molecular evolution of rdna in sturgeons: features and mechanisms
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Molecular evolution of rDNA in sturgeons: features and
mechanisms
Constantine V. RozhkovanGalina N. Chelomina
Diagram of the rDNA array of eukaryotes
NTS – non-transcribed spacer; ETS – external transcribed spacer; ITS – internal transcribed spacer. The detail of the small subunit (18S) rRNA gene shows PCR primers (and their orientations) used for amplification and sequencing of the gene. Cross-hatched box indicates the cloned and sequenced 486 bp part of the entire gene.
Model for concerted evolution of tandemly repeated multi-gene families (Liao, 1999)
The coding sequences are depicted as unblackened arrows, and the
intergenic spacers are depicted as lines. The flanking
sequences of the two arrays are differently labeled (as either
blackenedor cross-hatched boxes).
mutation
intrachromosomal homogenization
interchromosomal gene conversion (rate-limiting step)
interchromosomal homogenization
Taxa n S h Hd Pi k
Acipenser fulvescens* 18 31 12 0.935 0.01138 5.510
Acipenser schrenckii 22 20 11 0.714 0.00878 4.251
Huso dauricus 38 13 16 0.863 0.00979 4.649
Total 78 44 34 0.871 0.01123 5.335
18S rDNA diversity in sturgeon species and hybrids
n – sample size; S – number of polymorphic (segregating) sites; h – number of haplotypes; Hd – haplotypic diversity; Pi – nucleotide diversity; k – average number of nucleotide differences.
Taxa n S h Hd Pi k
A. schrenckii × H. dauricus 26 42 21 0.978 0.01666 8.031
A. schrenckii × A. baerii 14 18 10 0.890 0.01258 6.088
Total 40 50 29 0.955 0.01530 7.373
Hd-30 Hd-13
Hd-9 SD-11
Hd-20 Hd-3 SD-24
SB-12 Hd-10 As-22 Hd-26
SD-6 Hd-37 As-19 SD-18 As-17
SB-6 As-20 SB-5 As-11 Hd-38
Hd-22 As-9 As-16 Hd-17
As-3 Hd-15 As-5 SD-25
As-7 As-2 As-8
SD-14 Hd-4 Af-D**
SB-10 SD-2
Af-13** As-13 As-10 Af-7** SD-9
Hd-23 Af-11*
Hd-6 SB-7 As-6
SD-12 Hd-32
SB-8 Hd-1 SD-23 SD-10 Hd-12
Hd-34 Hd-19 Hd-24 As-21 Hd-5
SD-19 Af-5*
Hd-2 As-12
SB-11 Hd-35
Hd-28 Hd-36
Hd-14 As-14 SB-1
SD-15 SD-3
Af-29* SD-26 SD-17
SD-8 SD-4
As-18 SD-16
SD-7 Af-18*
Af-9* Af-3* Af-2* Af-1*
Af-31* Af-19* Af-10* Af-26* Af-6*
Af-33* Af-17*
SD-20 SB-2
Hd-21 Hd-27 SD-22 SB-3 Hd-8 Hd-11 Hd-29 Hd-18 SD-13 SB-9 Hd-7 Hd-25 SD-1 SB-14 SB-13 Hd-16 As-1 Hd-31 Hd-33 SB-4
As-15 As-4
SD-21 SD-5
S.salar* S.trutta*
78
75
75
64
63
63
5358
62
59
56
55
0,005
“G
E
N
E
S”
“P
S
E
U
D
O
G
E
N
E
S”
Af – Acipenser fulvescens;
As – Acipenser schrenckii;
Hd – Huso dauricus;
SD – A. schrenckii × H. dauricus;
SB – A. schrenckii × A. baerii;
* - here and further – Genebank data
Af-7,Af-d, Af-13,
As (n=12), Hd (n=11), A. sturio
As (n=1) Hd (n=2) Hd-12
Hd-22
As-7 As-3
Hd (n=2)
As-6
A.ruth Hd-13
Hd-5
Hd-2
Hd-14 As-14
Hd-36
Hd-34
10
As-12
Af-5
14
A.br-1
Hd-6 Hd-23
Af-11
As-1 Hd (n=9)
Af (n=4) A.br (n=2)
Hd-21 Hd-27
Hd-28
Hd-35
As-15
As-4
Af-29
As-18
Af-17 Af-33 8
Af-1, 2
A.br-2 Af-3
Af-31
Af-18
Af-9
Af – A. fulvescens*, As – A. schrenckii, Hd – H. dauricus, A.br – A. brevirostrum*, A.ruth – A. ruthenus*. Number of bars and numerals on connecting lines corresponds to a number of mutation steps, n – number of clones.
