Comparison between a coffee single copy chromosomal region and Arabidopsis duplicated counterparts evidenced high level synteny between the coffee genome and the ancestral Arabidopsis genome

Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.

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Metronidazole Resistance in Prevotella spp. and Description of a New nim Gene in Prevotella baroniae

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01003-09 ◽

2009 ◽

Vol 54 (1) ◽

pp. 60-64 ◽

Cited By ~ 36

Author(s):

C. Alauzet ◽

F. Mory ◽

C. Teyssier ◽

H. Hallage ◽

J. P. Carlier ◽

...

Keyword(s):

Sequence Analysis ◽

Prolonged Exposure ◽

Tertiary Care ◽

Single Copy ◽

Clinical Isolates ◽

Teaching Hospitals ◽

Rrna Gene ◽

Prolonged Incubation ◽

Sequence Elements ◽

High Level

ABSTRACT Nonduplicate clinical isolates of Prevotella spp. recovered from patients hospitalized between 2003 and 2006 in two French tertiary-care teaching hospitals were investigated for their susceptibility to metronidazole and the presence of nim genes. Of the 188 strains tested, 3 isolates displayed reduced susceptibility to metronidazole after 48 h of incubation, while 27 additional isolates exhibited heterogeneous resistance after prolonged incubation; all 30 of the isolates were nim negative. Among the remaining 158 isolates, 7 nim-positive isolates were detected. All of these strains were identified as Prevotella baroniae by 16S rRNA gene sequence analysis and contained a new nim gene, named nimI, as determined by DNA sequence analysis. Chromosomal localization of this single-copy gene was demonstrated in all clinical isolates as well as in type strain P. baroniae DSM 16972 by using Southern hybridization. No known associated insertion sequence elements were detected upstream of the nimI gene in any of the nim-positive strains by PCR mapping. After prolonged exposure to metronidazole, stable resistant subpopulations could be selected in nimI-positive Prevotella isolates (n = 6) as well as in nim-negative Prevotella isolates (n = 6), irrespective of their initial susceptibility to this antibiotic. This study is the first description of a new nitroimidazole resistance gene in P. baroniae which seems to be silent and which might be intrinsic in this species. Moreover, our findings highlight the fact that high-level resistance to metronidazole may be easily induced in both nim-positive and nim-negative Prevotella sp. strains.

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Genetic Analysis of Azole Resistance in the Darlington Strain of Candida albicans

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.44.11.2985-2990.2000 ◽

2000 ◽

Vol 44 (11) ◽

pp. 2985-2990 ◽

Cited By ~ 54

Author(s):

Hiroshi Kakeya ◽

Yoshitsugu Miyazaki ◽

Haruko Miyazaki ◽

Katherine Nyswaner ◽

Brian Grimberg ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Amino Acids ◽

Candida Albicans ◽

Amino Acid ◽

Genetic Analysis ◽

Expression System ◽

Single Copy ◽

Gene Replacement ◽

Azole Resistance ◽

High Level

ABSTRACT High-level azole resistance in the Darlington strain ofCandida albicans was investigated by gene replacement inC. albicans and expression in Saccharomyces cerevisiae. We sequenced the ERG11 gene, which encodes the sterol C14α-demethylase, from our copy of the Darlington strain. Both alleles contained the histidine for tyrosine substitution at position 132 (Y132H) reported in Darlington by others, but we also found a threonine-for-isoleucine substitution (I471T) not previously reported in the C. albicans ERG11. The encoded I471T change in amino acids conferred azole resistance when overexpressed alone and increased azole resistance when added to the Y132H amino acid sequence in an S. cerevisiae expression system. Replacement of one copy of ERG11 in an azole-susceptible strain of C. albicans with a single copy of the Darlington ERG11 resulted in expression of the integrated copy and a modest increase in azole resistance. The profound azole resistance of the Darlington strain is the result of multiple mutations.

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Detection of Bifidobacterium animalis subsp. lactis (Bb12) in the Intestine after Feeding of Sows and Their Piglets

Applied and Environmental Microbiology ◽

10.1128/aem.00309-08 ◽

2008 ◽

Vol 74 (20) ◽

pp. 6338-6347 ◽

Cited By ~ 24

Author(s):

Gloria Solano-Aguilar ◽

Harry Dawson ◽

Marta Restrepo ◽

Kate Andrews ◽

Bryan Vinyard ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Protein Biosynthesis ◽

