Data · dataset · 2026
CDS sequences of homologous genes
Listed in ScienceDB
The gene_sequence.txt file comprises CDS sequences of homologous genes, together with their 2 kb upstream flanking regions, retrieved from multiple accessions based on the NCBI Accession Numbers listed in Table S1.
Description
Homology searches were conducted via blastx alignment (BLAST v2.15.0+) against the reference genomes of T. turgidum (Svevo_v1), T. urartu (Tu2.1), T. monococcum (PI306540_Tmono), Ae. longissima, and Ae. sharonensis.
Candidate homologous gene sets were further validated by integration with species-specific genome annotation information. CDS of the identified homologous genes were extracted using gffread v0.12.7. Multiple sequence alignment was performed using MAFFT v7.526 with the auto strategy, to achieve an optimal balance between alignment accuracy and computational efficiency. Gene structural characteristics, pairwise alignment identity, and variant loci were statistically summarized and visualized in R v4.1.1 using the ggplot2 and dplyr packages.
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A Neighbor-Joining (NJ) phylogenetic tree was constructed in MEGA 11 based on the generated alignment, with 1000 bootstrap replicates applied to assess the topological reliability of the tree. The resulting tree was visualized and further refined using the ggtree v3.2.1 package in R.Putative promoter regions, defined as the 2000 bp sequence upstream of the transcription start site of each gene, were extracted using seqkit v2.11.0.
Cis-regulatory elements within these promoter regions were predicted using the PlantCARE online platform, and their distribution patterns and quantitative differences across accessions were analyzed and visualized in R using the ComplexHeatmap and ggplot2 packages.
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.j00210.00077 ↗
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
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.j00210.00077 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].anzsrc:group:3105 | enrichment · scidb cn | taxonomy-embedding@1.0.0 | title+keywords+description (72%) |
| 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:tabular | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (65%) |
| 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 |