Data · dataset · 2024
Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboo
Listed in ScienceDB
This dataset includes raw data, assembly, and annotation for the genome of Bambusa odashimae.
Description
The raw data consists of Next Generation Sequencing (NGS) data (NGS_*.fa.gz), Hi-C data (HIC*_raw_*.fa.gz), and Oxford Nanopore Technology (ONT) data (ONT*.pass.fastq.gz). The results of the assembly and annotation are provided in the following files: phased.bod.cds, phased.bod.gff, phased.bod.pep, and phased.genome.fasta.
Below is a detailed description of each data source. Raw Data: Fresh leaves of B. odashimae were collected, and DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method. For NGS sequencing, PCR-free libraries were constructed and sequenced on the MGISEQ2000 platform. For ONT sequencing, high-quality DNA was extracted with the QIAGEN Genomic kit, followed by library construction with the LSK109 kit and sequencing on the ONT platform.
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To position hybrid scaffolds onto the chromosome, Hi-C samples were prepared, a Hi-C library was constructed, and data were obtained using the Illumina NovaSeq platform. Genome Assembly and Annotation Data: The methods for genome assembly and annotation are detailed in the article "Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboos," which has been accepted by Horticulture Research.
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.12511 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Bioinformatics and computational biology 69% · Sequencing 75%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.12511 | 10 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].anzsrc:group:3102 | enrichment · scidb cn | taxonomy-embedding@1.0.0 | title+keywords+description (69%) |
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[modality].local:modality:sequencing | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/rights |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |