Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots, and eudicots

Genome ◽  
2010 ◽  
Vol 53 (7) ◽  
pp. 533-544 ◽  
Author(s):  
Haiying Liang ◽  
Abdelali Barakat ◽  
Scott E. Schlarbaum ◽  
Dina F. Mandoli ◽  
John E. Carlson
Keyword(s):  
Artificial Chromosome ◽  
Amino Acid Sequences ◽  
Basal Angiosperm ◽  
Yellow Poplar ◽  
Bac Clone ◽  
Poplar Genome ◽  
Photoperiodic Flowering ◽  
Angiosperm Species ◽  
Pyrosequencing Technology ◽  
Angiosperm Genome

GIGANTEA plays an important role in the control of circadian rhythms and photoperiodic flowering. The GIGANTEA gene has been studied in various species, but not in basal angiosperms. Moreover, to the best of our knowledge, no study of the genome organization of a basal angiosperm has yet been published. In this study, we sequenced a bacterial artificial chromosome (BAC) harboring GIGANTEA from yellow-poplar ( Liriodendron tulipifera L.) and compared the genomic organization of this gene in yellow-poplar with that in other species from various angiosperm clades. This is the first report on the gene structure and organization of a large contig in any basal angiosperm species. The BAC clone, covering a region of approximately 122 kb from the yellow-poplar genome, was sequenced and assembled by coupling the 454 pyrosequencing technology with ABI capillary sequencing. In addition to GIGANTEA, the gene RPS18.A (encoding ribosomal protein S18.A) was found in this segment of the genome. We found that gene content and order in this region of the yellow-poplar genome were similar to those in the corresponding region in eudicots but not in Oryza sativa and Sorghum bicolor , implying that clustering of the GIGANTEA and RPS18.A genes is ancestral and separation of the genes occurred after the phylogenetic split of monocots from dicots. Phylogenetic analysis of GIGANTEA amino acid sequences placed yellow-poplar closer to eudicots than to monocots. In addition, evidence for transposition and large insertions and duplications was found, suggesting multiple and complex mechanisms of basal angiosperm genome evolution.

scholarly journals Large-scale survey reveals pervasiveness and potential function of endogenous geminiviral sequences in plants

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Vikas Sharma ◽  
Pierre Lefeuvre ◽  
Philippe Roumagnac ◽  
Denis Filloux ◽  
Pierre-Yves Teycheney ◽  
...  
Keyword(s):  
Large Scale ◽  
Green Plant ◽  
Tea Plant ◽  
Basal Angiosperm ◽  
Copy Numbers ◽  
The Family ◽  
Camellia Species ◽  
Large Scale Survey ◽  
Angiosperm Species ◽  
Host Genes

Abstract The family Geminiviridae contains viruses with single-stranded DNA genomes that have been found infecting a wide variety of angiosperm species. The discovery within the last 25 years of endogenous geminivirus-like (EGV) elements within the nuclear genomes of several angiosperms has raised questions relating to the pervasiveness of EGVs and their impacts on host biology. Only a few EGVs have currently been characterized and it remains unclear whether any of these have influenced, or are currently influencing, the evolutionary fitness of their hosts. We therefore undertook a large-scale search for evidence of EGVs within 134 genome and 797 transcriptome sequences of green plant species. We detected homologues of geminivirus replication-associated protein (Rep) genes in forty-two angiosperm species, including two monocots, thirty-nine dicots, and one ANITA-grade basal angiosperm species (Amborella trichopoda). While EGVs were present in the members of many different plant orders, they were particularly common within the large and diverse order, Ericales, with the highest copy numbers of EGVs being found in two varieties of tea plant (Camellia sinensis). Phylogenetic and clustering analyses revealed multiple highly divergent previously unknown geminivirus Rep lineages, two of which occur in C.sinensis alone. We find that some of the Camellia EGVs are likely transcriptionally active, sometimes co-transcribed with the same host genes across several Camellia species. Overall, our analyses expand the known breadths of both geminivirus diversity and geminivirus host ranges, and strengthens support for the hypothesis that EGVs impact the biology of their hosts.

scholarly journals Use of Recombination-Mediated Genetic Engineering for Construction of Rescue Human Cytomegalovirus Bacterial Artificial Chromosome Clones

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Kalpana Dulal ◽  
Benjamin Silver ◽  
Hua Zhu
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Homologous Recombination ◽  
Human Cytomegalovirus ◽  
Artificial Chromosome ◽  
Bac Clone ◽  
Dna Viruses ◽  
E Coli ◽  
Recombination System ◽  
Capture Method

Bacterial artificial chromosome (BAC) technology has contributed immensely to manipulation of larger genomes in many organisms including large DNA viruses like human cytomegalovirus (HCMV). The HCMV BAC clone propagated and maintained insideE. coliallows for accurate recombinant virus generation. Using this system, we have generated a panel of HCMV deletion mutants and their rescue clones. In this paper, we describe the construction of HCMV BAC mutants using a homologous recombination system. A gene capture method, or gap repair cloning, to seize large fragments of DNA from the virus BAC in order to generate rescue viruses, is described in detail. Construction of rescue clones using gap repair cloning is highly efficient and provides a novel use of the homologous recombination-based method inE. colifor molecular cloning, known colloquially as recombineering, when rescuing large BAC deletions. This method of excising large fragments of DNA provides important prospects forin vitrohomologous recombination for genetic cloning.

scholarly journals The Avr1b Locus of Phytophthora sojae Encodes an Elicitor and a Regulator Required for Avirulence on Soybean Plants Carrying Resistance Gene Rps1b

2004 ◽  
Vol 17 (4) ◽  
pp. 394-403 ◽  
Author(s):  
Weixing Shan ◽  
Minh Cao ◽  
Dan Leung ◽  
Brett M. Tyler
Keyword(s):  
Resistance Gene ◽  
Artificial Chromosome ◽  
Phytophthora Sojae ◽  
Secreted Protein ◽  
Bac Clone ◽  
Bac Contig ◽  
Soybean Plants ◽  
Substitution Mutations ◽  
Race 2 ◽  
Soybean Leaves

We have used map-based approaches to clone a locus containing two genes, Avr1b-1 and Avr1b-2, required for avirulence of the oomycete pathogen Phytophthora sojae (Kaufmann & Gerdemann) on soybean plants carrying resistance gene Rps1b. Avr1b-1 was localized to a single 60-kb bacterial artificial chromosome (BAC) clone by fine-structure genetic mapping. Avr1b-1 was localized within the 60-kb region by identification of an mRNA that is expressed in a race-specific and infection-specific manner and that encodes a small secreted protein. When the Avr1b-1 protein was synthesized in the yeast Pichia pastoris and the secreted protein infiltrated into soybean leaves, it triggered a hypersensitive response specifically in host plants carrying the Rps1b resistance gene. This response eventually spread to the entire inoculated plant. In some isolates of P. sojae virulent on Rps1b-containing cultivars, such as P7081 (race 25) and P7076 (race 19), the Avr1b-1 gene had numerous substitution mutations indicative of strong divergent selection. In other isolates, such as P6497 (race 2) and P9073 (race 25), there were no substitutions in Avr1b-1, but Avr1b-1 mRNA did not accumulate. Genetic complementation experiments with P6497 revealed the presence of a second gene, Avr1b-2, required for the accumulation of Avr1b-1 mRNA. Avr1b-2 was genetically mapped to the same BAC contig as Avr1b-1, using a cross between P7064 (race 7) and P6497. The Avr1k gene, required for avirulence on soybean cultivars containing Rps1k, was mapped to the same interval as Avr1b-1.

scholarly journals Cloning of the Koi Herpesvirus Genome as an Infectious Bacterial Artificial Chromosome Demonstrates That Disruption of the Thymidine Kinase Locus Induces Partial Attenuation in Cyprinus carpio koi

2008 ◽  
Vol 82 (10) ◽  
pp. 4955-4964 ◽  
Author(s):  
B. Costes ◽  
G. Fournier ◽  
B. Michel ◽  
C. Delforge ◽  
V. Stalin Raj ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Thymidine Kinase ◽  
Artificial Chromosome ◽  
Wild Type ◽  
Bac Clone ◽  
Recombinant Viruses ◽  
Koi Herpesvirus ◽  
Cyprinus Carpio Koi

ABSTRACT Koi herpesvirus (KHV) is the causative agent of a lethal disease in koi and common carp. In the present study, we describe the cloning of the KHV genome as a stable and infectious bacterial artificial chromosome (BAC) clone that can be used to produce KHV recombinant strains. This goal was achieved by the insertion of a loxP-flanked BAC cassette into the thymidine kinase (TK) locus. This insertion led to a BAC plasmid that was stably maintained in bacteria and was able to regenerate virions when permissive cells were transfected with the plasmid. Reconstituted virions free of the BAC cassette but carrying a disrupted TK locus (the FL BAC-excised strain) were produced by the transfection of Cre recombinase-expressing cells with the BAC. Similarly, virions with a wild-type revertant TK sequence (the FL BAC revertant strain) were produced by the cotransfection of cells with the BAC and a DNA fragment encoding the wild-type TK sequence. Reconstituted recombinant viruses were compared to the wild-type parental virus in vitro and in vivo. The FL BAC revertant strain and the FL BAC-excised strain replicated comparably to the parental FL strain. The FL BAC revertant strain induced KHV infection in koi carp that was indistinguishable from that induced by the parental strain, while the FL BAC-excised strain exhibited a partially attenuated phenotype. Finally, the usefulness of the KHV BAC for recombination studies was demonstrated by the production of an ORF16-deleted strain by using prokaryotic recombination technology. The availability of the KHV BAC is an important advance that will allow the study of viral genes involved in KHV pathogenesis, as well as the production of attenuated recombinant candidate vaccines.

