scholarly journals Duplication of the Phytoene Synthase Gene in the Carotenoid Biosynthetic Pathway of Watermelon

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 1007A-1007 ◽  
Author(s):  
Haejeen Bang ◽  
Sunggil Kim ◽  
Daniel I. Leskovar ◽  
Angela Davis ◽  
Stephen R. King
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Gene Expression Pattern ◽  
Gene Families ◽  
Phytoene Synthase ◽  
Pcr Analysis ◽  
Long Time ◽  
Phytoene Synthase Gene ◽  
Relationship Of ◽  
Identification And Characterization

Gene identification and characterization can be utilized for the identification of respective functions and their relationship to flesh color inheritance. Phytoene synthase (PSY), which converts two molecules of GGPP into phytoene, is the first committed step of the pathway. Previous phylogenetic analysis of PSY has indicated that PSY duplication is common in Poaceae, but rare in dicots. Degenerate PCR and RACE were used for PSY cloning. Three members of PSY gene family (PSY-A, PSY-B and PSY-C) were identified. PSY-A shared higher identity with PSY-C than PSY-B. PSYC shared 96% identity with melon PSY. PSY-C also showed a high homology with tomato PSY1, even higher than PSY-A and PSY-B. It showed a similar gene expression pattern, so we propose that PSY-C is a homologue to PSY1. RT-PCR analysis indicated that PSY-B has a different transcriptional behavior from PSY-A, similar to tomato PSY2. Therefore, PSY genes appear to be under different regulatory mechanisms. Deduced protein sequence of PSY1 or PSY2 between species has higher homology than between PSY1 and PSY2 within species. Phylogenetic analysis indicated that watermelon PSY gene family is very distantly related. Watermelon and carrot PSY gene families did not appear to cluster as closely as in Poaceae or tomato. This indicates that watermelon and carrot PSY genes are not conserved as much as PSY in tomato or Poaceae. There was no particular pattern in phylogenetic relationship of dicots. Poaceae PSY genes showed a clustering into a PSY1 group and PSY2 group. PSY duplication in watermelon provides additional evidence that PSY duplication may be a common phenomenon in dicots. They are likely to be duplicated evolutionarily a long time ago, possibly even prior to the evolution of monocot and dicot divergence.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals The phytoene synthase gene family in the Grasses

2009 ◽  
Vol 4 (3) ◽  
pp. 208-211 ◽  
Author(s):  
Faqiang Li ◽  
Oren Tzfadia ◽  
Eleanore T. Wurtzel
Keyword(s):  
Gene Family ◽  
Phytoene Synthase ◽  
Phytoene Synthase Gene

scholarly journals Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance

2020 ◽  
Author(s):  
Yinbo Ma ◽  
Sushil Satish Chhapekar ◽  
Lu Lu ◽  
Sangheon Oh ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Raphanus Sativus ◽  
Expression Profiles ◽  
Recent Common Ancestor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Encoding Genes ◽  
Identification And Characterization

Abstract Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.

scholarly journals Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family in Solanum pimpinellifolium and Arabidopsis thaliana

2020 ◽  
Vol 16 ◽  
pp. 117693432091105
Author(s):  
Huawei Wei ◽  
Jia Liu ◽  
Qinwei Guo ◽  
Luzhao Pan ◽  
Songlin Chai ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Phylogenetic Analysis ◽  
Gene Family ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Chromosome Mapping ◽  
Gene Families ◽  
Gene Clusters ◽  
Motif Analysis ◽  
Solanum Pimpinellifolium

