Hypervariable noncoding sequences in Saccharomyces cerevisiae

Genetics. 2005 Aug;170(4):1575-87. doi: 10.1534/genetics.105.042283. Epub 2005 Jun 14.

Abstract

Compared to protein-coding sequences, the evolution of noncoding sequences and the selective constraints placed on these sequences is not well characterized. To compare the evolution of coding and noncoding sequences, we have conducted a survey for DNA polymorphism at five randomly chosen loci among a diverse collection of 81 strains of Saccharomyces cerevisiae. Average rates of both polymorphism and divergence are 40% lower at noncoding sites and 90% lower at nonsynonymous sites in comparison to synonymous sites. Although noncoding and coding sequences show substantial variability in ratios of polymorphism to divergence, two of the loci, MLS1 and PDR10, show a higher rate of polymorphism at noncoding compared to synonymous sites. The high rate of polymorphism is not accompanied by a high rate of divergence and is limited to a few small regions. These hypervariable regions include sites with three segregating bases at a single site and adjacent polymorphic sites. We show that this clustering of polymorphic sites is significantly greater than one would expect on the basis of the spacing between polymorphic fourfold degenerate sites. Although hypervariable noncoding sequences could result from selection on regulatory mutations, they could also result from transient mutational hotspots.

Publication types

  • Comparative Study

MeSH terms

  • Base Pairing
  • Base Sequence
  • Conserved Sequence
  • DNA, Fungal
  • Evolution, Molecular
  • Genetic Variation*
  • Haplotypes
  • Linkage Disequilibrium
  • Molecular Sequence Data
  • Polymorphism, Genetic
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic
  • Recombination, Genetic
  • Saccharomyces cerevisiae / genetics*
  • Selection, Genetic
  • Sequence Homology, Nucleic Acid
  • Species Specificity