Genes Pseudogenes
A
BC
SD (n=3) SB (n=5) SD-21 SB-11
SD-17 SD-26
SD-7
SD-3
SD-4 SD-8
SD-16
5
10
SD-20
SB-1
SD-5 SB-2
SD (n=3) SB-5
SD-15
SD-19
SD-12 SB-7
SD-23
SD-2
SB-12
SD-10 SB-6
SD-6
SD-14
SD-24
SB-10
SD-11
SB-8
Genes Pseudogenes
SD – A. schrenckii × H. dauricus, SB – A. schrenckii × A. baerii. Number of bars and numerals on connecting lines corresponds to a number of mutation steps, n – number of clones.
Groups compared n S h Hd Pi k
Genes
Species
Hybrids
31
12
9
16
6
9
0.301
0.909
0.00120
0.00578
0.581
2.803
Pseudogenes
Species
Hybrids
47
28
38
36
28
20
0.944
0.923
0.01117
0.01379
5.306
6.648
Groups compared ZnS (CT) + (GA) : other substitution
La-Lb Z
Species
Genes
Pseudogenes
0.182
0.082
1 : 2.5
1 : 1
-0.010836 2.540
Hybrids
Genes
Pseudogenes
0.226
0.276
1 : 2
1 : 1.5
-0.010587 2.083
n – sample size; S – number of polymorphic (segregating) sites; h – number of haplotypes; Hd – haplotypic diversity; Pi – nucleotide diversity; k – average number of nucleotide differences.
ZnS – Kelly’s neutrality test; L – relative evolution rate; La and Lb – the average distances (number of nucleotide substitutions per site) between genes and pseudogenes clusters in comparison with the common ancestor; if Z1.96, than hypothesis of constant evolutionary rate is rejected.
Recombination eventsTaxa Rg Ras 4 gt Rm S d
A. fulvescens* 13.7 0.0283 10 2 31 483.22
A. schrenckii 0.50 0.0010 12 2 20 483.77
H. dauricus 5.80 0.0120 30 4 13 483.39
A. schrenckii × H. dauricus 12.50 0.0285 20 2 18 483.57
A. schrenckii × A. baerii 23.60 0.0488 22 5 42 483.69
Taxa Rg (genes/ψgenes)
Ras (genes/ψgenes)
4 gt (genes/ψgenes)
Rm (genes/ψgenes)
A. fulvescens*
A. schrenckii
H. dauricus
Species
0.000/7.9
0.001/76.4
0.001/10.5
0.001/23.7
0/0.0164
0/0.1580
0/0.0217
0/0.0491
0/2
0/12
0/30
0/24
0/1
0/2
0/4
0/5
A. schrenckii × H. dauricus
A. schrenckii × A. baerii
Hybrids
81.4/31.0
>10 000/6.6
160/23.9
0.1682/0.0641
0/0.0137
0.3306/0.0494
0/22
0/16
0/26
0/5
0/2
0/5
R – recombination parameters: Rg – estimate of R per gene, Ras – estimate of R, between adjacent sites; 4 gt – number of pairs of sites with four gametic types; Rm – minimum number of recombination events; S – number of polymorphic (segregating) sites; d – average nucleotide distance between the most distant sites.
