) motif. These UGT genes were clustered into 16 major groups through phylogenetic analysis of these genes with other plant UGTs (A-P). Pomelo UGTs were distributed unevenly among the chromosomes. At least 10 intron insertion events were observed in these UGT genome sequences, and I-5 was identified to be the highest conserved one. The expression profile analysis of pomelo UGT genes in different fruit tissues during development and ripening was carried out by RNA-seq. Conclusions: We identified 145 UGTs in pomelo fruit through transcriptome data and citrus genome database. Our research provides available information on UGTs studies in pomelo, and provides an important research foundation for screening and identification of functional UGT genes.

Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in Teak (Tectona Grandis)

2020 ◽  
Author(s):  
Xi-Yang Wang ◽  
Jie Song ◽  
Jia-Hui Xing ◽  
Jun-Feng Liang ◽  
Bi-ying Ke
Keyword(s):  
Profile Analysis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Large Family ◽  
Tectona Grandis ◽  
Duplication Event ◽  
Whole Genome Sequence ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background: WRKY proteins comprise a large family of transcription factors that play vital roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in teak (Tectona grandis). The recent release of the whole-genome sequence of teak allowed us to perform a genome-wide investigation into the organization and expression profiling of teak WRKY genes. Results: In the present study, 102 teak WRKY (TgWRKY) genes were identified and renamed as per their positions on chromosome and scaffolds. According to their structural and phylogenetic analysis, the 102 TgWRKYs were further classified into three main groups with seceral subgroups. The segmental duplication event played a major role in the expansion of teak WRKY gene family and three WGD events were inferred. Expression profiles derived from transcriptome data exhibited distinct expression patterns of TgWRKY genes in various tissues and inresponse to different abiotic stress.Conclusions: 102 TgWRKY genes were identified in teak and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This study generated an important resource that will provide helpful information for further exploration of the TgWRKY genes role in the regulatory mechanism in response to abiotic stresses.

The graft response to transplantation: a gene expression profile analysis

2003 ◽  
Vol 15 (1) ◽  
pp. 52-64 ◽  
Author(s):  
Kenneth Christopher ◽  
Thomas F. Mueller ◽  
Rachel DeFina ◽  
Yurong Liang ◽  
Jianhua Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Constitutive Expression ◽  
Biological Processes ◽  
Heart Transplants ◽  
Self Organizing Maps ◽  
Gene Ontology Database ◽  
Expression Profile Analysis

Little is known regarding the graft response to transplantation injury. This study investigates the posttransplantation response of genes that are constitutively expressed in the heart. Constitutive heart and lymph node tissue-restricted gene expression was first analyzed with DNA microarrays. To demonstrate changes following transplantation in genes constitutively expressed in the heart, we performed vascularized murine heart transplants in allogeneic (BALB/c to B6), syngeneic (B6 to B6), and alymphoid (BALB/c-RAG2−/− to B6-RAG1−/−) experimental groups. Temporal induction of genes posttransplant relative to constitutive expression was evaluated with DNA microarrays. Dendrograms and self-organizing maps were generated to determine the dissimilarity between the experimental groups and to identify subsets of differentially expressed genes within the groups, respectively. Expression patterns of selected genes were confirmed by real-time PCR. Biological processes were assigned to genes induced posttransplant using the AnnBuilder package via the Gene Ontology Database. Post-transplant, a shift was noted in genes classified as defense, communication, and metabolism. Our results identify novel components of the graft response to transplantation injury and rejection.

scholarly journals Loss of Rb1 in the gastrointestinal tract of Apc1638N mice promotes tumors of the cecum and proximal colon

2008 ◽  
Vol 105 (40) ◽  
pp. 15493-15498 ◽  
Author(s):  
Melanie H. Kucherlapati ◽  
Kan Yang ◽  
Kunhua Fan ◽  
Mari Kuraguchi ◽  
Dmitriy Sonkin ◽  
...  
Keyword(s):  
Small Intestine ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tumor Location ◽  
Proximal Colon ◽  
Gi Tract ◽  
Expression Profile Analysis ◽  
Tumor Types

