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Genomic Structural Variation Resource

BGCNVdb: Bottle Gourd CNV Database

Exploring Copy Number Variations in Lagenaria siceraria

Analysis — BGCNVdb
BGCNVdb — Genome-Wide Study

CNV Analysis

🌿
145
Accessions
📈
26,660
Total CNVs
▼
68.7%
Deletions
▲
31.3%
Duplications
⚖
2.2:1
DEL:DUP Ratio
📌
1,024
CNVRs
Distribution

CNV & CNVR Type Proportions

Structural Variation

Type Distribution

Raw CNVs — 26,660 total
▼ Deletion
68.7%
▲ Duplication
31.3%
CNVRs — 1,024 total
▼ DEL-CNVR
63.4%
▲ DUP-CNVR
36.6%
649 DEL-CNVRs 375 DUP-CNVRs
Summary

Key Findings

  • 26,660 CNVs detected genome-wide across all 11 chromosomes in 145 bottle gourd accessions
  • Deletion bias with 18,322 deletions (68.7%) versus 8,338 duplications (31.3%)
  • CNVs per genotype ranged from 80 (Grif 970) to 1,063 (PI 381834), median 179
  • Chromosome 1 carried the most deletions (2,910) and duplications (1,364); chromosome 10 the fewest CNVs
  • Overlapping CNVs merged into 1,024 CNVRs (649 DEL, 375 DUP) at 50% reciprocal overlap, present in ≥3 accessions
  • CNVR-based clustering resolved five subpopulations broadly separating African from Eurasian germplasm
Pipeline Overview

Analysis Workflow

CNV analysis flowchart for Lagenaria siceraria

Fig. 1 — Schematic overview of the genome-wide CNV detection and CNVR construction pipeline in Lagenaria siceraria.