FINAL REPORT CANDIDATE GENES
- Genes found following all 4 approximations!
- In total 14 genes!
- Mc-Donald - Kreitman test  alpha:
𝛼=1 −
- Fisher exact test:
𝐷𝑠
𝑃𝑛
(
)
𝐷𝑛 𝑃𝑠 + 1
Gene ID
FBgn0031365
FBgn0021856
FBgn0033683
FBgn0025578
FBgn0011694
FBgn0036469
FBgn0037114
FBgn0052450
FBgn0037184
FBgn0027866
FBgn0004436
FBgn0014342
FBgn0025821
FBgn0038363
Chr
2L
2L
2R
2R
2R
3L
3L
3L
3L
3R
3R
3R
3R
3R
Start
1758286
21261168
8026200
20667502
21061320
15046668
21659552
22322878
22719334
153536
774477
1373837
7529752
11618410
End
1759093
21262411
8026829
20667951
21061729
15047235
21660080
22323757
22720889
159793
778404
1376354
7530638
11619209
1
1) FBgn004436


class
5’ UTR



Ubc6: ubiquitin conjugating enzyme 6  ubiquitin-protein transferase activity
3R: 774477-778404 (near centromere)
max
186
k
syn_k
0.25641 0.147059
pi
0
syn_pi
0.000226
Dn
10
Pn
0
Ds
10
Ps
1
recomb
0.108814
Ka/Ks ratio: 1.74358
alpha (MKT): 1
p-value (Fisher): 1
- GO: Molecular function  p53 binding, ubiquitin-protein transferase activity
- GO: Biological process  centrome organization and separation, DNA repair, endocyting recycling,
mitochondrion degradation, mitotic spindle organization, negative regulation of apoptotic process,
proteasome-mediated ubiquitin-dependent protein catabolic process
- GO: Cellular component: nucleus
- Ortho DB:



Group EOG7G7Z4H: 54 genes in 53 species
InterPro Domains
 54 genes with IPR016135: Ubiquitin-conjugating enzyme/RWD-like;
 54 genes with IPR000608: Ubiquitin-conjugating enzyme, E2;
Evolutionary Rate: 0.57
- Evidences of selection: NO
2
2) FBgn0011694


PebII: protein ejaculatory bulb II  multicellular organism reproduction
2R: 21061320-21061729 (near telomere)
class
CDS 2f



max
201
k
syn_k
0.235294 0.16667
pi
0
syn_pi
0
Dn
16
Pn
2
Ds
6
Ps
0
recomb
0
Ka/Ks ratio: 1.41176
alpha (MKT): 0.25
p-value (Fisher): 1
- GO: Molecular function: - GO: Biological process: multicellular organism reproduction, negative regulation of female receptivity,
post-mating behaviour
- GO: Cellular component: extracellular space
- Table S1. Young genes  Parental gene: NA; Mechanism: de novo; Age: 25 ~ 35 Myr.
- Ortho DB



Group EOG7XMFF5: 5 genes in 5 species
InterPro Domains: No domains identified.
Evolutionary Rate: 1.15
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: 201 - 207 > 85.07
- Evidences of selection: YES

Zhang, Clark, et al., 2013. Natural genetic variation in male reproductive genes contributes to
nontransitivity of sperm competitive ability in Drosophila melanogaster. Mol. Ecoll. 22: 1400-15.
3
3) FBgn0014342


class
CDS 2f



mia: meiosis I arrest  male meiosis, spermatogenesis, spermatid differentiation and
development.
3R: 1373837-1376354 (near centromere)
max
1770
k
0.2471
syn_k
pi
syn_pi
0.223881 0.000173 0.000275
Dn
190
Pn
2
Ds
60
Ps
3
recomb
0
Ka/Ks ratio: 1.10368
alpha (MKT): 0.842105
p-value (Fisher): 0.0983547
- GO: Molecular function: protein heterodimerization activity.
- GO: Biological process: male meiosis I, regulation of gene expression, spermatid differentiation,
spermatogenesis, meiotic nuclear division, spermatid development.
- GO: Cellular component: male germ cell nucleus, nucleolus
- OrthoDB:



