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photocyte / PPYR_OGS

Official Geneset (OGS) for Photinus pyralis, at least until I figure out a long term alternative
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PPYR_06392 has lantern enriched splice variant with PTS1 #19

Closed photocyte closed 5 years ago

photocyte commented 5 years ago

See: JBrowse link

Solution: Make Ppyr1.3_Trinity-PASA_stranded-DCGM_transdecoder_asmbl_27909.p1 the A isoform (standard isoform, clearly the preferred variant in non adult male light organ tissues, no peroxisomal targeting sequence) Make Ppyr1.3_Trinity-PASA_stranded-DCGM_transdecoder_asmbl_27914.p1 the B isoform (adult male lantern preferred isoform, peroxisomal targeting sequence) Make Ppyr1.3_Trinity-PASA_stranded-DCGM_transdecoder_asmbl_27913.p1 the C isoform? (Poor expression support?)

Note: This gene has an artifactual duplicate with PPYR_06428-PA

photocyte commented 5 years ago

See here for alignment of 3 splice variants:

asmbl_27914.p1  MIYHVLKTFLLGNVVRKSRTGKAFLNSFTQATFNRQSQVAMSYGIVERGSPFSQDYRVYI
asmbl_27909.p1  MIYHVLKTFLLGNVVRKSRTGKAFLNSFTQATFNRQSQVAMSYGIVERGSPFSQDYRVYI
asmbl_27913.p1  MIYHVLKTFLLGNVVRKSRTGKAFLNSFTQATFNRQSQVAMSYGIVERGSPFSQDYRVYI
                ************************************************************

asmbl_27914.p1  TDNNVPISPLHDIPLFSDQEKNLYNMVVEVPRWTNAKMEITMKEVLNPIKQDIKKGKPRF
asmbl_27909.p1  TDNNVPISPLHDIPLFSDQEKNLYNMVVEVPRWTNAKMEITMKEVLNPIKQDIKKGKPRF
asmbl_27913.p1  TDNNVPISPLHDIPLFSDQEKNLYNMVVEVPRWTNAKMEITMKEVLNPIKQDIKKGKPRF
                ************************************************************

asmbl_27914.p1  VSNCFPHHGYIWNYGALPQTWENPDHLDDGTGAKGDNDPIDVIEIGYRIAKRGEILQVKI
asmbl_27909.p1  VSNCFPHHGYIWNYGALPQTWENPDHLDDGTGAKGDNDPIDVIEIGYRIAKRGEILQVKI
asmbl_27913.p1  VSNCFPHHGYIWNYGALPQTWENPDHLDDGTGAKGDNDPIDVIEIGYRIAKRGEILQVKI
                ************************************************************

asmbl_27914.p1  IGTIALIDEGETDWKLIAIDINDPLANDINDVGDLDKHFPGLLKATVEWFKIYKIPDGKP
asmbl_27909.p1  IGTIALIDEGETDWKLIAIDINDPLANDINDVGDLDKHFPGLLKATVEWFKIYKIPDGKP
asmbl_27913.p1  IGTIALIDEGETDWKLIAIDINDPLANDINDVGDLDKHFPGLLKATVEWFKIYKIPDGKP
                ************************************************************

asmbl_27914.p1  ENQFAFNGEAKPADFALGVVDQVHKFWKQLVGKEVDAKGISCINTSLEGNSFMISNDEAM
asmbl_27909.p1  ENQFAFNGEAKPADFALGVVDQVHKFWKQLVGKEVDAKGISCINTSLEGNSFMISNDEAM
asmbl_27913.p1  ENQFAFNGEAKPADFALGVVDQVHKFWKQLVGKEVDAKGISCINTSLEGNSFMISNDEAM
                ************************************************************

asmbl_27914.p1  EIINKTPLLQPPQPVDPIVDKIYFTSTNSYLAAHL-
asmbl_27909.p1  EIINKTPLLQPPQPVDPIVDKWHYV--------HLK
asmbl_27913.p1  EIINKTPLLQPPQPVDPIGNNIIQI-----IYAFF-
                ****************** ::            .:
photocyte commented 5 years ago

Expression quantification of different isoforms:

./non_strand_specific_results/Ppyr_FatBody_1/abundance.tsv
asmbl_27909.p1  103.381
asmbl_27913.p1  10.6628
asmbl_27914.p1  76.5731
./non_strand_specific_results/Ppyr_FatBody_2/abundance.tsv
asmbl_27909.p1  130.391
asmbl_27913.p1  2.24427
asmbl_27914.p1  16.4873
./non_strand_specific_results/Ppyr_FatBody_3/abundance.tsv
asmbl_27909.p1  131.436
asmbl_27913.p1  7.40205
asmbl_27914.p1  26.8839
./non_strand_specific_results/Ppyr_FatBody_Mated/abundance.tsv
asmbl_27909.p1  133.947
asmbl_27913.p1  1.63853
asmbl_27914.p1  17.9552
./non_strand_specific_results/Ppyr_FThorax/abundance.tsv
asmbl_27909.p1  58.4808
asmbl_27913.p1  1.09114
asmbl_27914.p1  14.888
./non_strand_specific_results/Ppyr_Lantern_1A/abundance.tsv
asmbl_27909.p1  321.893
asmbl_27913.p1  85.0852
asmbl_27914.p1  791.559
./non_strand_specific_results/Ppyr_Lantern_2/abundance.tsv
asmbl_27909.p1  251.941
asmbl_27913.p1  57.9708
asmbl_27914.p1  818.8
./non_strand_specific_results/Ppyr_Lantern_3/abundance.tsv
asmbl_27909.p1  296.842
asmbl_27913.p1  67.5221
asmbl_27914.p1  695.551
./non_strand_specific_results/Ppyr_MThorax_1/abundance.tsv
asmbl_27909.p1  58.9505
asmbl_27913.p1  1.84524
asmbl_27914.p1  16.9943
./non_strand_specific_results/Ppyr_MThorax_2/abundance.tsv
asmbl_27909.p1  35.8813
asmbl_27913.p1  4.76121
asmbl_27914.p1  28.2881
./non_strand_specific_results/Ppyr_MThorax_3/abundance.tsv
asmbl_27909.p1  27.807
asmbl_27913.p1  0
asmbl_27914.p1  24.699
./non_strand_specific_results/Ppyr_OAG_1A/abundance.tsv
asmbl_27909.p1  845.789
asmbl_27913.p1  1.50247
asmbl_27914.p1  11.4477
./non_strand_specific_results/Ppyr_OAG_1B/abundance.tsv
asmbl_27909.p1  689.913
asmbl_27913.p1  1.24957
asmbl_27914.p1  6.33525
./non_strand_specific_results/Ppyr_OAG_2/abundance.tsv
asmbl_27909.p1  581.053
asmbl_27913.p1  5.24604
asmbl_27914.p1  2.99213
./non_strand_specific_results/Ppyr_OAG_Mated/abundance.tsv
asmbl_27909.p1  572.498
asmbl_27913.p1  1.60626
asmbl_27914.p1  6.26392
./non_strand_specific_results/Ppyr_SDGBursa/abundance.tsv
asmbl_27909.p1  725.37
asmbl_27913.p1  8.68798
asmbl_27914.p1  18.4714
./non_strand_specific_results/Ppyr_SG_Mated/abundance.tsv
asmbl_27909.p1  216.451
asmbl_27913.p1  0.407617
asmbl_27914.p1  0.660154
./non_strand_specific_results/Ppyr_Spermatheca/abundance.tsv
asmbl_27909.p1  468.115
asmbl_27913.p1  0.392072
asmbl_27914.p1  4.62684
./non_strand_specific_results/Ppyr_SpiralGland_1/abundance.tsv
asmbl_27909.p1  204.345
asmbl_27913.p1  0.943201
asmbl_27914.p1  2.16316
./non_strand_specific_results/Ppyr_SpiralGland_2/abundance.tsv
asmbl_27909.p1  128.892
asmbl_27913.p1  0
asmbl_27914.p1  1.74112
./non_strand_specific_results/Ppyr_SpiralGland_3/abundance.tsv
asmbl_27909.p1  152.377
asmbl_27913.p1  0
asmbl_27914.p1  0
./non_strand_specific_results/SRA_8175_Photinus_pyralis_male_head_adult_transcriptome/abundance.tsv
asmbl_27909.p1  50.0549
asmbl_27913.p1  3.53852
asmbl_27914.p1  11.4777
./non_strand_specific_results/SRA_8176_Photinus_pyralis_male_light_organ_adult_transcriptome/abundance.tsv
asmbl_27909.p1  261.586
asmbl_27913.p1  12.6881
asmbl_27914.p1  164.509
./non_strand_specific_results/SRA_8819_Photinus_pyralis_light_organ_larval_transcriptome/abundance.tsv
asmbl_27909.p1  90.4848
asmbl_27913.p1  1.63303
asmbl_27914.p1  12.5874
./non_strand_specific_results/TF_VA2017_3pooled_larval_lantern_CAGATC-s_2/abundance.tsv
asmbl_27909.p1  1089.15
asmbl_27913.p1  12.9693
asmbl_27914.p1  685.771
./strand_specific_results/Ppyr_eggs_GCCAAT/abundance.tsv
asmbl_27909.p1  128.291
asmbl_27913.p1  6.81665
asmbl_27914.p1  14.3381
./strand_specific_results/Ppyr_FemaleWhole_ACTTGA/abundance.tsv
asmbl_27909.p1  126.279
asmbl_27913.p1  3.90129
asmbl_27914.p1  131.586
./strand_specific_results/Ppyr_larvae_CAGATC/abundance.tsv
asmbl_27909.p1  150.094
asmbl_27913.p1  4.62317
asmbl_27914.p1  25.809
./strand_specific_results/Ppyr_MaleWhole_GATCAG/abundance.tsv
asmbl_27909.p1  230.624
asmbl_27913.p1  8.60493
asmbl_27914.p1  175.061
./strand_specific_results/SRA_9_Photinus_sp_1_lantern/abundance.tsv
asmbl_27909.p1  67.2689
asmbl_27913.p1  60.8811
asmbl_27914.p1  292.888
photocyte commented 5 years ago

Added PPYR_06392-PB in 978d54243193f28a3b67c32ac6b2d10186bbbb7a

Just a note: PPYR_06392-PB doesn't have its stop codon on the last exon (so it should be degraded by nonsense mediated decay), but apparently if the stop codon is within 50 bp of the last exon-exon junction, NMD doesn't occur.