Dear colleagues, I have amplified and sequenced (Sanger sequencing) three candidate genes (730-1600 bp) from 150 teak (Tectona grandis) genotypes. After alignment and variant detection using NovoSNP, I obtained a list of SNPs and indels. One of the genotypes was used as the reference sequence during the analysis in NovoSNP. All the corresponding gene sequences have been submitted to NCBI.
Now, I need to submit these variants to the European Variation Archive (EVA), which requires a VCF file including chromosomal positions for each variant. However, the whole genome assembly of teak is not yet available in NCBI, and only short reads (SRA entries ~101 bp) are accessible.
My questions are:
Thank you in advance for any guidance.
Best regards, Nuzhat Bano
Nuzhat Bano Yes, you can still submit SNPs/indels to EVA even without a genome assembly. Since you've sequenced specific genes and submitted them to NCBI, treat those gene sequences (e.g., GenBank accessions) as "contigs" in your VCF file. Use the gene accession as the CHROM field and the variant position relative to that sequence as POS.
EVA accepts contig-based submissions for non-model species. You'll also need to provide:
- A reference FASTA file (with the same gene sequences used in the VCF),
- A manifest file explaining your reference setup,
- Metadata describing the study.
This approach is common in gene-targeted studies for species without a reference genome. Let me know if you need help formatting the VCF or manifest!
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