Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft Plastid and Mitochondrial Genome Sequences from Antarctic Alga Prasiola crispa.

ABSTRACT: The organelle genomes of the Antarctic alga Prasiola crispa (Lightfoot) Kützing have been sequenced. The plastid and mitochondrial genomes have a total length of 196,502 bp and 89,819 bp, respectively. These genomes have 19 putative photosynthesis-related genes and 17 oxidative metabolism-related genes, respectively.

SUBMITTER: Carvalho EL

PROVIDER: S-EPMC4599086 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Draft Plastid and Mitochondrial Genome Sequences from Antarctic Alga Prasiola crispa.

Carvalho Evelise Leis EL Wallau Gabriel da Luz Gda L Rangel Darlene Lopes DL Machado Laís Ceschini LC da Silva Alexandre Freitas AF da Silva Luiz Fernando Duarte LF Macedo Pablo Echeverria PE Pereira Antonio Batista AB Victoria Filipe de Carvalho Fde C Boldo Juliano Tomazzoni JT Dal Belo Cháriston André CA Pinto Paulo Marcos PM

Genome announcements 20151008 5

The organelle genomes of the Antarctic alga Prasiola crispa (Lightfoot) Kützing have been sequenced. The plastid and mitochondrial genomes have a total length of 196,502 bp and 89,819 bp, respectively. These genomes have 19 putative photosynthesis-related genes and 17 oxidative metabolism-related genes, respectively. ...[more]

PMID: 26450727

Similar Datasets

Prasiola crispa

Project description:Prasiola crispa Transcriptome or Gene expression

| PRJNA329112 | ENA

Draft genome sequence of the Antarctic green alga <i>Chlamydomonas</i> sp. UWO241.

Project description:Antarctica is home to an assortment of psychrophilic algae, which have evolved various survival strategies for coping with their frigid environments. Here, we explore Antarctic psychrophily by examining the ?212 Mb draft nuclear genome of the green alga Chlamydomonas sp. UWO241, which resides within the water column of a perennially ice-covered, hypersaline lake. Like certain other Antarctic algae, UWO241 encodes a large number (?37) of ice-binding proteins, putatively originating from horizontal gene transfer. Even more striking, UWO241 harbors hundreds of highly similar duplicated genes involved in diverse cellular processes, some of which we argue are aiding its survival in the Antarctic via gene dosage. Gene and partial gene duplication appear to be an ongoing phenomenon within UWO241, one which might be mediated by retrotransposons. Ultimately, we consider how such a process could be associated with adaptation to extreme environments but explore potential non-adaptive hypotheses as well.

| S-EPMC7887394 | biostudies-literature

Mitochondrial and plastid genome analysis of the marine red alga <i>Coeloseira compressa</i> (Champiaceae, Rhodophyta).

Project description:The classification of species originally assigned to the marine red algal genus Coeloseira G.J. Hollenberg remains univestigated using molecular data. Paired-end 36?bp Illumina sequences (Illumina Inc, San Diego, CA) were generated from a specimen of Coeloseira compressa G. J. Hollenberg and used to assemble the partial mitochondrial and complete plastid genomes. The mitogenome is 25,391?bp in length and contains 46 genes, and the plastome is 176,291?bp with 233 genes. Both organellar genomes show high gene synteny with previously published Florideophyceae. Comparison of organellar and nuclear phylogenetic markers (rbcL, CO1, LSU) of C. compressa to other genera in the Champiaceae supports its removal from Gastroclonium Kützing and the reinstatement of the name Coeloseira compressa.

| S-EPMC7800148 | biostudies-literature

Draft Genome Sequences of Bacterial Strains Capable of Degrading Ulvan from the Green Alga Ulva ohnoi.

Project description:We present here the draft genome sequences of four marine bacterial strains which can use ulvan as their sole carbon source. We used ulvan extracted from the green alga Ulva ohnoi Each bacterium contains a polysaccharide-utilizing locus, which is necessary for the complete degradation of ulvan.

| S-EPMC6965591 | biostudies-literature

Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida.

Project description:In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.

| S-EPMC4591262 | biostudies-literature

Draft Genome Sequences of the Alga-Degrading Bacteria Aeromonas hydrophila Strain AD9 and Pseudomonas pseudoalcaligenes Strain AD6.

