Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Callitris sulcata

ABSTRACT: Chloroplast genome sequencing of endangered plant species

PROVIDER: PRJDB5242 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR075506.fastq.gz	Fastqsanger.gz
	DRR075507.fastq.gz	Fastqsanger.gz
	DRR075508.fastq.gz	Fastqsanger.gz
	DRR075509.fastq.gz	Fastqsanger.gz
	DRR075510.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Callitris sulcata

Project description:Callitris sulcata overview

| PRJNA416956 | ENA

Callitris sulcata

Project description:Ecological genomics of New Caledonian conifers

| PRJDB3827 | ENA

Development of nuclear and chloroplast microsatellite markers for the endangered conifer Callitris sulcata (Cupressaceae).

Project description:Microsatellite markers were developed for Callitris sulcata (Cupressaceae), an endangered conifer species in New Caledonia. Using sequencing by synthesis (SBS) of an RNA-Seq library, 15 polymorphic nuclear and chloroplast microsatellite markers were developed. When evaluated with 48 individuals, these markers showed genetic variations ranging from two to 15 alleles and expected heterozygosity ranging from 0 to 0.881. These markers will be useful for examining the genetic diversity and structure of remaining wild populations and improving the genetic status of ex situ populations.

| S-EPMC4542945 | biostudies-literature

An Integrated OMICs Approach of Assembly and Annotation of Indian Sandalwood (Santalum album L.) plant genome provides insights into an array of genes involved in Santalol biosynthesis

Project description:Indian sandalwood (Santalum album) is an economically important plant known for its aromatic wood. This highly valued plant has also been reported as an endangered species. Despite its economic value, the genome sequence of this plant is not yet available. In the current study,we report the draft genome sequence of sandalwood generated using Illumina HiSeq1000 sequencing platform. Genome annotation was carried out using InterProScan tool and Uniprot database,which was further facilitated using in-house RNA-Seq data. Further, we carried out in-depth proteome analysis of samples derived from four tissues viz., shoot meristem, leaf, stem and fruit using high-resolution tandem mass spectrometry. Proteogenomics analysis was performed to identify novel gene models, revise the predicted gene structures and provide experimental evidence for the predicted genes. Our analysis resulted in the identification of 72,325 peptides mapping to 10,076 genes predicted in the sandalwood genome thereby validating the expression of these gene models. Additionally, this study also provides evidence for 53 novel protein coding genes and revision of 121existing gene models.

2019-05-29 | PXD006283 | Pride

Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants [ChIP-seq]

Project description:The coordination of chloroplast and nuclear genome status are critical for plant cell function, but the mechanism remain largely unclear. In this study, we report that Arabidopsis thaliana CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in both the chloroplast and the nucleus.

2022-12-13 | GSE220489 | GEO

Transcriptomic profiling permits the identification of pollutant sources and effects in ambient water samples

Project description:The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls.

2012-09-20 | GSE40991 | GEO

Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants [RNA-seq]

2022-12-13 | GSE220490 | GEO

Ribosome footprinting of wild-type Col-0 and rlmnl3 mutant

Project description:In the present study, we discover the presence of m2A in chloroplast rRNA and tRNA, as well as cytosolic tRNA, in multiple plant species. We identify six m2A-modified chloroplast tRNAs and two m2A-modified cytosolic tRNAs across different plants. Furthermore, we characterize three Arabidopsis m2A methyltransferases—RLMNL1, RLMNL2, and RLMNL3—which methylate chloroplast rRNA, chloroplast tRNA, and cytosolic tRNA, respectively. Our findings demonstrate that m2A37 promotes a relaxed conformation of tRNA, enhancing translation efficiency in chloroplast and cytosol by facilitating decoding of tandem m2A-tRNA-dependent codons. This study provides insights into the molecular function and biological significance of m2A, uncovering a layer of translation regulation in plants.

2024-02-03 | GSE127146 | GEO

Project description:complete chloroplast genome of herbal plant species

| PRJNA878453 | ENA

Project description:Sequencing of the chloroplast genome of a critically endangered tree species Gonystylus bancanus.

| PRJNA1137116 | ENA