Table 5 Identified genes, their UniProt accession IDs and the number of corresponding contigs for the Amazon molly ( P. formosa; Pofo ) and the Atlantic molly ( P. mexicana; Pome )

Ago1

Argonaute 1, Eukaryotic translation initiation factor 2C 1

Q8CJG1

1

7

Ago2

Argonaute 2, Eukaryotic translation initiation factor 2C 2

Q8CJG0

10

2

Ago3

Argonaute 3, Eukaryotic translation initiation factor 2C 3

Q9H9G7

8

9

Ago4

Argonaute 4, Eukaryotic translation initiation factor 2C 4

Q9HCK5

9

0

C15orf60

Meiotic recombination protein REC114-like

Q7Z4M0

0

2

CcnA1

Cyclin-A1

Q92161

13

7

CcnA2

Cyclin-A2

P30274

20

8

CcnC

Cyclin-C

Q28F72

8

3

Cdk1

Cell division protein kinase/Cyclin-dependent kinase 1

Q9DG98

3

3

Cdk2

Cell division protein kinase/Cyclin-dependent kinase 2

P43450

1

1

Cdk4

Cyclin-dependent kinase 4

Q91727

9

4

Cdk7

Cyclin-dependent kinase 7

P51953

18

2

Cdk10

Cell division protein kinase/Cyclin-dependent kinase 10

Q2TBL8

1

1

Cdk14

Cell division protein kinase/Cyclin-dependent kinase 14

B0VXL7

3

0

Cdk16

Cell division protein kinase/Cyclin-dependent kinase 16

Q00536

3

0

Mcm2

DNA helicase MCM2, Minichromosome maintenance protein 2

Q6DIH3

10

1

Mcm3

DNA helicase MCM3, Minichromosome maintenance protein 3

Q5ZMN2

1

3

Mcm4

DNA helicase MCM4, Minichromosome maintenance protein 4

P33991

0

2

Mcm4B

DNA replication licensing factor MCM4-B, Minichromosome maintenance protein 4-B

P30664

3

3

Mcm5

DNA helicase MCM5, Minichromosome maintenance 5

Q561P5

18

2

Mcm6

DNA helicase MCM6, Minichromosome maintenance 6

Q14566

3

4

Mcm7

DNA helicase MCM7, Minichromosome maintenance 7

Q6NX31

18

3

Mcm8

DNA helicase MCM8, Minichromosome maintenance 8

Q9UJA3

15

2

Mcm9

DNA helicase MCM9, Minichromosome maintenance 9

Q6NRM6

19

1

Zmcm3

Zygotic minichromosome maintenance protein 3

Q7ZXZ0

0

4

Mei1*

Meiosis inhibitor protein 1

Q5TIA1

11

11

Mlh1*

DNA mismatch repair protein Mlh1, MutL protein homolog 1

P40692

7

4

Mlh3*

DNA mismatch repair protein Mlh3, MutL protein homolog 3

Q9UHC1

6

1

Mnd1*

Meiotic nuclear division protein 1 homolog

Q32L19

11

3

Mns1*

Meiosis-specific nuclear structural protein 1

Q6PBA8

1

2

Mre11

Double-strand break repair protein MRE11

Q9W6K1

2

1

Msh2*

DNA mismatch repair protein Msh2, MutS protein homolog 2

Q5XXB5

10

6

Msh3*

DNA mismatch repair protein Msh3, MutS protein homolog 3

P20585

8

4

Msh4*

DNA mismatch repair protein Msh4, MutS protein homolog 4

O15457

7

4

Msh5*

DNA mismatch repair protein Msh5, MutS protein homolog 5

O43196

0

4

Msh6*

DNA mismatch repair protein Msh6, MutS protein homolog 6

P52701

26

6

Piwil1

Piwi-like protein 1

Q8UVX0

13

6

Piwil2

Piwi-like protein 2

A6P7L8

7

2

Pms2

DNA mismatch repair protein (endonuclease) PMS2

P54278

12

1

Psmc3ip*

Homologous-pairing protein 2 homolog (HOP2)

Q63ZL2

3

2

Rad1

Cell cycle checkpoint protein RAD1

Q5R7X9

4

0

Rad21*

Double-strand-break repair protein rad21 homolog

O60216

9

12

Rad50

DNA repair protein RAD50

P70388

2

2

Rad51B*

DNA repair protein RAD51 homolog B

Q91917

23

3

Rad51C*

DNA repair protein RAD51 homolog 3

O43502

7

1

Rad51D*

DNA repair protein RAD51 homolog 4/D

O75771

7

5

Rad52

DNA repair protein RAD52 homolog

P39022

10

11

Rad54A*

DNA repair and recombination protein RAD54-like

Q92698

18

6

Rad54B*

DNA repair and recombination protein RAD54B

Q9DG67

9

1

Rad9A

Cell cycle checkpoint control protein RAD9A

Q99638

8

3

Rad9B

Cell cycle checkpoint control protein RAD9B

Q6WBX8

0

1

Rec8*

Meiotic recombination protein REC8 homolog

O95072

3

2

RecQl1

ATP-dependent DNA helicase Q1

Q9Z129

3

3

RecQl4

ATP-dependent DNA helicase Q4

O94761

3

6

RecQl5

ATP-dependent DNA helicase Q5

O94762

5

2

Rmi1

RecQ-mediated genome instability protein 1

A4IF98

15

1

Rmi2

RecQ-mediated genome instability protein 2

Q5ZM20

0

2

Sfr1*

Swi5-dependent recombination DNA repair protein 1 homolog, Meiosis protein 5 homolog

B7ZD04

2

1

Smarca2

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2

Q6DIC0

11

0

Smarca4

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4

A7Z019

10

0

Smc1a*

Structural maintenance of chromosomes protein 1A

Q9CU62

10

2

Smc1b*

Structural maintenance of chromosomes protein 1B

Q8NDV3

2

2

Smc2*

Structural maintenance of chromosomes protein 2

P50533

9

2

Smc3*

Structural maintenance of chromosomes protein 3

Q9CW03

2

3

Smc4*

Structural maintenance of chromosomes protein 4

P50532

7

8

Smc5*

Structural maintenance of chromosomes protein 5

Q802R9

4

1

Smc6*

Structural maintenance of chromosomes protein 6

Q6P9I7

24

3

Smchd1

Structural maintenance of chromosomes flexible hinge domain-containing protein 1

A6NHR9

25

37

Spo11*

Meiotic recombination protein

Q9Y5K1

4

11

Stag1*

Cohesin subunit SA-1

Q8WVM7

3

13

Stag2*

Cohesin subunit SA-2

Q8N3U4

7

14

Xrcc1

DNA repair protein XRCC1

Q60596

21

3

Xrcc2*

DNA repair protein XRCC2

Q9CX47

19

12

Xrcc3*

DNA repair protein XRCC3

Q08DH8

2

0

Xrcc4

DNA repair protein XRCC4

Q924T3

24

6