Ontology highlight
ABSTRACT:
PROVIDER: PRJNA847710 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19611691_1.fastq.gz | Fastqsanger.gz | |||
| SRR19611691_2.fastq.gz | Fastqsanger.gz |
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Project description:The draft genome of L. sativa (lettuce) cv. Tizian was sequenced in two Illumina sequencing runs, mate pair and shotgun. This entry contains the RAW sequencing data.
2018-02-09 | E-MTAB-6347 | biostudies-arrayexpress
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
Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
2019-12-16 | PXD016522 | Pride
Project description:Background Trombidid mites have a unique lifecycle in which only the larval stage is ectoparasitic. In the superfamily Trombiculoidea (“chiggers”), the larvae feed preferentially on vertebrates, including humans. Species in the genus Leptotrombidium are vectors of a potentially fatal bacterial infection, scrub typhus, which affects 1 million people annually. Moreover, chiggers can cause pruritic dermatitis (trombiculiasis) in humans and domesticated animals. In the Trombidioidea (velvet mites), the larvae feed on other arthropods and are potential biological control agents for agricultural pests. Here, we present the first trombidid mites genomes, obtained both for a chigger, Leptotrombidium deliense, and for a velvet mite, Dinothrombium tinctorium. Results Sequencing was performed on the Illumina MiSeq platform. A 180 Mb draft assembly for D. tinctorium was generated from two paired-end and one mate-pair library using a single adult specimen. For L. deliense, a lower-coverage draft assembly (117 Mb) was obtained using pooled, engorged larvae with a single paired-end library. Remarkably, both genomes exhibited evidence of ancient lateral gene transfer from soil-derived bacteria or fungi. The transferred genes confer functions that are rare in animals, including terpene and carotenoid synthesis. Thirty-seven allergenic protein families were predicted in the L. deliense genome, of which nine were unique. Preliminary proteomic analyses identified several of these putative allergens in larvae. Conclusions Trombidid mite genomes appear to be more dynamic than those of other acariform mites. A priority for future research is to determine the biological function of terpene synthesis in this taxon and its potential for exploitation in disease control. Project was jointly supervised by Stuart Armstrong and Ben Makepeace.
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2016-04-21 | PXD003564 | Pride
Project description:Plutella xylostella is the major cosmopolitan pest of brassica and other crucifer crops,the larval midgut of which is a dynamic organ that interfaces with a diversearray of physiological and toxicological processes.The draft sequence of the P.xylostella genome was recently released,but its annotation remains chanllenging because of the low coverage of this branch of life.Peptide sequencing by computational assignment of tandem mass spectra to a database of putative protein sequences provides an independent approach to confirm or refute protein prediction,which has been termed proteogenomics.In this study,we carried out an in-depth proteogenomic analysis using shotgun HPLC-ESI-MS/MS approach with a multi-algorithme peipline to complement genome annotation in the P.xylostella larval midgut.
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Project description:Plutella xylostella is the major cosmopolitan pest of brassica and other crucifer crops,the larval midgut of which is a dynamic organ that interfaces with a diversearray of physiological and toxicological processes.The draft sequence of the P.xylostella genome was recently released,but its annotation remains chanllenging because of the low coverage of this branch of life.Peptide sequencing by computational assignment of tandem mass spectra to a database of putative protein sequences provides an independent approach to confirm or refute protein prediction,which has been termed proteogenomics.In this study,we carried out an in-depth proteogenomic analysis using shotgun HPLC-ESI-MS/MS approach with a multi-algorithme peipline to complement genome annotation in the P.xylostella larval midgut.
2016-04-11 | PXD003567 | Pride
Project description:Plutella xylostella is the major cosmopolitan pest of brassica and other crucifer crops,the larval midgut of which is a dynamic organ that interfaces with a diversearray of physiological and toxicological processes.The draft sequence of the P.xylostella genome was recently released,but its annotation remains chanllenging because of the low coverage of this branch of life.Peptide sequencing by computational assignment of tandem mass spectra to a database of putative protein sequences provides an independent approach to confirm or refute protein prediction,which has been termed proteogenomics.In this study,we carried out an in-depth proteogenomic analysis using shotgun HPLC-ESI-MS/MS approach with a multi-algorithme peipline to complement genome annotation in the P.xylostella larval midgut.
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