Project description:Background:An economically viable production of biofuels and biochemicals from lignocellulose requires microorganisms that can readily convert both the cellulosic and hemicellulosic fractions into product. The yeast Candida intermedia displays a high capacity for uptake and conversion of several lignocellulosic sugars including the abundant pentose d-xylose, an underutilized carbon source since most industrially relevant microorganisms cannot naturally ferment it. Thus, C. intermedia constitutes an important source of knowledge and genetic information that could be transferred to industrial microorganisms such as Saccharomyces cerevisiae to improve their capacity to ferment lignocellulose-derived xylose. Results:To understand the genetic determinants that underlie the metabolic properties of C. intermedia, we sequenced the genomes of both the in-house-isolated strain CBS 141442 and the reference strain PYCC 4715. De novo genome assembly and subsequent analysis revealed C. intermedia to be a haploid species belonging to the CTG clade of ascomycetous yeasts. The two strains have highly similar genome sizes and number of protein-encoding genes, but they differ on the chromosomal level due to numerous translocations of large and small genomic segments. The transcriptional profiles for CBS 141442 grown in medium with either high or low concentrations of glucose and xylose were determined through RNA-sequencing analysis, revealing distinct clusters of co-regulated genes in response to different specific growth rates, carbon sources and osmotic stress. Analysis of the genomic and transcriptomic data also identified multiple xylose reductases, one of which displayed dual NADH/NADPH co-factor specificity that likely plays an important role for co-factor recycling during xylose fermentation. Conclusions:In the present study, we performed the first genomic and transcriptomic analysis of C. intermedia and identified several novel genes for conversion of xylose. Together the results provide insights into the mechanisms underlying saccharide utilization in C. intermedia and reveal potential target genes to aid in xylose fermentation in S. cerevisiae.
Project description:Prevotella intermedia has long been known to be as the principal etiologic agent of periodontal diseases and associated with various systemic diseases. Previous studies showed that the intra-species difference exists in capacity of biofilm formation, antibiotic resistance, and serological reaction among P. intermedia strains. Here we report the genome sequence of P. intermedia SUNY aB G8-9K-3 (designated ATCC49046) that displays a relatively high antimicrobial resistant and biofilm-forming capacity. Genome sequencing information provides important clues in understanding the genetic bases of phenotypic differences among P. intermedia strains.
Project description:Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the monocot order Alismatales. They display the most rapid growth among flowering plants, vary?~?14-fold in genome size and comprise five genera. Spirodela is the phylogenetically oldest genus with only two mainly asexually propagating species: S. polyrhiza (2n?=?40; 160 Mbp/1C) and S. intermedia (2n?=?36; 160 Mbp/1C). This study combined comparative cytogenetics and de novo genome assembly based on PacBio, Illumina and Oxford Nanopore (ON) reads to obtain the first genome reference for S. intermedia and to compare its genomic features with those of the sister species S. polyrhiza. Both species' genomes revealed little more than 20,000 putative protein-coding genes, very low rDNA copy numbers and a low amount of repetitive sequences, mainly Ty3/gypsy retroelements. The detection of a few new small chromosome rearrangements between both Spirodela species refined the karyotype and the chromosomal sequence assignment for S. intermedia.
Project description:Prevotella intermedia, a major periodontal pathogen, is increasingly implicated in human respiratory tract and cystic fibrosis lung infections. Nevertheless, the specific mechanisms employed by this pathogen remain only partially characterized and poorly understood, largely due to its total lack of genetic accessibility. Here, using Single Molecule, Real-Time (SMRT) genome and methylome sequencing, bisulfite sequencing, in addition to cloning and restriction analysis, we define the specific genetic barriers to exogenous DNA present in two of the most widespread laboratory strains, P. intermedia ATCC 25611 and P. intermedia Strain 17. We identified and characterized multiple restriction-modification (R-M) systems, some of which are considerably divergent between the two strains. We propose that these R-M systems are the root cause of the P. intermedia transformation barrier. Additionally, we note the presence of conserved Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) systems in both strains, which could provide a further barrier to exogenous DNA uptake and incorporation. This work will provide a valuable resource during the development of a genetic system for P. intermedia, which will be required for fundamental investigation of this organism's physiology, metabolism, and pathogenesis in human disease.