To examine the role of Rb1 in gastrointestinal (GI) tumors, we generated mice with an Apc1638N allele, Rbtm2brn floxed alleles, and a villin-cre transgene (RBVCA). These animals had exon 19 deleted from Rb1 throughout the GI tract. We have shown previously that Rb1 deficiency is insufficient for GI tumor initiation, with inactivation of an Apc allele capable of overcoming the insufficiency. In this study we demonstrate that RBVCA mice have reduced median survival because of an increase in tumor incidence and multiplicity in the cecum and the proximal colon. Large intestinal tumors are predominantly adenomas, whereas the tumors of the small intestine are a mixture of adenomas and adenocarcinomas. We find truncation mutations to the second Apc allele in tumors of both the large and small intestine. Expression profiles of duodenal and cecal tumors relative to each other show unique gene subsets up and down regulated. Substantial expression patterns compare to human colorectal cancer, including recapitulation of embryonic genes. Our results indicate that Rb1 has significant influence over tumor location in the GI tract, and that both cecal and duodenal tumors initiate through inactivation of Apc. Expression profile analysis indicates the two tumor types differentially regulate distinct sets of genes that are over-expressed in a majority of human colorectal carcinomas.

scholarly journals Genome-wide characterization, evolution and expression profiling of UDP-glycosyltransferase family in pomelo (Citrus grandis) fruit

2020 ◽  
Author(s):  
Boping Wu ◽  
Xiaohong Liu ◽  
Kai Xu ◽  
Bo Zhang
Keyword(s):  
Secondary Metabolites ◽  
Profile Analysis ◽  
Intron Insertion ◽  
Genome Database ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Major Species ◽  
Screening And Identification ◽  
Available Information

Abstract Background: Pomelo is one of the three major species of citrus. The fruit accumulates a variety of abundant secondary metabolites that affect the flavor. UDP-glycosyltransferases (UGTs) are involved in the glycosylation of secondary metabolites. Results: In the present study, we performed a genome-wide analysis of pomelo UGT family, a total of 145 UGTs was identified based on the conserved plant secondary product glycosyltransferase (PSPG) motif. These UGT genes were clustered into 16 major groups through phylogenetic analysis of these genes with other plant UGTs (A-P). Pomelo UGTs were distributed unevenly among the chromosomes. At least 10 intron insertion events were observed in these UGT genome sequences, and I-5 was identified to be the highest conserved one. The expression profile analysis of pomelo UGT genes in different fruit tissues during development and ripening was carried out by RNA-seq. Conclusions: We identified 145 UGTs in pomelo fruit through transcriptome data and citrus genome database. Our research provides available information on UGTs studies in pomelo, and provides an important research foundation for screening and identification of functional UGT genes.

scholarly journals Functional Conservation and Divergence of Five AP1/FUL-like Genes in Marigold (Tagetes erecta L.)

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 2011
Author(s):  
Chunling Zhang ◽  
Yalin Sun ◽  
Xiaomin Yu ◽  
Hang Li ◽  
Manzhu Bao ◽  
...  
Keyword(s):  
Profile Analysis ◽  
Floral Organ ◽  
Tagetes Erecta ◽  
Flower Buds ◽  
Functional Conservation ◽  
Expression Profile Analysis ◽  
Petal Identity ◽  
Organ Identity ◽  
Tagetes Erecta L ◽  
Two Hybrid

Members of AP1/FUL subfamily genes play an essential role in the regulation of floral meristem transition, floral organ identity, and fruit ripping. At present, there have been insufficient studies to explain the function of the AP1/FUL-like subfamily genes in Asteraceae. Here, we cloned two euAP1 clade genes TeAP1-1 and TeAP1-2, and three euFUL clade genes TeFUL1, TeFUL2, and TeFUL3 from marigold (Tagetes erecta L.). Expression profile analysis demonstrated that TeAP1-1 and TeAP1-2 were mainly expressed in receptacles, sepals, petals, and ovules. TeFUL1 and TeFUL3 were expressed in flower buds, stems, and leaves, as well as reproductive tissues, while TeFUL2 was mainly expressed in flower buds and vegetative tissues. Overexpression of TeAP1-2 or TeFUL2 in Arabidopsis resulted in early flowering, implying that these two genes might regulate the floral transition. Yeast two-hybrid analysis indicated that TeAP1/FUL proteins only interacted with TeSEP proteins to form heterodimers and that TeFUL2 could also form a homodimer. In general, TeAP1-1 and TeAP1-2 might play a conserved role in regulating sepal and petal identity, similar to the functions of MADS-box class A genes, while TeFUL genes might display divergent functions. This study provides a theoretical basis for the study of AP1/FUL-like genes in Asteraceae species.

scholarly journals Genome-Wide Identification and Characterization of NODULE-INCEPTION-Like Protein (NLP) Family Genes in Brassica napus

2018 ◽  
Vol 19 (8) ◽  
pp. 2270 ◽  
Author(s):  
Miao Liu ◽  
Wei Chang ◽  
Yonghai Fan ◽  
Wei Sun ◽  
Cunmin Qu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Nitrogen Deficiency ◽  
Three Dimensional ◽  
Group Iii ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Brassicaceae Species ◽  
History Of

