The preservation of our genetic resources and production of high-quality seeds depends on their ability to remain viable and vigorous during storage. In a quantitative trait locus analysis on seed ...longevity in Medicago truncatula, we identified the bZIP transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5). Characterization of Mt-abi5 insertion mutant seeds revealed that both the acquisition of longevity and dormancy were severely impaired. Using transcriptomes of developing Mt-abi5 seeds, we created a gene coexpression network and revealed ABI5 as a regulator of gene modules with functions related to raffinose family oligosaccharide (RFO) metabolism, late embryogenesis abundant (LEA) proteins, and photosynthesis-associated nuclear genes (PhANGs). Lower RFO contents in Mt-abi5 seeds were linked to the regulation of SEED IMBIBITION PROTEIN1. Proteomic analysis confirmed that a set of LEA polypeptides was reduced in mature Mt-abi5 seeds, whereas the absence of repression of PhANG in mature Mt-abi5 seeds was accompanied by chlorophyll and carotenoid retention. This resulted in a stress response in Mt-abi5 seeds, evident from an increase in a-tocopherol and upregulation of genes related to programmed cell death and protein folding. Characterization of abi5 mutants in a second legume species, pea (Pisum sativum), confirmed a role for ABI5 in the regulation of longevity, seed degreening, and RFO accumulation, identifying ABI5 as a prominent regulator of late seed maturation in legumes.
A novel bacterial strain was isolated from industrially contaminated waste water. In the presence of crude oil, this strain was shown to reduce the rate of total petroleum hydrocarbons (TPH) up to ...97.10% in 24 h. This bacterium was subsequently identified by 16S rRNA gene sequence analysis and affiliated to the
Serratia
genus by the RDP classifier. Its genome was sequenced and annotated, and genes coding for catechol 1,2 dioxygenase and naphthalene 1,2-dioxygenase system involved in aromatic hydrocarbon catabolism, and LadA
-
type monooxygenases involved in alkane degradation, were identified. Gas Chromatography-Mass Spectrometry (GC–MS) analysis of crude oil after biological treatment showed that
Serratia
sp. Tan611 strain was able to degrade n-alkanes (from C
13
to C
25
). This bacterium was also shown to produce a biosurfactant, the emulsification index (E24) reaching 43.47% and 65.22%, against vegetable and crude oil, respectively. Finally, the formation of a biofilm was increased in the presence of crude oil. These observations make
Serratia
sp. Tan611 a good candidate for hydrocarbon bioremediation.
Abstract
The evolutionary and adaptive potential of a pathogen is a key determinant for successful host colonization and proliferation but remains poorly known for most of the pathogens. Here, we ...used experimental evolution combined with phenotyping, genomics, and transcriptomics to estimate the adaptive potential of the bacterial plant pathogen Ralstonia solanacearum to overcome the quantitative resistance of the tomato cultivar Hawaii 7996. After serial passaging over 300 generations, we observed pathogen adaptation to within-plant environment of the resistant cultivar but no plant resistance breakdown. Genomic sequence analysis of the adapted clones revealed few genetic alterations, but we provide evidence that all but one were gain of function mutations. Transcriptomic analyses revealed that even if different adaptive events occurred in independently evolved clones, there is convergence toward a global rewiring of the virulence regulatory network as evidenced by largely overlapping gene expression profiles. A subset of four transcription regulators, including HrpB, the activator of the type 3 secretion system regulon and EfpR, a global regulator of virulence and metabolic functions, emerged as key nodes of this regulatory network that are frequently targeted to redirect the pathogen’s physiology and improve its fitness in adverse conditions. Significant transcriptomic variations were also detected in evolved clones showing no genomic polymorphism, suggesting that epigenetic modifications regulate expression of some of the virulence network components and play a major role in adaptation as well.
A novel thermophilic, anaerobic bacterium, strain F1F22
, was isolated from hot spring water collected in northern Tunisia. The cells were non-motile, Gram-negative and helical with hooked ends, ...0.5×10-32 µm in size. Growth of the strain was observed at 45-70 °C (optimum, 55 °C), in 0.0-1.0 % (w/v) NaCl (optimum without NaCl) and at pH 6.5-8.5 (optimum, pH 7.5). Yeast extract was required for growth, and the strain grew on glucose, sucrose and maltose. The major fatty acids were C
(40.2 %), iso-C
(30.2 %) and C
DMA (14.5 %). The genome consisted of a circular chromosome (2.5 Mb) containing 2672 predicted protein-encoding genes with a G+C content of 43.15 mol %. Based on a comparative 16S rRNA gene sequence analysis, strain F1F22
formed a deeply branching lineage within the phylum
, class
, order
, and had only low sequence similarity to other species of the phylum (lower than 83 %). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain F1F22
with
DSM 7334
,
ATCC 43811
and
DSM 6578
showed values between 63.26 and 63.52 %, and between 20 and 25 %. Hence, we propose strain F1F22
as a representative of a novel family (
fam. nov.), genus and species of
:
gen. nov., sp. nov. (type strain F1F22
=JCM 31314
=DSM 101182
).