Project description:Prevotella intermedia, a Gram-negative black-pigmented anaerobic rod, is frequently isolated from not only periodontal pockets but also purulent infections. We report here the complete genome sequence of P. intermedia strain 17-2, which is a non-exopolysaccharide-producing variant obtained from exopolysaccharide (EPS)-producing P. intermedia strain 17 stock culture.
Project description:Here, we report a draft genome sequence of <i>Ramalina intermedia</i> strain YAF0013. The functional annotation of <i>R. intermedia</i> provides important information related to its ability to produce secondary metabolites. The genome sequence reported here builds the basis for further genome mining.
Project description:We improved upon the previously reported draft genome of Hydrogenophaga intermedia strain PBC, a 4-aminobenzenesulfonate-degrading bacterium, by supplementing the assembly with Nanopore long reads which enabled the reconstruction of the genome as a single contig. From the complete genome, major genes responsible for the catabolism of 4-aminobenzenesulfonate in strain PBC are clustered in two distinct genomic regions. Although the catabolic genes for 4-sulfocatechol, the deaminated product of 4-aminobenzenesulfonate, are only found in H. intermedia, the sad operon responsible for the first deamination step of 4-aminobenzenesulfonate is conserved in various Hydrogenophaga strains. The absence of pabB gene in the complete genome of H. intermedia PBC is consistent with its p-aminobenzoic acid (pABA) auxotrophy but surprisingly comparative genomics analysis of 14 Hydrogenophaga genomes indicate that pABA auxotrophy is not an uncommon feature among members of this genus. Of even more interest, several Hydrogenophaga strains do not possess the genomic potential for hydrogen oxidation, calling for a revision to the taxonomic description of Hydrogenophaga as "hydrogen eating bacteria."
Project description:The Intermediate Egret <i>Ardea intermedia</i> belongs to family Ardeidae, and it is widely distributed over east Africa across the Indian subcontinent to Southeast Asia and Australia. In the present study, the total mitochondrial genome of <i>A. intermedia</i> was determined. The genome is 18,578 bases in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (CR and CRR), with a base composition of A 30.8%, G 14.0%, T 24.3% and C 30.9%. The dn/ds values of ten PCGs (ND1, ND2, ATP8, ATP6, Cox3, ND3, ND4L, ND4, ND5 and ND6) are below 1. Bayesian inference (BI) and maximum likelihood (ML) methods generated similar topologies. Phylogenies showed that <i>Ardea novaehollandiae</i> and <i>A. intermedia</i> should be assign to <i>Egretta</i> and <i>Ardea</i>, respectively. The mitogenomic data of <i>A. intermedia</i> will be useful in the conservation genetics and phylogeny of the species.
Project description:The <i>Mycalesis intermedia</i> belongs to Nymphalidae in Lepidoptera. We described the complete mitogenome of <i>M. intermedia</i>, which is typical circular duplex molecules and 15,386 bp in length, containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an A + T-rich region with macro-repeat sequences. All the inferred tRNA secondary structures show the common cloverleaf pattern, with the exception of <i>trnS1(AGN)</i> which lacks the DHU arm. The <i>M. intermedia</i> mitochondrial genome has the same gene order with other lepidopterans.
Project description:<i>Anneissia intermedia</i> (A.H. Clark, 1916) is a common crinoid found in waters along the coastlines of China, Japan, and Korea. In this study, we determined the complete mitogenome of <i>A. intermedia</i>. The genome was found to be 15,874 bp in length and consists of 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. With the exception of <i>Antedon mediterranea</i>, the gene order and genetic characteristics of the <i>A. intermedia</i> mitogenome are identical with those of the mitogenomes of other crinoids. The complete mitogenome of <i>A. intermedia</i> will contribute to enhance our understanding of the phylogeny of crinoids.