NODULE-INCEPTION-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in responses to nitrogen deficiency. However, the evolutionary relationships and characteristics of NLP family genes in Brassica napus are unclear. In this study, we identified 31 NLP genes in B. napus, including 16 genes located in the A subgenome and 15 in the C subgenome. Subcellular localization predictions indicated that most BnaNLP proteins are localized to the nucleus. Phylogenetic analysis suggested that the NLP gene family could be divided into three groups and that at least three ancient copies of NLP genes existed in the ancestor of both monocots and dicots prior to their divergence. The ancestor of group III NLP genes may have experienced duplication more than once in the Brassicaceae species. Three-dimensional structural analysis suggested that 14 amino acids in BnaNLP7-1 protein are involved in DNA binding, whereas no binding sites were identified in the two RWP-RK and PB1 domains conserved in BnaNLP proteins. Expression profile analysis indicated that BnaNLP genes are expressed in most organs but tend to be highly expressed in a single organ. For example, BnaNLP6 subfamily members are primarily expressed in roots, while the four BnaNLP7 subfamily members are highly expressed in leaves. BnaNLP genes also showed different expression patterns in response to nitrogen-deficient conditions. Under nitrogen deficiency, all members of the BnaNLP1/4/5/9 subfamilies were upregulated, all BnaNLP2/6 subfamily members were downregulated, and BnaNLP7/8 subfamily members showed various expression patterns in different organs. These results provide a comprehensive evolutionary history of NLP genes in B. napus, and insight into the biological functions of BnaNLP genes in response to nitrogen deficiency.

scholarly journals Genome-wide characterization, evolution and expression profiling of UDP-glycosyltransferase family in pomelo (Citrus grandis) fruit

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Boping Wu ◽  
Xiaohong Liu ◽  
Kai Xu ◽  
Bo Zhang
Keyword(s):  
Secondary Metabolites ◽  
Profile Analysis ◽  
Intron Insertion ◽  
Genome Database ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Major Species ◽  
Screening And Identification ◽  
Available Information

Abstract Background Pomelo is one of the three major species of citrus. The fruit accumulates a variety of abundant secondary metabolites that affect the flavor. UDP-glycosyltransferases (UGTs) are involved in the glycosylation of secondary metabolites. Results In the present study, we performed a genome-wide analysis of pomelo UGT family, a total of 145 UGTs was identified based on the conserved plant secondary product glycosyltransferase (PSPG) motif. These UGT genes were clustered into 16 major groups through phylogenetic analysis of these genes with other plant UGTs (A-P). Pomelo UGTs were distributed unevenly among the chromosomes. At least 10 intron insertion events were observed in these UGT genome sequences, and I-5 was identified to be the highest conserved one. The expression profile analysis of pomelo UGT genes in different fruit tissues during development and ripening was carried out by RNA-seq. Conclusions We identified 145 UGTs in pomelo fruit through transcriptome data and citrus genome database. Our research provides available information on UGTs studies in pomelo, and provides an important research foundation for screening and identification of functional UGT genes.

scholarly journals Genome-wide Characterization, Evolution and Expression Profiling of Udp-glycosyltransferase Family in Pomelo (Citrus Grandis) Fruit

2020 ◽  
Author(s):  
Boping Wu ◽  
Xiaohong Liu ◽  
kai xu ◽  
Bo Zhang
Keyword(s):  
Secondary Metabolites ◽  
Profile Analysis ◽  
Intron Insertion ◽  
Genome Database ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Major Species ◽  
Screening And Identification ◽  
Available Information

Abstract Background: Pomelo is one of the three major species of citrus. The fruit accumulates a variety of abundant secondary metabolites that affect the flavor. UDP-glycosyltransferases (UGTs) are involved in the glycosylation of secondary metabolites.Results: In the present study, we performed a genome-wide analysis of pomelo UGT family, a total of 145 UGTs was identified based on the conserved plant secondary product glycosyltransferase (PSPG) motif. These UGT genes were clustered into 16 major groups through phylogenetic analysis of these genes with other plant UGTs (A-P). Pomelo UGTs were distributed unevenly among the chromosomes. At least 10 intron insertion events were observed in these UGT genome sequences, and I-5 was identified to be the highest conserved one. The expression profile analysis of pomelo UGT genes in different fruit tissues during development and ripening was carried out by RNA-seq.Conclusions: We identified 145 UGTs in pomelo fruit through transcriptome data and citrus genome database. Our research provides available information on UGTs studies in pomelo, and provides an important research foundation for screening and identification of functional UGT genes.

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