Group EOG7GBTB5: 10 genes in 9 species
InterPro Domains
 9 genes with IPR011442: Domain of unknown function DUF1546;
 1 gene with IPR009072: Histone-fold;
Evolutionary Rate: 1.55
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: 1770 - 1674 > 80.29
- Evidences of selection: YES

Aquadro et al., 2015. Adaptative Evolution of Genes Involved in the Regulation of Germline Stem
Cells in Drosophila melanogaster and Drosophila simulans. G3 Journal: February.
4
4) FBgn0021856


class
3’ UTR



l(2)k14505: lethal (2) k14505  ovarian follicle stem cells (+ oogenesis), essential for viability or
fertility
2L: 21261168-21262411 (near centromere)
max
148
k
syn_k
0.411765 0.231405
pi
0
syn_pi
0.0002541
Dn
7
Pn
0
Ds
28
Ps
1
recomb
0.1173
Ka/Ks ratio: 1.779412
alpha (MKT): 1
p-value (Fisher): 1
- GO: Molecular function: - GO: Biological process: proton-transporting ATP synthase complex assembly
- GO: Cellular component: - OrthoDB:



Group EOG74RD5S: 50 genes in 49 species
InterPro Domains: 49 genes with IPR011419: ATP12, ATPase F1F0-assembly protein;
Evolutionary Rate: 1.06
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: -
- Evidences of selection: YES

Zhang, Clark, et al., 2013. Natural genetic variation in male reproductive genes contributes to
nontransitivity of sperm competitive ability in Drosophila melanogaster. Mol. Ecoll. 22: 1400-15.
5
5) FBgn0025578


Lcp9: larval cuticle protein 9  development
2R: 20667502-20667951
class
introns



max
56
k
0.3091
syn_k
0.0909
pi
0
syn_pi
0
Dn
17
Pn
0
Ds
4
Ps
0
recomb
1.8439
Ka/Ks ratio: 3.4
alpha (MKT): 1
p-value (Fisher): 1
- GO: Molecular function: structural constituent of chitin-based (larval) cuticle
- GO: Biological process: (larval) chitin-based cuticle development
- GO: Cellular component: extracellular matrix, extracellular region
- OrthoDB:



Group EOG7PCWZT: 10 genes in 10 species
InterPro Domains: 10 genes with IPR000618: Insect cuticle protein;
Evolutionary Rate: 0.95
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: 56 - 57 > 71.43
- Evidences of selection: YES (Indirect)


Gojobori and Moriyama 1989. J Mol Evol May; 28(5):391-7 Evolution of nested genes with
special reference to cuticle proteins in Drosophila melanogaster.
Riddiford et al., 1997. Nov:147(3):1213-24. A cluster of cuticle protein genes of Drosophila
melanogaster at 65A: sequence, structure and evolution.
6
6) FBgn0025821


class
CDS 2f



I-t: inhibitor-T  testis specific inhibitor
3R: 7529752-7530638
max
555
k
syn_k
0.327731 0.293103
pi
0
syn_pi
0
Dn
67
Pn
7
Ds
17
Ps
0
recomb
1.30577
Ka/Ks ratio: 1.118143
alpha (MKT): -0.776119
p-value (Fisher): 0.340244
- GO: Molecular function: protein phosphatase inhibitor activity
- GO: Biological process: negative regulation of protein dephosphorylation
- GO: Cellular component: - OrthoDB:



Group EOG722WQZ: 10 genes in 7 species
InterPro Domains: 2 genes with IPR007062: Protein phosphatase inhibitor 2 (IPP-2);
Evolutionary Rate: 1.73
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: 555 - 504 > 78.17
- Evidences of selection: YES (Indirect)


Zhang, Clark, et al., 2013. Natural genetic variation in male reproductive genes contributes to
nontransitivity of sperm competitive ability in Drosophila melanogaster. Mol. Ecoll. 22: 1400-15.
Aquadro et al., 2015. Adaptative Evolution of Genes Involved in the Regulation of Germline Stem
Cells in Drosophila melanogaster and Drosophila simulans. G3 Journal: February.
7
7) FBgn27866


class
5’ UTR



CG9776 (zinc finger protein)  (stress and immune pathways?)
3R: 153536-159793 (near centromere)
max
159
k
0.3333
syn_k
0.228477
pi
0
syn_pi
0.000226
Dn
9
Pn
0
Ds
138
Ps
4
recomb
0
Ka/Ks ratio: 1.458935
alpha (MKT): 1
p-value (Fisher): 1
- GO: Molecular function: - GO: Biological process: - GO: Cellular component: - OrthoDB:



Group EOG7XMFBP: 62 genes in 57 species
InterPro Domains
 47 genes with IPR003604: Zinc finger, U1-type;
 6 genes with IPR015880: Zinc finger, C2H2-like;
 2 genes with IPR008474: Protein of unknown function DUF755;
Evolutionary Rate: 1.29
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: -
- Evidences of selection: NO
8
8) FBgn0031365


class
CDS 2f



CG17650  oxidative stress susceptivility / resistance
2L: 1758286-1759093 (near telomere)
max
378
k
syn_k
pi
0.28125 0.205128 0.000162
syn_pi
0
Dn
41
Pn
5
Ds
8
Ps
0
recomb
2.22823
Ka/Ks ratio: 1.3711
alpha (MKT): 0.02439
p-value (Fisher): 1
- GO: Molecular function: - GO: Biological process: - GO: Cellular component: - Table S1. Young genes  Parental gene: NA; Mechanism: de novo; Age: 11 ~ 25 Myr.
- OrthoDB:



Group EOG72VVNR: 7 genes in 7 species
InterPro Domains: No domains identified.
Evolutionary Rate: 1.76
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: 378 - 402 > 79.37
- Evidences of selection: YES


Weber et al., 2012, PLoS ONE 7(4): e3474. Genome-Wide Association Analysis of Oxidative
Stress Resistance in Drosophila melanogaster. oxidative stress susceptivility/resistance genes
 evolutionary conserved.
Chen et al., 2012, Cell Rep. 1(2): 118--132. Frequent Recent Origination of Brain Genes Shaped
the Evolution of Foraging Behavior in Drosophila.  Table S1. List of young genes and their
origin.
9
9) FBgn0033683


CG18343  regeneration process (wing imaginal discs), development
2R: 8026200-8026829
class
CDS 2f



max
300
k
syn_k
0.32203 0.26923
pi
0
syn_pi
0
Dn
44
Pn
2
Ds
14
Ps
0
recomb
2.6031
Ka/Ks ratio: 1.196125
alpha (MKT): 0.36363636
p-value (Fisher): 1
- GO: Molecular function: - GO: Biological process: - GO: Cellular component: - Table S1. Young genes  Parental gene: NA; Mechanism: de novo; Age: 11 ~ 25 Myr.
- OrthoDB:



Group EOG7X9TQ3: 5 genes in 5 species
InterPro Domains: No domains identified.
Evolutionary Rate: 1.62
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: 300 - 333 > 69.67
- Evidences of selection: YES

Chen et al., 2012, Cell Rep. 1(2): 118--132. Frequent Recent Origination of Brain Genes Shaped
the Evolution of Foraging Behavior in Drosophila.  Table S1. List of young genes and their
origin.
10
10) FBgn0036469


class
CDS 2f



CG18649
3L: 15046668-15047235
max
279
k
syn_k
0.242857 0.178571
pi
0
syn_pi
0
Dn
7
Pn
5
Ds
5
Ps
0
recomb
0.761484
Ka/Ks ratio: 1.3600024
alpha (MKT): -2.57142857
p-value (Fisher): 0.244505
- GO: Molecular function: - GO: Biological process: - GO: Cellular component: - OrthoDB:

Your search returned no hits.  Please modify your search parameters and try again.
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: -
- Evidences of selection: YES (conserved)

Ranade et al., 2008, Dev. Biol. 315(2): 521--534. Analysis of the Otd-dependent transcriptome
supports the evolutionary conservation of CRX/OTX/OTD functions in flies and vertebrates
11) FBgn0037114


class
3’ UTR



Cpr78E: cuticular protein 78E  regeneration process (wing imaginal discs), development
3L: 21659552-21660080 (near centromere)
max
25
k
syn_k
0.291667 0.142857
pi
0
syn_pi
0
Dn
7
Pn
0
Ds
10
Ps
0
recomb
0.346129
Ka/Ks ratio: 2.041671
alpha (MKT): 1
p-value (Fisher): 1
11
- GO: Molecular function: structural constituent of chitin-based (larval) cuticle
- GO: Biological process: chitin-based cuticle development
- GO: Cellular component: extracellular matrix
- OrthoDB:



Group EOG7C33GT: 14 genes in 13 species
InterPro Domains: 14 genes with IPR000618: Insect cuticle protein;
Evolutionary Rate: 1.02
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: -
- Evidences of selection: YES (Indirect)



Gojobori and Moriyama 1989. J Mol Evol May; 28(5):391-7 Evolution of nested genes with
special reference to cuticle proteins in Drosophila melanogaster.
Riddiford et al., 1997. Nov:147(3):1213-24. A cluster of cuticle protein genes of Drosophila
melanogaster at 65A: sequence, structure and evolution.
Ranade et al., 2008, Dev. Biol. 315(2): 521--534. Analysis of the Otd-dependent transcriptome
supports the evolutionary conservation of CRX/OTX/OTD functions in flies and vertebrates.
12
12) FBgn0037184


class
CDS 0f



CG14450
3L: 22719334-22720889 (near centromere)
max
1119
k
0.137931
syn_k
0.21
pi
0
syn_pi
0
Dn
16
Pn
0
Ds
6
Ps
0
recomb
0
Ka/Ks ratio: 0.574712
alpha (MKT): 1
p-value (Fisher): 1
- GO: Molecular function: - GO: Biological process: - GO: Cellular component: - OrthoDB:



Group EOG7D2SVG: 36 genes in 36 species
InterPro Domains: No domains identified.
Evolutionary Rate: 1.77
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: 1119-1122 > 87.13
- Evidences of selection: NO
13
13) FBgn0038363


Acyp2: acylphosphatase 2  acylphosphatase and hydrolase activity
3R: 11618410-11619209
class
CDS 0f



max
309
k
0.142857
syn_k
0.225
pi
0
syn_pi
0
Dn
29
Pn
0
Ds
9
Ps
0
recomb
2.82917
Ka/Ks ratio: 0.63492
alpha (MKT): 1
p-value (Fisher): 1
- GO: Molecular function: acylphosphatase activity, hydrolase activity
- GO: Biological process: (cellular metabolic process)
- GO: Cellular component: cytoplasm
- OrthoDB:



Group EOG7HXR6N: 150 genes in 55 species
InterPro Domains: 150 genes with IPR001792: Acylphosphatase-like;
Evolutionary Rate: 0.96
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score: 309 - 375 > 62.78
- Evidences of selection: YES

Blanco et al., 2008, Genome Biol. 9(9): R134. Conserved chromosomal clustering of genes
governed by chromatin regulators in Drosophila.  gene upregulated
14
14) FBgn0052450


CG32450  aging process
3L: 22322878-22323757 (near centromere)
class
CDS 2f



max
477
k
syn_k
0.22549 0.173913
pi
0
syn_pi
0
Dn
30
Pn
0
Ds
12
Ps
0
recomb
0.13845
Ka/Ks ratio: 1.2965678
alpha (MKT): 1
p-value (Fisher): 1
- GO: Molecular function: - GO: Biological process: - GO: Cellular component: - OrthoDB:



Group EOG710B3H: 11 genes in 9 species
InterPro Domains: No domains identified.
Evolutionary Rate: 1.77
- Alignment with d. yakuba orthologous gene:

Length d. mel - Length d.yak > clustalW score:
- Evidences of selection: NO
15
Plots: genes by chr