A novel heavy metal resistant actinobacterial strain was isolated from an old lead and zinc mine in north-eastern Algeria. This strain was shown to resist high concentrations of heavy metals, ...including up to 500 ppm arsenic, 700 ppm cadmium, 1750 ppm chromium, 1250 ppm cobalt, 1000 ppm copper, 2750 ppm iron, 2750 ppm lead, 800 ppm mercury, 1750 ppm nickel, and 2750 ppm zinc. In addition, it was able to degrade dyes of the most used families, i.e., triphenylmethane (Malachite Green), azo (Ponceau S), and anthraquinone (Remazol Brilliant Blue R) dyes at 97.79%, 62.93%, and 39.41%, respectively. This bacterium was identified by sequencing the 16S rRNA encoding gene and affiliated to the genus
Streptomyces
by the RDP Naive Bayesian rDNA Classifier Version 2.11. The genome of
Streptomyces
sp. KY75 was sequenced using Illumina MiSeq and Oxford Nanopore. It was annotated by the MicroScope platform, and gene codings for resistance to heavy metals and dye biodecolorization were identified. It has a single linear chromosome with 7,837,660 bp and a GC content of 71.58%, 7509 of coding sequences (CDS), 66 tRNA genes, 18 rRNA genes, and 11 pseudogenes. The effect of hexavalent chromium on the dye biodegradation in liquid medium was also tested. Surprisingly, the dye biodegradation was not affected by the addition of hexavalent chromium. These observations make the actinobacterial strain
Streptomyces
sp. KY75 a good candidate for the bioremediation of textile dyeing industry effluents.
Primary root growth in the absence or presence of exogenous $\mathrm{N}{\mathrm{O}}_{3}^{-}$ was studied by a quantitative genetic approach in a recombinant inbred line (RIL) population of Medicago ...truncatula. A quantitative trait locus (QTL) on chromosome 5 appeared to be particularly relevant because it was seen in both N-free medium (LOD score 5.7; R 2 =13.7) and medium supplied with $\mathrm{N}{\mathrm{O}}_{3}^{-}$ (LOD score, 9.5; R 2 =21.1) which indicates that it would be independent of the general nutritional status. Due to its localization exactly at the peak of this QTL, the putative NRT1- $\mathrm{N}{\mathrm{O}}_{3}^{-}$ transporter (Medtr5g093170.1), closely related to Arabidopsis AtNRT1.3, a putative low-affinity nitrate transporter, appeared to be a significant candidate involved in the control of primary root growth and $\mathrm{N}{\mathrm{O}}_{3}^{-}$ sensing. Functional characterization in Xenopus oocytes using both electrophysiological and ^{15}\mathrm{N}{\mathrm{O}}_{3}^{-}$ uptake approaches showed that Medtr5g093170.1, named MtNRT1.3, encodes a dual-affinity $\mathrm{N}{\mathrm{O}}_{3}^{-}$ transporter similar to the AtNRT1.1 'transceptor' in Arabidopsis. MtNRT1.3 expression is developmentally regulated in roots, with increasing expression after completion of germination in N-free medium. In contrast to members of the NRT1 superfamily characterized so far, MtNRT1.3 is environmentally up-regulated by the absence of $\mathrm{N}{\mathrm{O}}_{3}^{-}$ and down-regulated by the addition of the ion to the roots. Split-root experiments showed that the increased expression stimulated by the absence of $\mathrm{N}{\mathrm{O}}_{3}^{-}$ was not the result of a systemic signalling of plant N status. The results suggest that MtNRT1.3 is involved in the response to N limitation, which increases the ability of the plant to acquire $\mathrm{N}{\mathrm{O}}_{3}^{-}$ under N-limiting conditions.
Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. ...Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of
cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of
belong mainly to one phylogenetic clade.
Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated
isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of
strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of
-related diseases.
DNA methylations play an important role in the biology of bacteria. Often associated with restriction modification (RM) systems, they are important drivers of bacterial evolution interfering in ...horizontal gene transfer events by providing a defence against foreign DNA invasion or by favouring genetic transfer through production of recombinogenic DNA ends. Little is known regarding the methylome of the
genus, which encompasses several pathogenic species with small genomes. Here, genome-wide detection of DNA methylations was conducted using single molecule real-time (SMRT) and bisulphite sequencing in several strains of
, an important ruminant pathogen and a model organism. Combined with whole-genome analysis, this allowed the identification of 19 methylated motifs associated with three orphan methyltransferases (MTases) and eight RM systems. All systems had a homolog in at least one phylogenetically distinct
spp. Our study also revealed that several superimposed genetic events may participate in the
dynamic epigenomic landscape. These included (i) DNA shuffling and frameshift mutations that affect the MTase and restriction endonuclease content of a clonal population and (ii) gene duplication, erosion, and horizontal transfer that modulate MTase and RM repertoires of the species. Some of these systems were experimentally shown to play a major role in mycoplasma conjugative, horizontal DNA transfer. While the versatility of DNA methylation may contribute to regulating essential biological functions at cell and population levels, RM systems may be key in mycoplasma genome evolution and adaptation by controlling horizontal gene transfers.
is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple
strains has ...identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of
is unknown. Sequencing of
strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of
methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete
spp. genomes and across the
, as well as a methylation motif associated to a phage-borne methylase unique to
UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in
UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in
evolution and its adaptation to different plants.
Abstract Background The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis ...mellifera mellifera , often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses. Results Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants. Conclusions Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes.
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