scholarly journals Bmp2 Transcription in Osteoblast Progenitors Is Regulated by a Distant 3′ Enhancer Located 156.3 Kilobases from the Promoter

2007 ◽  
Vol 27 (8) ◽  
pp. 2934-2951 ◽  
Author(s):  
Ronald L. Chandler ◽  
Kelly J. Chandler ◽  
Karen A. McFarland ◽  
Douglas P. Mortlock
Keyword(s):  
Risk Factor ◽  
Osteoblast Differentiation ◽  
Expression Patterns ◽  
Artificial Chromosome ◽  
Regulatory Elements ◽  
Bone Morphogenetic Protein 2 ◽  
Regulatory Function ◽  
Regulatory Sequences ◽  
Bac Clone ◽  
Osteoblast Progenitor

ABSTRACT Bone morphogenetic protein 2 (encoded by Bmp2) has been implicated as an important signaling ligand for osteoblast differentiation and bone formation and as a genetic risk factor for osteoporosis. To initially survey a large genomic region flanking the mouse Bmp2 gene for cis-regulatory function, two bacterial artificial chromosome (BAC) clones that extend far upstream and downstream of the gene were engineered to contain a lacZ reporter cassette and tested in transgenic mice. Each BAC clone directs a distinct subset of normal Bmp2 expression patterns, suggesting a modular arrangement of distant Bmp2 regulatory elements. Strikingly, regulatory sequences required for Bmp2 expression in differentiating osteoblasts, as well as tooth buds, hair placodes, kidney, and other tissues, are located more than 53 kilobases 3′ to the promoter. By testing BACs with engineered deletions across this distant 3′ region, we parsed these regulatory elements into separate locations and more closely refined the location of the osteoblast progenitor element. Finally, a conserved osteoblast progenitor enhancer was identified within a 656-bp sequence located 156.3 kilobases 3′ from the promoter. The identification of this enhancer should permit further investigation of upstream regulatory mechanisms that control Bmp2 transcription during osteoblast differentiation and are relevant to further studies of Bmp2 as a candidate risk factor gene for osteoporosis.

Cytological characterization of sunflower by in situ hybridization using homologous rDNA sequences and a BAC clone containing highly represented repetitive retrotransposon-like sequences

Genome ◽  
2010 ◽  
Vol 53 (3) ◽  
pp. 172-179 ◽  
Author(s):  
P. Talia ◽  
E. Greizerstein ◽  
C. Díaz Quijano ◽  
L. Peluffo ◽  
L. Fernández ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Chromosome Complement ◽  
Artificial Chromosome ◽  
Bac Clone ◽  
Clear Cut ◽  
Rdna Sequences ◽  
Rdna Signal ◽  
Or Genes ◽  
Sunflower Genome

In the present work we report new tools for the characterization of the complete chromosome complement of sunflower ( Helianthus annuus L.), using a bacterial artificial chromosome (BAC) clone containing repetitive sequences with similarity to retrotransposons and a homologous rDNA sequence isolated from the sunflower genome as probes for FISH. The rDNA signal was found in 3 pairs of chromosomes, coinciding with the location of satellites. The BAC clone containing highly represented retroelements hybridized with all the chromosome complement in FISH, and used together with the rDNA probe allowed the discrimination of all chromosome pairs of sunflower. Their distinctive distribution pattern suggests that these probes could be useful for karyotype characterization and for chromosome identification. The karyotype could be subdivided into 3 clear-cut groups of 12 metacentric pairs, 1 submetacentric pair, and 4 subtelocentric pairs, thus resolving previously described karyotype controversies. The use of BAC clones containing single sequences of specific markers and (or) genes associated with important agricultural traits represents an important tool for future locus-specific identification and physical mapping.

