Question: Why do Drosophila genomes look haploid?
0
gravatar for predeus
3.4 years ago by
predeus1.3k
Russia
predeus1.3k wrote:

Hello all,

I have next to zero experience with D. melanogaster biology, but I've processed quite a few mouse and human experiments.As a task for students I've chosen D.melanogaster RNA-seq experiment - since the genome is so much smaller and I figures it would work faster on their machines. Here's the experiment I've used - it's a cell line:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2055139

I've aligned the experiment to dm6 reference with hisat2 and visualized the BAM with IGV. What I can't understand is why do all of the variants look homozygous? Is that normal? Is that because they are very inbred?

Thank you for any input.

enter image description here

igv rna-seq • 769 views
ADD COMMENTlink written 3.4 years ago by predeus1.3k
2

inbreeding does create runs of homozygosity. I think fruit flies have a quick generation time, and are likely inbred. Then you're looking at a cell line, which is going to be derived from another unique individual. Should research the data files to see what the source material is. It is labeled "S2 cell line" only.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by karl.stamm3.6k
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