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Molecular evolution of r. DNA in sturgeons: features and mechanisms Constantine V. Rozhkovan Galina Molecular evolution of r. DNA in sturgeons: features and mechanisms Constantine V. Rozhkovan Galina N. Chelomina

Diagram of the r. DNA array of eukaryotes NTS – non-transcribed spacer; ETS – Diagram of the r. DNA array of eukaryotes NTS – non-transcribed spacer; ETS – external transcribed spacer; ITS – internal transcribed spacer. The detail of the small subunit (18 S) r. RNA 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) mutation intrachromosomal homogenization Model for concerted evolution of tandemly repeated multi-gene families (Liao, 1999) mutation intrachromosomal homogenization interchromosomal gene conversion (rate-limiting step) interchromosomal homogenization 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 blackened or cross-hatched boxes).

18 S r. DNA diversity in sturgeon species and hybrids Taxa n S h 18 S r. DNA diversity in sturgeon species and hybrids 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 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 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.

“G E N E S” “P S E U D O G E N “G E N E S” “P S E U D O G E N Af – Acipenser fulvescens; As – Acipenser schrenckii; Hd – Huso dauricus; E SD – A. schrenckii × H. dauricus; S” SB – A. schrenckii × A. baerii; * - here and further – Genebank data

Genes Pseudogenes A B C Af – A. fulvescens*, As – A. schrenckii, Hd Genes Pseudogenes A B C 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 SD – A. schrenckii × H. dauricus, SB – A. schrenckii × 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 Species 31 9 6 0. 301 Groups compared n S h Hd Pi k Species 31 9 6 0. 301 0. 00120 0. 581 Hybrids 12 16 9 0. 909 0. 00578 2. 803 Species 47 38 28 0. 944 0. 01117 5. 306 Hybrids 28 36 20 0. 923 0. 01379 6. 648 Genes Pseudogenes Groups compared (C T) + (G A) : other substitution 0. 182 1 : 2. 5 Pseudogenes 0. 082 0. 226 2. 540 2. 083 1: 1 Genes Z -0. 010587 Species La-Lb -0. 010836 Genes Zn. S 1: 2 Hybrids Pseudogenes 0. 276 1 : 1. 5 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. Zn. S – 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 Z 1. 96, than hypothesis of constant evolutionary rate is rejected.

Recombination events Taxa Rg Ras 4 gt Rm S d A. fulvescens* 13. 7 Recombination events Taxa 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 Taxa Ngc Psi Nis Conversion tracts A. fulvescens* 2 0. 00723 7 Gene conversion 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 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

Linkage disequilibrium Species and hybrids Taxa Af* As Hd SD SB Sites with linkage Linkage disequilibrium Species and hybrids Taxa Af* As Hd SD SB Sites with linkage disequilibrium 68 68 68 35 68 68 F=48. 8%; B=18. 2% 236 236 236 260 367 381 392 396 435 436 452 260 372 392 435 436 452 260 275 372 392 435 436 452 260 295 333 392 435 436 452 260 275 372 392 435 436 452 F=89. 3%; B=32% F=100%; B=86. 1% 68 68 452 Acipenser schrenckii 68 236 260 275 372 392 435 436 260 372 392 435 436 452 Acipenser fulvescens* 35 68 236 260 376 381 392 396 435 436 F=61. 1%; B=22. 7% 68 236 260 275 295 333 372 392 436 452 Huso dauricus 435 SD 452 SB Af – A. fulvescens, As – A. schrenckii, Hd – H. dauricus, SD – A. schrenckii × H. dauricus, SB – A. schrenckii × A. baerii; Light grey rectangle – 0. 01

Linkage disequilibrium Pseudogenes Taxa Sites with linkage disequilibrium 68 366 380 395 435 68 Linkage disequilibrium Pseudogenes Taxa Sites with linkage disequilibrium 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 Af* As Hd SD SB F=16. 6%; B=0% F=10. 7%; B=0% F=35. 5%; B=31. 2% F=63. 8%; B=56. 5% 35 68 68 366 380 395 435 Af* F=13. 9%; B=0% 235 259 371 391 434 435 451 As 68 68 235 259 274 371 391 434 435 451 Hd 236 260 295 333 392 435 436 452 SD 236 260 275 372 392 435 436 452 SB Af – A. fulvescens, As – A. schrenckii, Hd – H. dauricus, SD – A. schrenckii × H. dauricus, SB – A. schrenckii × A. baerii; Light grey rectangle – 0. 01

Linkage disequilibrium D D Acipenser schrenckii 0. 4 0. 2 0. 0 -0. 1 Linkage disequilibrium D D Acipenser schrenckii 0. 4 0. 2 0. 0 -0. 1 -0. 2 Huso dauricus -0. 2 0 D 100 200 Nucleotide distance 400 300 0 D Acipenser schrenckii × Huso dauricus 0. 4 Acipenser schrenckii × Acipenser baerii -0. 1 -0. 2 400 0. 0 -0. 1 300 0. 2 0. 0 200 Nucleotide distance 0. 4 0. 2 100 -0. 2 0 100 200 300 Nucleotide distance 400 0 100 200 Nucleotide distance 300 400