Bifidobacterium Longum ◽

Elongation Factor ◽

Single Copy ◽

Bifidobacterium Animalis ◽

Gene Copies ◽

Intestinal Contents ◽

High Level

ABSTRACT A real-time PCR method has been developed to distinguish Bifidobacterium animalis subspecies in the gastrointestinal tracts of pigs. Identification of a highly conserved single-copy tuf gene encoding the elongation factor Tu involved in bacterial protein biosynthesis was used as a marker to differentiate homologous Bifidobacterium animalis subsp. lactis (strain Bb12) from Bifidobacterium animalis subsp. animalis, as well as Bifidobacterium suis, Bifidobacterium breve, Bifidobacterium longum, several species of Lactobacillus, and Enterococcus faecium. Real-time PCR detection of serially diluted DNA extracted from a pure culture of Bb12 was linear for bacterial numbers ranging from 10 to 10,000 tuf gene copies per PCR (r 2 = 0.99). Relative differences in Bb12 bacterial numbers in pigs fed daily with Bb12 were determined after detection of Bb12 tuf gene copies in DNA extracted from the intestinal contents. Piglets treated with Bb12 immediately after birth maintained a high level of Bb12 in their large intestines with continuous daily administration of Bb12. Piglets born to Bb12-treated sows during the last third of their gestation and also treated with Bb12 at birth (T/T group) had a higher number of Bb12 organisms per gram of intestinal contents compared to placebo-treated piglets born to placebo-treated sows (C/C group), Bb12-treated sows (T/C group), or piglets born to placebo sows but treated with Bb12 immediately after birth (C/T group). In addition, there was a significant increase in gene expression for Toll-like receptor 9 (TLR9) in piglets from the T/T group, with no change in TLR2 and TLR4. These findings suggest that the tuf gene represents a specific and functional marker for detecting Bifidobacterium animalis subsp. lactis strain Bb12 within the microbiota of the intestine.

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bcgTree: automatized phylogenetic tree building from bacterial core genomes

Genome ◽

10.1139/gen-2015-0175 ◽

2016 ◽

Vol 59 (10) ◽

pp. 783-791 ◽

Cited By ~ 46

Author(s):

Markus J. Ankenbrand ◽

Alexander Keller

Keyword(s):

Markov Models ◽

Bacterial Species ◽

Single Copy ◽

Bacterial Strains ◽

Bacterial Genomes ◽

Sequencing Technologies ◽

Genus Lactobacillus ◽

Standard Task ◽

Tree Building ◽

High Level

The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate its performance in both low- and high-level taxonomy test sets. The tool is freely available at github ( https://github.com/iimog/bcgTree ) and our institutional homepage ( http://www.dna-analytics.biozentrum.uni-wuerzburg.de ).

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Role of upstream DNase I hypersensitive sites in the regulation of human alpha globin gene expression

Blood ◽

10.1182/blood.v82.5.1666.bloodjournal8251666 ◽

1993 ◽

Vol 82 (5) ◽

pp. 1666-1671

Author(s):

JA Sharpe ◽

RJ Summerhill ◽

P Vyas ◽

G Gourdon ◽

DR Higgs ◽

...

Keyword(s):

Gene Expression ◽

Globin Gene ◽

Single Copy ◽

Beta Globin ◽

Hypersensitive Sites ◽

Alpha Globin ◽

Alpha Gene ◽

High Level ◽

Globin Gene Expression

Erythroid-specific DNase 1 hypersensitive sites have been identified at the promoters of the human alpha-like genes and within the region from 4 to 40 kb upstream of the gene cluster. One of these sites, HS-40, has been shown previously to be the major regulator of tissue-specific alpha-globin gene expression. We have now examined the function of other hypersensitive sites by studying the expression in mouse erythroleukemia (MEL) cells of various fragments containing these sites attached to HS-40 and an alpha-globin gene. High level expression of the alpha gene was observed in all cases. When clones of MEL cells bearing a single copy of the alpha-globin gene fragments were examined, expression levels were similar to those of the endogenous mouse alpha genes and similar to MEL cells bearing beta gene constructs under the control of the beta-globin locus control region. However, there was no evidence that the additional hypersensitive sites increased the level of expression or conferred copy number dependence on the expression of a linked alpha gene in MEL cells.

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Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

Plants ◽

10.3390/plants9030296 ◽

2020 ◽

Vol 9 (3) ◽

pp. 296 ◽

Cited By ~ 3

Author(s):

Jacinta N. Munyao ◽

Xiang Dong ◽

Jia-Xin Yang ◽

Elijah M. Mbandi ◽

Vincent O. Wanga ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Important Species ◽

Genomic Resources ◽

Phylogenetic Studies ◽

Chloroplast Genomes ◽

Cp Genome ◽

High Level

The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.

