RNA seq and SNP discovery

[tripta]

Hi!
Iam new to this area of science and intend to go for RNA seq and SNP discovery of a highly heterozygous~4.8GB,tetraploid plant (without any reference).
what would be advisable Illumina PE Hiseq2000 or Roche 454

Best,
Tripta

[zhidkov.ilia]

You can start with literature review (look for papers of plant genomes de-novo assembly and what strategies were used). There is a review by McCombie WR et al (PMID: 22546054), which might be useful to get better understand the challenges in de-novo assembly of plant genome.

[tripta]

RNA seq and SNP DISCOVERY

Hi Ilia,
Thanks for the reference,may for hybrid approach will be more appropriate here.
thanks for the suggestion
Best,
tripta

[Melissa]

I think your primary concern should be the SNPs detection approach rather than sequencing approach. I would advise you to go for Illumina sequencing due to low cost and high coverage. My experience with SNPs discovery using de novo transcriptome sequencing of a diploid plant is high false positive rate, which i believed was mainly caused by highly duplicated nature of the genome (or paralogous genes). In your case, there can be up to four alleles for a particular SNP segregating in the genome and this is further complicated by several copies of the genes. Some relevant studies like alfalfa, soybean and polyploid wheat might be useful for you.