Gene conversion
Ngc – number of gene conversion tracts identified; Psi – average number of informative nucleotide sites per site; Nis – number of sites with information. First nucleotide of 486 bp fragment corresponds to 960 nucleotide of entire gene sequence
Taxa Ngc Psi Nis Conversion tracts
A. fulvescens* 2 0.00723 7 391-451 – Af-05; 235-259 – Af-11
A. schrenckii 2 0.00826 11 259-274 – As-12; 68-274 – As-14
H. dauricus 8 0.01174 9 235-274 – Hd-02; 68-371 – Hd-06; 371-391 – Hd-13; 235-274 – Hd-14; 235-274 – Hd-23; 434-435 – Hd-28; 434-451 – Hd-35; 235-371 – Hd-36
A. schrenckii × H. dauricus 3 0.01676 11 236-275 – SH-05; 435-436 – SH-07; 68-236 – SH-16
A. schrenckii × A. baerii 3 0.01609 9 68-275 – SB-01; 435-436 – SB-07; 435-452 – SB-11
Taxa Sites with linkage disequilibrium
Af*
As
Hd
SD
SB
68 236 260 367 381 392 396 435 436 452
68 236 260 372 392 435 436 452
68 236 260 275 372 392 435 436 452
35 68 236 260 295 333 392 435 436 452
68 236 260 275 372 392 435 436 452
Linkage disequilibriumSpecies and hybrids
Af – A. fulvescens, As – A. schrenckii, Hd – H. dauricus, SD – A. schrenckii × H. dauricus, SB – A. schrenckii × A. baerii;
Light grey rectangle – 0.01<P<0.05; dark grey rectangle – 0.001<P<0.01; black rectangle – P<0.001; F – sites, significant by Fisher’s exact test, B – sites, significant with Bonferroni correction procedure.
First nucleotide of 486 bp fragment corresponds to 960 nucleotide of entire gene sequence
68236
260
376381
396
435436
452
392
Acipenser fulvescens*
68
236260
372392
435436
452
Acipenser schrenckii
68
236260
275372
392
435436
452
Huso dauricus
3568
236260
295333
392435
436452
68236
260275
372392
435436
452
SD SB
F=48.8%; B=18.2% F=89.3%; B=32% F=89.3%; B=32% F=100%; B=86.1% F=61.1%; B=22.7%
Taxa Sites with linkage disequilibrium
Af*
As
Hd
SD
SB
68 366 380 395 435
68 235 259 371 391 434 435 451
68 235 259 274 371 391 434 465 451
35 68 236 260 295 333 372 392 435 452
68 236 260 275 392 435 436 452
Linkage disequilibriumPseudogenes
Af – A. fulvescens, As – A. schrenckii, Hd – H. dauricus, SD – A. schrenckii × H. dauricus, SB – A. schrenckii × A. baerii;
Light grey rectangle – 0.01<P<0.05; dark grey rectangle – 0.001<P<0.01; black rectangle – P<0.001; F – sites, significant by Fisher’s exact test, B – sites, significant with Bonferroni correction procedure.
First position of 486 bp fragment corresponds to 960 position of entire gene sequence
366
380395
435
68235
259
371391
434435
451
68235
259274
371391
434435
451
68
35
236
260295
333392
435436
452
68236
260
275372
392
435436
452
Af* As Hd SD SB
F=16.6%; B=0%
F=10.7%; B=0% F=63.8%; B=56.5% F=35.5%; B=31.2% F=13.9%; B=0%
-0.2
-0.1
0.0
0.2
0.4
0 100 200 300 400
-0.2
-0.1
0.0
0.2
0.4
0 100 200 300 400
-0.2
-0.1
0.0
0.2
0.4
0 100 200 300 400
-0.2
-0.1
0.0
0.2
0.4
0 100 200 300 400
Nucleotide distance Nucleotide distance
Nucleotide distance
Acipenser schrenckii Huso dauricus
Acipenser schrenckii × Huso dauricus Acipenser schrenckii × Acipenser baerii
D D
D D
Nucleotide distance
Linkage disequilibrium
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