NBS-LRR (nucleotide-binding site and leucine-rich repeat) is one of the largest resistance gene families in plants. The completion of the genome sequencing of wild tomato Solanum pimpinellifolium provided an opportunity to conduct a comprehensive analysis of the NBS-LRR gene superfamily at the genome-wide level. In this study, gene identification, chromosome mapping, and phylogenetic analysis of the NBS-LRR gene family were analyzed using the bioinformatics methods. The results revealed 245 NBS-LRRs in total, similar to that in the cultivated tomato. These genes are unevenly distributed on 12 chromosomes, and ~59.6% of them form gene clusters, most of which are tandem duplications. Phylogenetic analysis divided the NBS-LRRs into 2 subfamilies (CNL-coiled-coil NBS-LRR and TNL-TIR NBS-LRR), and the expansion of the CNL subfamily was more extensive than the TNL subfamily. Novel conserved structures were identified through conserved motif analysis between the CNL and TNL subfamilies. Compared with the NBS-LRR sequences from the model plant Arabidopsis thaliana, wide genetic variation occurred after the divergence of S. pimpinellifolium and A thaliana. Species-specific expansion was also found in the CNL subfamily in S. pimpinellifolium. The results of this study provide the basis for the deeper analysis of NBS-LRR resistance genes and contribute to mapping and isolation of candidate resistance genes in S. pimpinellifolium.

scholarly journals The Maize Phytoene Synthase Gene Family: Overlapping Roles for Carotenogenesis in Endosperm, Photomorphogenesis, and Thermal Stress Tolerance

2008 ◽  
Vol 147 (3) ◽  
pp. 1334-1346 ◽  
Author(s):  
Faqiang Li ◽  
Ratnakar Vallabhaneni ◽  
Jane Yu ◽  
Torbert Rocheford ◽  
Eleanore T. Wurtzel
Keyword(s):  
Thermal Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Phytoene Synthase ◽  
Phytoene Synthase Gene

scholarly journals Identification and Characterization of Wall-Associated Kinase (WAK) and WAK-like (WAKL) Gene Family in Juglans regia and Its Wild Related Species Juglans mandshurica

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 134
Author(s):  
Mengdi Li ◽  
Jiayu Ma ◽  
Hengzhao Liu ◽  
Mengwei Ou ◽  
Hang Ye ◽  
...  
Keyword(s):  
Gene Family ◽  
Related Species ◽  
Juglans Regia ◽  
Critical Role ◽  
Gene Expression Pattern ◽  
Gene Families ◽  
Plant Response ◽  
Potential Candidate ◽  
Evolutionary Analysis ◽  
Juglans Mandshurica

Wall-associated kinase (WAK) and WAK-like kinase (WAKL) are receptor-like kinases (RLKs), which play important roles in signal transduction between the cell wall and the cytoplasm in plants. WAK/WAKLs have been studied in many plants, but were rarely studied in the important economic walnut tree. In this study, 27 and 14 WAK/WAKL genes were identified in Juglans regia and its wild related species Juglans mandshurica, respectively. We found tandem duplication might play a critical role in the expansion of WAK/WAKL gene family in J. regia, and most of the WAK/WAKL homologous pairs underwent purified selection during evolution. All WAK/WAKL proteins have the extracellular WAK domain and the cytoplasmic protein kinase domain, and the latter was more conserved than the former. Cis-acting elements analysis showed that WAK/WAKL might be involved in plant growth and development, plant response to abiotic stress and hormones. Gene expression pattern analysis further indicated that most WAK/WAKL genes in J. regia might play a role in the development of leaves and be involved in plant response to biotic stress. Our study provides a new perspective for the evolutionary analysis of gene families in tree species and also provides potential candidate genes for studying WAK/WAKL gene function in walnuts.

scholarly journals Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance

2020 ◽  
Author(s):  
Yinbo Ma ◽  
Sushil Satish Chhapekar ◽  
Lu Lu ◽  
Sangheon Oh ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Raphanus Sativus ◽  
Expression Profiles ◽  
Recent Common Ancestor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Encoding Genes ◽  
Identification And Characterization

Abstract Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.

scholarly journals Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance

2020 ◽  
Author(s):  
Yinbo Ma ◽  
Sushil Satish Chhapekar ◽  
Lu Lu ◽  
Sangheon Oh ◽  
Sonam Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Fusarium Oxysporum ◽  
Raphanus Sativus ◽  
Expression Profiles ◽  
Recent Common Ancestor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Encoding Genes ◽  
Identification And Characterization

