Dendronephthya gigantea
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ABSTRACT:
PROVIDER: PRJNA507917 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Dendronephthya gigantea Raw sequence reads
| PRJNA507943 | ENA
Project description:Dendronephthya gigantea isolate:DGI-Jeju-01 Genome sequencing and assembly
| PRJNA507923 | ENA
Project description:Coral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities of octocorallian species, appear more resilient. The genomes of several cnidarians species have been published, including from stony corals, sea anemones, and hydra. To fill the phylogenetic gap for octocoral species of cnidarians, we sequenced the octocoral, Dendronephthya gigantea, a nonsymbiotic soft coral, commonly known as the carnation coral. The D. gigantea genome size is ∼276 Mb. A high-quality genome assembly was constructed from PacBio long reads (29.85 Gb with 108× coverage) and Illumina short paired-end reads (35.54 Gb with 128× coverage) resulting in the highest N50 value (1.4 Mb) reported thus far among cnidarian genomes. About 12% of the genome is repetitive elements and contained 28,879 predicted protein-coding genes. This gene set is composed of 94% complete BUSCO ortholog benchmark genes, which is the second highest value among the cnidarians, indicating high quality. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence times were estimated at 544 MYA. There is a clear difference in Hox gene composition between these species: unlike hexacorals, the Antp superclass Evx gene was absent in D. gigantea. Here, we present the first genome assembly of a nonsymbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including stony and soft corals, both symbiotic and nonsymbiotic. The D. gigantea genome may also provide clues to mechanisms of differential coping between the soft and stony corals in response to scenarios of global warming.
| S-EPMC6447388 | biostudies-literature
Project description:Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high pitch content, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of pitch were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s pitch metabolism. These results contribute to our fundamental understanding of conifer colonization and carbon cycling processes. Phlebiopsis gigantea was cultivated in media containing one of three carbon sources: freshly harvested loblolly pine (3 replicates), acetone extracted lobollly pine (3 replicates), or glucose (2 replicates). RNA was extracted and processed for Illumina sequencing as described below.
2014-10-01 | E-GEOD-53112 | biostudies-arrayexpress
Project description:Bipolaris gigantea Genome sequencing and assembly
| PRJNA830924 | ENA
Project description:Crassadoma gigantea Genome sequencing and assembly
| PRJNA523973 | ENA
Project description:Liparis gigantea Genome sequencing and assembly
| PRJNA1103398 | ENA
Project description:In this study, C. gigantea miRNAs and their target genes were investigated by extracting RNA from young roots, tender stems, young leaves, and flower buds of C. gigantea to establish a small RNA (sRNA) library and a degradome library to further sequence. This study identified 194 known miRNAs belonging to 52 miRNA families and 23 novel miRNAs. Among the miRNA families, 158 miRNAs from 27 miRNA families were highly conserved and existed in a plurality of plants. In addition, 60 different targets for 30 known families and one target for novel miRNA were identified by high-throughput sequencing and degradome analysis in C. gigantea. Our analyses showed that conserved miRNAs have higher expression levels and more family members as well as more targets than other miRNAs. Meanwhile, these conserved miRNAs were found to be involved in auxin signal transduction, regulation of transcription, and other developmental processes in plants, which will help further understanding regulatory mechanisms of C. gigantea miRNAs. The samples were collected from the young roots, tender shoots, young leaves and flower buds of wild C. gigantea growing in Jiangsu Province. TRIzol reagent (Invitrogen, USA) was used to extract the total RNAs [20]. An Illumina next-generation sequencing system, i.e. the 1 G Genome Analyzer sequencing platform, was utilized for sRNA sequencing. An Illumina HiSeq 2000 (LC Sciences, USA) was used for degradome sequencing.
2016-03-10 | E-GEOD-66754 | biostudies-arrayexpress