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Polychlorinated Biphenyl Rhizoremediation by Pseudomonas fluorescens F113 Derivatives, Using a Sinorhizobium meliloti nod System To Drive bph Gene Expression

Applied and Environmental Microbiology ◽

10.1128/aem.71.5.2687-2694.2005 ◽

2005 ◽

Vol 71 (5) ◽

pp. 2687-2694 ◽

Cited By ~ 100

Author(s):

Marta Villacieros ◽

Clare Whelan ◽

Martina Mackova ◽

Jesper Molgaard ◽

María Sánchez-Contreras ◽

...

Keyword(s):

Gene Expression ◽

Pseudomonas Fluorescens ◽

Sinorhizobium Meliloti ◽

Polychlorinated Biphenyl ◽

Expression System ◽

Single Copy ◽

Bacterial Strains ◽

High Level Expression ◽

High Level ◽

Biodegradation Genes

ABSTRACT Rhizoremediation of organic chemicals requires high-level expression of biodegradation genes in bacterial strains that are excellent rhizosphere colonizers. Pseudomonas fluorescens F113 is a biocontrol strain that was shown to be an excellent colonizer of numerous plant rhizospheres, including alfalfa. Although a derivative of F113 expressing polychlorinated biphenyl (PCB) biodegradation genes (F113pcb) has been reported previously, this strain shows a low level of bph gene expression, limiting its rhizoremediation potential. Here, a high-level expression system was designed from rhizobial nod gene regulatory relays. Nod promoters were tested in strain F113 by using β-galactosidase transcriptional fusions. This analysis showed that nodbox 4 from Sinorhizobium meliloti has a high level of expression in F113 that is dependent on an intact nodD1 gene. A transcriptional fusion of a nodbox cassette containing the nodD1 gene and nodbox 4 fused to a gfp gene was expressed in the alfalfa rhizosphere. The bph operon from Burkholderia sp. strain LB400 was cloned under the control of the nodbox cassette and was inserted as a single copy into the genome of F113, generating strain F113L::1180. This new genetically modified strain has a high level of BphC activity and grows on biphenyl as a sole carbon and energy source at a growth rate that is more than three times higher than that of F113pcb. Degradation of PCBs 3, 4, 5, 17, and 25 was also much faster in F113L::1180 than in F113pcb. Finally, the modified strain cometabolized PCB congeners present in Delor103 better than strain LB400, the donor of the bph genes used.

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Identification and characterization of microsatellites in Norway spruce (Picea abies K.)

Genome ◽

10.1139/g97-055 ◽

1997 ◽

Vol 40 (4) ◽

pp. 411-419 ◽

Cited By ~ 111

Author(s):

Antonella Pfeiffer ◽

Angelo M. Olivieri ◽

Michele Morgante

Keyword(s):

Picea Abies ◽

Norway Spruce ◽

Repetitive Dna ◽

Genome Mapping ◽

Single Copy ◽

Mendelian Inheritance ◽

Single Locus ◽

Dot Blot ◽

Genomic Libraries ◽

High Level

Norway spruce (Picea abies) genomic libraries were screened for presence of dinucleotide AC/GT and AG/CT microsatellites (or simple sequence repeats). On average, one (AG)n microsatellite every 194 kb and one (AC)n microsatellite every 406 kb were found. Forty-six positive clones were sequenced and primers flanking 24 AG microsatellites and 12 AC microsatellites designed. Only seven (20%) of them produced the expected single-locus polymorphic pattern when used to amplify Norway spruce DNAs. The other primer pairs gave either multiple bands or bad amplification, or a single monomorphic fragment. Such a small proportion of successful primer pairs was attributed to the high level of complexity of the Norway spruce genome. Dot blot analysis of the clones showed that many of them contained repetitive DNA and that those giving the single-locus polymorphic patterns usually corresponded to single-copy sequences. A family of repetitive DNA that contained AG repeats was identified and was present in about 40 000 copies per haploid genome. Simple Mendelian inheritance was observed for all the polymorphisms tested. The average number of alleles was 13, ranging from 6 to 22, and the expected heterozygosity was 0.79 when seven microsatellites were used to genotype a panel of 18 trees representing different populations. Compared with isozymes, microsatellites are about five times more informative and could provide an extremely valuable source of markers for genome mapping and genetic diversity studies.Key words: microsatellite, repetitive DNA, hypervariability, Picea abies, genome complexity.

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Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

GigaScience ◽

10.1093/gigascience/giaa013 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 1

Author(s):

Xupo Ding ◽

Wenli Mei ◽

Qiang Lin ◽

Hao Wang ◽

Jun Wang ◽

...

Keyword(s):

Genome Assembly ◽

Gene Annotation ◽

Draft Genome ◽

Single Copy ◽

Aquilaria Sinensis ◽

Final Size ◽

Plant Resources ◽

Protein Coding ◽

High Level ◽

Chromosome Level

Abstract Backgroud Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information. Findings We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18–84.37 million years ago. Conclusions Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.

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