Pf4-Cre transgenic mice allow the generation of lineage-restricted gene knockouts for studying megakaryocyte and platelet function in vivo

Blood ◽  
2006 ◽  
Vol 109 (4) ◽  
pp. 1503-1506 ◽  
Author(s):  
Ralph Tiedt ◽  
Tibor Schomber ◽  
Hui Hao-Shen ◽  
Radek C. Skoda
Keyword(s):  
Transgenic Mice ◽  
Platelet Function ◽  
Artificial Chromosome ◽  
Cre Recombinase ◽  
Integrin Β1 ◽  
Bac Clone ◽  
Platelet Factor ◽  
Conditional Allele ◽  
Platelet Formation

Abstract To generate transgenic mice that express Cre-recombinase exclusively in the megakaryocytic lineage, we modified a mouse bacterial artificial chromosome (BAC) clone by homologous recombination and replaced the first exon of the platelet factor 4 (Pf4), also called CXCL4, with a codon-improved Cre cDNA. Several strains expressing the transgene were obtained and one strain, Q3, was studied in detail. Crossing Q3 mice with the ROSA26-lacZ reporter strain showed that Cre-recombinase activity was confined to megakaryocytes. These results were further verified by crossing the Q3 mice with a strain containing loxP-flanked integrin β1. Excision of this conditional allele in megakaryocytes was complete at the DNA level, and platelets were virtually devoid of the integrin β1 protein. The Pf4-Cre transgenic strain will be a valuable tool to study megakaryopoiesis, platelet formation, and platelet function.

scholarly journals Oncogenicity of Virulent Marek's Disease Virus Cloned as Bacterial Artificial Chromosomes

2004 ◽  
Vol 78 (23) ◽  
pp. 13376-13380 ◽  
Author(s):  
Lawrence Petherbridge ◽  
Andrew C. Brown ◽  
Susan J. Baigent ◽  
Ken Howes ◽  
Melanie A. Sacco ◽  
...  
Keyword(s):  
Disease Virus ◽  
Artificial Chromosome ◽  
Marek's Disease Virus ◽  
Marek's Disease ◽  
Wild Type Virus ◽  
Marek’S Disease Virus ◽  
Marek’S Disease ◽  
Bac Clone ◽  
Artificial Chromosomes ◽  
Bac Clones

ABSTRACT Marek's disease virus (MDV) is an oncogenic alphaherpesvirus that induces T-cell lymphomas in poultry. We report the construction of bacterial artificial chromosome (BAC) clones of the highly oncogenic RB-1B strain by inserting mini-F vector sequences into the US2 locus. MDV reconstituted from two BAC clones induced rapid-onset lymphomas similar to those induced by the wild-type virus. Virus reconstituted from another BAC clone that showed a 7.7-kbp deletion in the internal and terminal unique long repeat regions was nononcogenic, suggesting that the deleted region may be associated with oncogenicity. The generation of the oncogenic BAC clones of MDV is a significant step in unraveling the oncogenic determinants of this virus.

scholarly journals The α- and β-subunits of the Human UDP-N-acetylglucosamine:Lysosomal Enzyme Phosphotransferase Are Encoded by a Single cDNA

2005 ◽  
Vol 280 (43) ◽  
pp. 36141-36149 ◽  
Author(s):  
Mariko Kudo ◽  
Ming Bao ◽  
Anil D'Souza ◽  
Fu Ying ◽  
Huaqin Pan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Catalytic Domain ◽  
Amino Acid Sequences ◽  
Subunit Structure ◽  
Bac Clone ◽  
Significant Similarity ◽  
Α Subunit ◽  
Γ Subunit ◽  
Mannose 6 Phosphate ◽  
Α And Β Subunits

Lysosomal enzymes are targeted to the lysosome through binding to mannose 6-phosphate receptors because their glycans are modified with mannose 6-phosphate. This modification is catalyzed by UDP-N-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase). Bovine GlcNAc-phosphotransferase was isolated using monoclonal antibody affinity chromatography, and an α2β2γ2-subunit structure was proposed. Although cDNA encoding the γ-subunit has been described, cDNAs for the α- and β-subunits have not. Using partial amino acid sequences from the bovine α- and β-subunits, we have isolated a human cDNA that encodes both the α- and β-subunits. Both subunits contain a single predicted membrane-spanning domain. The α- and β-subunits appear to be generated by a proteolytic cleavage at the Lys928-Asp929 bond. Transfection of 293T cells with the α/β-subunits-precursor cDNA with or without the γ-subunit cDNA results in a 3.6- or 17-fold increase in GlcNAc-phosphotransferase activity in cell lysates, suggesting that the precursor cDNA contains the catalytic domain. The sequence lacks significant similarity with any described vertebrate enzyme except for two Notch-like repeats in the α-subunit. However, a 112-amino acid sequence is highly similar to a group of bacterial capsular polymerases (46% identity). A BAC clone containing the gene that spanned 85.3 kb and was composed of 21 exons was sequenced and localized to chromosome 12q23. We now report the cloning of both the cDNA and genomic DNA of the precursor of Glc-NAc-phosphotransferase. The completion of cloning all three subunits of GlcNAc-phosphotransferase allows expression of recombinant enzyme and dissection of lysosomal targeting disorders.

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