Abstract Background: The nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.Results: A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740).Conclusions: The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.

scholarly journals Genetic diversity of Raspberry leaf blotch emaravirus in red raspberries from Serbia

2019 ◽  
Vol 17 (1) ◽  
pp. e1004 ◽  
Author(s):  
Darko Jevremović ◽  
Aleksandar Leposavić ◽  
Svetlana A Paunović
Keyword(s):  
Phylogenetic Analysis ◽  
Large Scale ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Leaf Blotch ◽  
High Incidence ◽  
Long Time ◽  
Large Scale Survey ◽  
Polymerase Chain ◽  
Degree Of Association

Raspberry leaf blotch emaravirus (RLBV) is a recently characterised virus infecting raspberries reported in several European countries. RLBV causes yellow blotching, the distortion of leaf margins, and the twisting of raspberry leaves. For a long time, similar symptoms were attributed to the feeding damage caused by raspberry leaf and bud mite (Phyllocoptes gracilis). From 2014−2017, a large-scale survey was conducted in Serbia to investigate the degree of association of the observed symptoms with the RLBV infection. A total of 98 symptomatic and asymptomatic samples were collected from 30 locations. All collected samples were tested on the RLBV presence by reverse transcription and polymerase chain reaction (RT-PCR) using three sets of RNA-specific primers targeting RNA-1, RNA-3, and RNA-5 of the RLBV genome. RT-PCR analysis revealed high incidence of RLBV in tested samples (68.7%). RLBV was confirmed in raspberries ‘Fertödi Zamatos’, ‘Glen Ample’, ‘Meeker’, ‘Polana’, ‘Tulameen’ and ‘Willamette’. Twenty-one isolates were selected for sequencing the portion of the nucleocapsid (NC) gene. The nucleotide sequences of the isolates showed 93.2−100% identity. Phylogenetic analysis confirmed significant genetic variability of the Serbian RLBV isolates based on the nucleocapsid-encoding sequences and revealed the existence of two main clusters. Phylogenetic analysis of the 45 RLBV sequences from Finland, Slovakia, Scotland, and this study also confirmed the existence of two main clusters of isolates.

scholarly journals Genome-Wide Identification and Characterization of HSP70 Gene Family in Aquilaria sinensis (Lour.) Gilg

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 8
Author(s):  
Cuicui Yu ◽  
Mei Rong ◽  
Yang Liu ◽  
Peiwen Sun ◽  
Yanhong Xu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Pcr Analysis ◽  
Hsp70 Gene ◽  
Aquilaria Sinensis ◽  
Genome Wide ◽  
Gene Structures ◽  
Systematic Identification ◽  
Identification And Characterization

The heat shock protein 70 (HSP70) gene family perform a fundamental role in protecting plants against biotic and abiotic stresses. Aquilaria sinensis is a classic stress-induced medicinal plant, producing a valuable dark resin in a wood matrix, known as agarwood, in response to environmental stresses. The HSP70 gene family has been systematic identified in many plants, but there is no comprehensive analysis at the genomic level in A. sinensis. In this study, 15 putative HSP70 genes were identified in A. sinensis through genome-wide bioinformatics analysis. Based on their phylogenetic relationships, the 15 AsHSP70 were grouped into six sub-families that with the conserved motifs and gene structures, and the genes were mapped onto six separate linkage groups. A qRT-PCR analysis showed that the relative expression levels of all the AsHSP70 genes were up-regulated by heat stress. Subcellular localization of all HSP70s was predicted, and three were verified by transiently expressed in Arabidopsis protoplasts. Based on the expression profiles in different tissues and different layers treated with Agar-Wit, we predict AsHSP70 genes are involved in different stages of agarwood formation. The systematic identification and expression analysis of HSP70s gene family imply some of them may play important roles in the formation of agarwood. Our findings not only provide a foundation for further study their biological function in the later research in A. sinensis, but also provides a reference for the analysis of HSPs in other species.

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