Project description:Aeromonas hydrophila AD9 and Pseudomonas pseudoalcaligenes AD6 have been linked to algal cell degradation. Here we report the draft genomes of A. hydrophila AD9 and P. pseudoalcaligenes AD6 for the investigation of causative agents for algal cell degradation.

| S-EPMC4102871 | biostudies-literature

A draft map of cis-regulatory sequences in the mouse genome

Project description:The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 billion bases of the mouse genome share a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. To date, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated. Comparative genomics has been a powerful tool for the discovery of these sequences, but it alone cannot resolve their temporal and spatial functions. Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including human, D. melanogaster and C. elegans. We have applied the same experimental approach to a diverse set of 19 tissues and cell types in the mouse, producing a map of nearly 300,000 murine cis-regulatory sequences. This map provides functional annotation to nearly 11% of the mouse genome, and over 70% of conserved, non-coding sequences (CNS). We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and study of mechanisms regulating tissue-specific gene expression. This SuperSeries is composed of the SubSeries listed below.

2012-07-01 | GSE29184 | GEO

Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti.

Project description:The Antarctic bathydraconid dragonfish, Parachaenichthys charcoti, is an Antarctic notothenioid teleost endemic to the Southern Ocean. The Southern Ocean has cooled to -1.8ºC over the past 30 million years, and the seawater had retained this cold temperature and isolated oceanic environment because of the Antarctic Circumpolar Current. Notothenioids dominate Antarctic fish, making up 90% of the biomass, and all notothenioids have undergone molecular and ecological diversification to survive in this cold environment. Therefore, they are considered an attractive Antarctic fish model for evolutionary and ancestral genomic studies. Bathydraconidae is a speciose family of the Notothenioidei, the dominant taxonomic component of Antarctic teleosts. To understand the process of evolution of Antarctic fish, we select a typical Antarctic bathydraconid dragonfish, P. charcoti. Here, we have sequenced, de novo assembled, and annotated a comprehensive genome from P. charcoti. The draft genome of P. charcoti is 709 Mb in size. The N50 contig length is 6145 bp, and its N50 scaffold length 178 362 kb. The genome of P. charcoti is predicted to contain 32 712 genes, 18 455 of which have been assigned preliminary functions. A total of 8951 orthologous groups common to 7 species of fish were identified, while 333 genes were identified in P. charcoti only; 2519 orthologous groups were also identified in both P. charcoti and N. coriiceps, another Antarctic fish. Four gene ontology terms were statistically overrepresented among the 333 genes unique to P. charcoti, according to gene ontology enrichment analysis. The draft P. charcoti genome will broaden our understanding of the evolution of Antarctic fish in their extreme environment. It will provide a basis for further investigating the unusual characteristics of Antarctic fishes.

| S-EPMC5597851 | biostudies-literature

Complete Plastid Genome of the Brown Alga Costaria costata (Laminariales, Phaeophyceae).

Project description:Costaria costata is a commercially and industrially important brown alga. In this study, we used next-generation sequencing to determine the complete plastid genome of C. costata. The genome consists of a 129,947 bp circular DNA molecule with an A+T content of 69.13% encoding a standard set of six ribosomal RNA genes, 27 transfer RNA genes, and 137 protein-coding genes with two conserved open reading frames (ORFs). The overall genome structure of C. costata is nearly the same as those of Saccharina japonica and Undaria pinnatifida. The plastid genomes of these three algal species retain a strong conservation of the GTG start codon while infrequently using TGA as a stop codon. In this regard, they differ substantially from the plastid genomes of Ectocarpus siliculosus and Fucus vesiculosus. Analysis of the nucleic acid substitution rates of the Laminariales plastid genes revealed that the petF gene has the highest substitution rate and the petN gene contains no substitution over its complete length. The variation in plastid genes between C. costata and S. japonica is lower than that between C. costata and U. pinnatifida as well as that between U. pinnatifida and S. japonica. Phylogenetic analyses demonstrated that C. costata and U. pinnatifida have a closer genetic relationship. We also identified two gene length mutations caused by the insertion or deletion of repeated sequences, which suggest a mechanism of gene length mutation that may be one of the key explanations for the genetic variation in plastid genomes.

| S-EPMC4596871 | biostudies-literature

A draft map of cis-regulatory sequences in the mouse genome [HiC]

Project description:As the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression.

2012-07-01 | GSE34587 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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