Post date: Jun 15, 2017 2:52:45 AM
14vi17.
summarizePips.R
sortedCombinedPips.txt
15v17. I used a pip cutoff of 0.1 to say which SNPs are associated with which traits (changed to 0.01 for scaf 5076 and 1636 since only one trait was showing up; see summrizePips.R for all scaffolds with a cutoff of 0.1). For the talk we might want to make a heatmap for each SNP showing where (traitxgroup) they "light up" (have a moderate or high pip).
scaffolds 203, 443 and 5076 either didn't hit anything or hit other lep scaffolds that lacked info.
scaffold 203 (chromosome 14): Anna and All a2 size, Anna and All a3 size, Anna and All a4 size, Anna a5 size
scaffold 443 (chromosome 17): SN a2 size, SN a3 size, SN a4 size
scaffold 5076 (chromosome ?): SN a3 y, sn A4 y, SN cu23 x, SN Sc y, All cu23 x, AN a2 y, AN 2a x, ID 2a x
scaffold1566 (chromosome 20): Anna M1 size, Anna M2 size, Anna Cu21A size
It sorta maps to Choline O-acetyltransferase (Drosophila melanogaster; involved in neurotransmitters ACh and acetyl CoA).
>SNP at position 17518 is 12518 bp away from Choline O-acetyltransferase.
This is the coolest one. scaffold 48 (chromosome Z) is responsible for aurorae size (a1-a6) in ME.
It maps to Nuclear hormone receptor FTZ-F1 (Bombyx mori) and plays a role in development (pupa to adult).
scaffold 48 is also responsible for USP6 N-terminal-like protein (Mus musculus; receptor traficking, golgi aparatus).
>SNP at position 166171 is 16171 bp away from FTZ-F1.
>SNP at position 166171 is 108829 bp away from USP6 N-terminal-like protein.
scaffold 157 (chromosome 2): ME Sc size, ME M1 size, ME M2 size.
It maps to probable muscarinic acetylcholine receptor gar-2 (C. elegans; acetycholine receptor).
>SNP at position 20350 is 156348 bp away from probable muscarinic acetylcholine receptor gar-2
scaffold 92 (chromosome Z): ME a4 size, ME Sc size, ME Rs size, ME M3 size, ME Cu21a size.
It sorta maps to: 1) Sterol regulatory element-binding protein cleavage-activating protein (Human; escort protein required for cholestrol), 2) Triple function domain protein (Humans: actin remodeling required for cell movement), 3) kalirin (human: exchange of GDP by GTP, affects actin cytoskeleton).
>SNP at position 104206 is about 155794 bp away from Sterol regulatory element-binding protein cleavage-activating protein (SREBP)
>SNP at position 104206 is about 25794 bp away from Triple function domain protein
**>SNP at position 104206 is within kalirin
scaffold 1636 (chromosome ?): MW sizes for 9 black spots in a row: M through Cu21a.
It maps to Mediator of RNA polymerase II transcription subunit 24 (Anopheles gambiae; regulated transcriptions of nearly all RNA polymerase II-dependent genes)
>SNP at position 44024 is 6524 bp away from Mediator of RNA polymerase II transcription subunit 24
scaffold 165 (chromosome Z): WA M1 x, WA M1 vein x.
It maps to Otoferlin (Human and Mus; calcium ion sensor, neurotransmitter release, cochlear inner hair cells specifically)
**>SNP at position 182769 is within Otoferlin
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I searched for our genes of interest in the Heliconius papers cited in the third paragraph of Belleghem et al. 2017. No hits.
Choline O-acetyltransferase
FTZ-F1
USP6 N-terminal-like protein
probable muscarinic acetylcholine receptor gar-2
Sterol regulatory element-binding protein cleavage-activating protein
Triple function domain protein
kalirin
Mediator of RNA polymerase II transcription subunit 24
Otoferlin
Then I did a google scholar search for each gene and "butterfly moth wing pattern"
Sahara et al. 2012 is interesting: Sex chromosome evolution in moths and butterflies. Our Z chromosome gene, FTZ-F1, has orthologues in Z chromosomes of other Lepidoptera (they looked at Bicyclus anynana and Heliconius melpomene and it wasn't found):
Bombyx mori (silkworm)
Ostrinia nubilalis (European corn borer)
Manduca sexta (tobacco hornworm)
Agrius convolvuli (Convolvulus Hawk-moth)
Plutella xylostella (diamondback moth)
See Majerowicz&Gondim_2013-SREBP.pdf for an explanation of what we know about Sterol regulatory element-binding protein (SREBP) in Drosophila:
-Mutant flies for this gene do not survive beyond the second instar, indicating that SREBP is essential
-the silencing of SREBP by RNAi causes a reduction in the size of both cells and organs in D. melanogaster