Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft Genome Sequence of Umbilicaria muehlenbergii KoLRILF000956, a Lichen-Forming Fungus Amenable to Genetic Manipulation.

ABSTRACT: Umbilicaria muehlenbergii strain KoLRILF000956 is amenable to Agrobacterium tumefaciens-mediated transformation (ATMT), making it the only known genetically tractable lichen-forming fungus to date. We report another advancement in lichen genetics, a draft genome assembly for U. muehlenbergii with a size of 34,812,353 bp and a GC content of 47.12%, consisting of seven scaffolds.

SUBMITTER: Park SY

PROVIDER: S-EPMC3999499 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Draft Genome Sequence of Umbilicaria muehlenbergii KoLRILF000956, a Lichen-Forming Fungus Amenable to Genetic Manipulation.

Park Sook-Young SY Choi Jaeyoung J Lee Gir-Won GW Jeong Min-Hye MH Kim Jung A JA Oh Soon-Ok SO Lee Yong-Hwan YH Hur Jae-Seoun JS

Genome announcements 20140424 2

Umbilicaria muehlenbergii strain KoLRILF000956 is amenable to Agrobacterium tumefaciens-mediated transformation (ATMT), making it the only known genetically tractable lichen-forming fungus to date. We report another advancement in lichen genetics, a draft genome assembly for U. muehlenbergii with a size of 34,812,353 bp and a GC content of 47.12%, consisting of seven scaffolds. ...[more]

PMID: 24762942

Similar Datasets

Draft Genome Sequence of Lichen-Forming Fungus Caloplaca flavorubescens Strain KoLRI002931.

Project description:Here we report a draft genome sequence of Caloplaca flavorubescens strain KoLRI002931, isolated from the bark of a gingko tree at Mt. Deogyu, Muju, South Korea. The genome sequence is 34,455,815 bp, with a GC content of 41.89%, consisting of 36 scaffolds.

| S-EPMC3757454 | biostudies-literature

Draft Genome Sequence of Lichen-Forming Fungus Cladonia metacorallifera Strain KoLRI002260.

Project description:The lichen-forming fungus Cladonia metacorallifera strain KoLRI002260 is capable of producing a number of secondary metabolites, including usnic, didymic, and squamatic acids, which have antitumor, antioxidant, and antibiotic activities. The draft genome assembly has a size of 36,682,060 bp, with a G+C content of 44.91%, and consists of 30 scaffolds.

| S-EPMC3924382 | biostudies-literature

Draft Genome Sequence and Annotation of the Lichen-Forming Fungus Arthonia radiata.

Project description:We report here the draft de novo genome assembly, transcriptome assembly, and annotation of the lichen-forming fungus Arthonia radiata (Pers.) Ach., the type species for Arthoniomycetes, a class of lichen-forming, lichenicolous, and saprobic Ascomycota. The genome was assembled using overlapping paired-end and mate pair libraries and sequenced on an Illumina HiSeq 2500 instrument.

| S-EPMC5887037 | biostudies-literature

Draft Genome Sequence of the Lichen-Forming Fungus Ramalina intermedia Strain YAF0013.

Project description:Here, we report a draft genome sequence of Ramalina intermedia strain YAF0013. The functional annotation of R. intermedia provides important information related to its ability to produce secondary metabolites. The genome sequence reported here builds the basis for further genome mining.

| S-EPMC5992360 | biostudies-literature

Draft Genome Sequence of Cladonia macilenta KoLRI003786, a Lichen-Forming Fungus Producing Biruloquinone.

Project description:The lichen-forming fungus Cladonia macilenta strain KoLRI003786 is capable of producing an acetylcholinesterase inhibitor, biruloquinone, which effectively prevents neurodegeneration in Alzheimer's disease. Laying the foundation to unravel the biruloquinone biosynthetic pathway, we present the 37.11-Mb draft genome sequence of strain KoLRI003786.

| S-EPMC3764418 | biostudies-literature

Isolation and draft genome sequence of <i>Enterobacter asburiae</i> strain i6 amenable to genetic manipulation.

Project description:Enterobacter asburiae is a species of Gram-negative bacteria that is found in soil, water, and sewage. E. asburiae is generally considered to be an opportunistic pathogen, but has also been reported as a plant growth-promoting bacterium (PGPB), which may have beneficial effects on plant growth and development. However, genetic analysis of E. asburiae has been limited, possibly due to its redundant enzymes that digest exogenous DNA in the cell. Here, an E. asburiae strain i6 was isolated from soil in Nara, Japan. This strain was amenable to transformation and the one-step gene inactivation method based on λ Red recombinase. The transformation efficiency of the i6 strain with the 10 kb plasmid DNA pCF430 was at least four orders of magnitude higher than that of the previously sequenced E. asburiae strain ATCC 35953, which could not be transformed with the same plasmid DNA. A draft genome sequence of the i6 strain was determined and deposited into the database, allowing several factors that may determine transformation efficiency to be perturbed and tested. Together with the amenability of the i6 strain to genetic manipulation, the information from the i6 genome will facilitate characterization and fine-tuning of the beneficial and detrimental traits of this species.

| S-EPMC10845240 | biostudies-literature

Draft genome sequence of a Sphingomonas sp., an endosymbiotic bacterium isolated from an arctic lichen Umbilicaria sp.

Project description:Sphingomonas sp. strain PAMC 26617 has been isolated from an Arctic lichen Umbilicaria sp. on the Svalbard Islands. Here we present the draft genome sequence of this strain, which represents a valuable resource for understanding the symbiotic mechanisms between endosymbiotic bacteria and lichens surviving in extreme environments.

| S-EPMC3370618 | biostudies-literature

Agrobacterium tumefaciens-mediated transformation of the lichen fungus, Umbilicaria muehlenbergii.

Project description:Transformation-mediated mutagenesis in both targeted and random manners has been widely applied to decipher gene function in diverse fungi. However, a transformation system has not yet been established for lichen fungi, severely limiting our ability to study their biology and mechanism underpinning symbiosis via gene manipulation. Here, we report the first successful transformation of the lichen fungus, Umbilicaria muehlenbergii, via the use of Agrobacterium tumefaciens. We generated a total of 918 transformants employing a binary vector that carries the hygromycin B phosphotransferase gene as a selection marker and the enhanced green fluorescent protein gene for labeling transformants. Randomly selected transformants appeared mitotically stable, based on their maintenance of hygromycin B resistance after five generations of growth without selection. Genomic Southern blot showed that 88% of 784 transformants contained a single T-DNA insert in their genome. A number of putative mutants affected in colony color, size, and/or morphology were found among these transformants, supporting the utility of Agrobacterium tumefaciens-mediated transformation (ATMT) for random insertional mutagenesis of U. muehlenbergii. This ATMT approach potentially offers a systematic gene functional study with genome sequences of U. muehlenbergii that is currently underway.

| S-EPMC3875497 | biostudies-literature

Transposable Elements in the Genome of the Lichen-Forming Fungus <i>Umbilicaria pustulata</i> and Their Distribution in Different Climate Zones along Elevation.

Project description:Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.

| S-EPMC8773270 | biostudies-literature

Complete Genome Sequence of an Australian Strain of the Lichen-Forming Fungus Endocarpon pusillum (Hedwig).

Project description:The cosmopolitan lichen-forming fungus Endocarpon pusillum (Hedwig) has previously been used as a model for the study of symbiosis and drought resistance. Here, we present the annotated genome of the Australian strain Endocarpon pusillum EPUS1.4. This genome sequence provides additional information on the ability of this species to produce secondary metabolites.

| S-EPMC7729407 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data