Top: gene name (FBgn00)
Bottom: recombination value (cM/Mb)
16
Evidences of selection:
Gene ID
Gene Name
FBgn0011694
Ubc6 (ubiquitin conjugating
enzyme 6)
PebII (protein ejaculatory bulb II)
FBgn0014342
mia (meiosis I arrest)
FBgn0021856
l(2)k14505 (lethal (2) k14505)
FBgn0025578
FBgn0025821
FBgn0027866
FBgn0031365
FBgn0033683
FBgn0036469
Lcp9 (larval cuticle protein 9)
I-t (inhibitor-T)
CG9776 (zinc finger protein)
CG17650
CG18343
CG18649
FBgn0037114
Cpr78E (cuticular protein 78E)
FBgn0037184
FBgn0038363
FBgn0052450
CG14450
Acyp2 (acylphosphatase 2)
CG32450
FBgn0004436
GO / process
Ev idence of selection
ubiquitin-protein transferase activity
NO
multicellular organism reproduction
male meiosis, spermatogenesis, spermatid
differentiation and development
ovarian follicle stem cells (+ oogenesis),
essential for viability or fertility
development
testis specific inhibitor
(stress and immune response pathways?)
oxidative stress susceptivility/resistance
regeneration process (wing imaginal discs)
regeneration process (wing imaginal discs),
development
acylphosphatase and hydrolase activity
aging process
YES [1]
YES [2]
YES [2]
YES (Indirect) [3, 4]
YES (Indirect) [1, 2]
NO
YES [5, 6]
YES [6]
YES (conserved!) [7]
YES (Indirect) [3, 4, 7]
NO
YES [8]
NO
[1]: Zhang, Clark, et. al., 2013, Mol. Ecol.22 1400--1415. Natural genetic variation in male reproductive genes
contributes to nontransitivity of sperm competitive ability in Drosophila melanogaster.
[2]: Aquadro et al., 2015. Adaptive Evolution of Genes Involved in the Regulation of Germline Stem Cells in
Drosophila melanogaster and Drosophila simulans.
[3]: Gojobori and Moriyama 1989. J Mol Evol May; 28(5):391-7 Evolution of nested genes with special reference to
cuticle proteins in Drosophila melanogaster.
[4]: Riddiford et al., 1997. Nov:147(3):1213-24. A cluster of cuticle protein genes of Drosophila melanogaster at
65A: sequence, structure and evolution.
[5]: Weber et al., 2012, PLoS ONE 7(4): e3474. Genome-Wide Association Analysis of Oxidative Stress Resistance in
Drosophila melanogaster. oxidative stress susceptivility/resistance genes  evolutionary conserved.
[6]: Chen et al., 2012, Cell Rep. 1(2): 118--132. Frequent Recent Origination of Brain Genes Shaped the Evolution of
Foraging Behavior in Drosophila.  Table S1. List of young genes and their origin.
[7]: Ranade et al., 2008, Dev. Biol. 315(2): 521--534. Analysis of the Otd-dependent transcriptome supports the
evolutionary conservation of CRX/OTX/OTD functions in flies and vertebrates.
[8]: Blanco et al., 2008, Genome Biol. 9(9): R134. Conserved chromosomal clustering of genes governed by
chromatin regulators in Drosophila.  gene upregulated
17
EXCLUSION CRITERIA
Gene ID
Gene Name
WEAKNESS
FBgn0004436
Ubiquitin conjugating
enzyme 6
recomb = 0.1
NO ES
near centromere
FBgn0011694
Protein ejaculatory bulb
II
recomb = 0
near telomere
FBgn0014342
meiosis I arrest
recomb = 0
FBgn0021856
lethal (2) k14505
recomb = 0.1
ES
FBgn0025578
Larval cuticle protein 9
near telomere
FBgn0025821
Inhibitor-T
recomb = 1.8
recomb = 1.3
(testis specific inhibitor?)
FBgn0027866
CG9776
recomb = 0
NO ES
near centromere
FBgn0031365
CG17650
NO GO
FBgn0033683
CG18343
NO GO
FBgn0036469
CG18649
FBgn0037114
Cuticular protein 78E
FBgn0037184
CG14450
FBgn0038363
Acylphosphatase 2
FBgn0052450
CG32450



no orthologous for d. yak
recomb = 0.7
max = 25 nt (Dn + Ds = 17; Pn + Ps = 0)
recomb = 0.3
Ka / Ks < 1
recomb = 0
NO GO
NO ES
Ka / Ks < 1
many orthologous!!!
recomb = 0.1
NO ES
STRENGTH
Young gene (table S1)
ES
GO: reproduction
ES
GO: male meiosis,
spermatogenesis
recomb = 2.2
Young gene (table S1)
ES
recomb = 2.6
Young gene (table S1)
ES
recomb = 2.8
ES
ES: evidence of selection
GO: gene onthology
recomb: recombination cM/Mb
18