Substances

  • DNA, Fungal

Associated data

  • GENBANK/AY942206
  • GENBANK/AY942207
  • GENBANK/AY942208
  • GENBANK/AY942209
  • GENBANK/AY942210
  • GENBANK/AY942211
  • GENBANK/AY942212
  • GENBANK/AY942213
  • GENBANK/AY942214
  • GENBANK/AY942215
  • GENBANK/AY942216
  • GENBANK/AY942217
  • GENBANK/AY942218
  • GENBANK/AY942219
  • GENBANK/AY942220
  • GENBANK/AY942221
  • GENBANK/AY942222
  • GENBANK/AY942223
  • GENBANK/AY942224
  • GENBANK/AY942225
  • GENBANK/AY942226
  • GENBANK/AY942227
  • GENBANK/AY942228
  • GENBANK/AY942229
  • GENBANK/AY942230
  • GENBANK/AY942231
  • GENBANK/AY942232
  • GENBANK/AY942233
  • GENBANK/AY942234
  • GENBANK/AY942235
  • GENBANK/AY942236
  • GENBANK/AY942237
  • GENBANK/AY942238
  • GENBANK/AY942239
  • GENBANK/AY942240
  • GENBANK/AY942241
  • GENBANK/AY942242
  • GENBANK/AY942243
  • GENBANK/AY942244
  • GENBANK/AY942245
  • GENBANK/AY942246
  • GENBANK/AY942247
  • GENBANK/AY942248
  • GENBANK/AY942249
  • GENBANK/AY942250
  • GENBANK/AY942251
  • GENBANK/AY942252
  • GENBANK/AY942253
  • GENBANK/AY942254
  • GENBANK/AY942255
  • GENBANK/AY942256
  • GENBANK/AY942257
  • GENBANK/AY942258
  • GENBANK/AY942259
  • GENBANK/AY942260
  • GENBANK/AY942261
  • GENBANK/AY942262
  • GENBANK/AY942263
  • GENBANK/AY942264
  • GENBANK/AY942265
  • GENBANK/AY942266
  • GENBANK/AY942267
  • GENBANK/AY942268
  • GENBANK/AY942269
  • GENBANK/AY942270
  • GENBANK/AY942271
  • GENBANK/AY942272
  • GENBANK/AY942273
  • GENBANK/AY942274
  • GENBANK/AY942275
  • GENBANK/AY942276
  • GENBANK/AY942277
  • GENBANK/AY942278
  • GENBANK/AY942279
  • GENBANK/AY942280
  • GENBANK/AY942281
  • GENBANK/AY942282
  • GENBANK/AY942283
  • GENBANK/AY942284
  • GENBANK/AY942285
  • GENBANK/AY942286
  • GENBANK/AY942287
  • GENBANK/AY942288
  • GENBANK/AY942289
  • GENBANK/AY942290
  • GENBANK/AY942291
  • GENBANK/AY942292
  • GENBANK/AY942293
  • GENBANK/AY942294
  • GENBANK/AY942295
  • GENBANK/AY942296
  • GENBANK/AY942297
  • GENBANK/AY942298
  • GENBANK/AY942299
  • GENBANK/AY942300
  • GENBANK/AY942301
  • GENBANK/AY942302
  • GENBANK/AY942303
  • GENBANK/AY942304
  • GENBANK/AY942305
  • GENBANK/AY942306
  • GENBANK/AY942307
  • GENBANK/AY942308
  • GENBANK/AY942309
  • GENBANK/AY942310
  • GENBANK/AY942311
  • GENBANK/AY942312
  • GENBANK/AY942313
  • GENBANK/AY942314
  • GENBANK/AY942315
  • GENBANK/AY942316
  • GENBANK/AY942317
  • GENBANK/AY942318
  • GENBANK/AY942319
  • GENBANK/AY942320
  • GENBANK/AY942321
  • GENBANK/AY942322
  • GENBANK/AY942323
  • GENBANK/AY942324
  • GENBANK/AY942325
  • GENBANK/AY942326
  • GENBANK/AY942327
  • GENBANK/AY942328
  • GENBANK/AY942329
  • GENBANK/AY942330
  • GENBANK/AY942331
  • GENBANK/AY942332
  • GENBANK/AY942333
  • GENBANK/AY942334
  • GENBANK/AY942335
  • GENBANK/AY942336
  • GENBANK/AY942337
  • GENBANK/AY942338
  • GENBANK/AY942339
  • GENBANK/AY942340
  • GENBANK/AY942341
  • GENBANK/AY942342
  • GENBANK/AY942343
  • GENBANK/AY942344
  • GENBANK/AY942345
  • GENBANK/AY942346
  • GENBANK/AY942347
  • GENBANK/AY942348
  • GENBANK/AY942349
  • GENBANK/AY942350
  • GENBANK/AY942351
  • GENBANK/AY942352
  • GENBANK/AY942353
  • GENBANK/AY942354
  • GENBANK/AY942355
  • GENBANK/AY942356
  • GENBANK/AY942357
  • GENBANK/AY942358
  • GENBANK/AY942359
  • GENBANK/AY942360
  • GENBANK/AY942361
  • GENBANK/AY942362
  • GENBANK/AY942363
  • GENBANK/AY942364
  • GENBANK/AY942365
  • GENBANK/AY942366
  • GENBANK/AY942367
  • GENBANK/AY942368
  • GENBANK/AY942369
  • GENBANK/AY942370
  • GENBANK/AY942371
  • GENBANK/AY942372
  • GENBANK/AY942373
  • GENBANK/AY942374
  • GENBANK/AY942375
  • GENBANK/AY942376
  • GENBANK/AY942377
  • GENBANK/AY942378
  • GENBANK/AY942379
  • GENBANK/AY942380
  • GENBANK/AY942381
  • GENBANK/AY942382
  • GENBANK/AY942383
  • GENBANK/AY942384
  • GENBANK/AY942385
  • GENBANK/AY942386
  • GENBANK/AY942387
  • GENBANK/AY942388
  • GENBANK/AY942389
  • GENBANK/AY942390
  • GENBANK/AY942391
  • GENBANK/AY942392
  • GENBANK/AY942393
  • GENBANK/AY942394
  • GENBANK/AY942395
  • GENBANK/AY942396
  • GENBANK/AY942397
  • GENBANK/AY942398
  • GENBANK/AY942399
  • GENBANK/AY942400
  • GENBANK/AY942401
  • GENBANK/AY942402
  • GENBANK/AY942403
  • GENBANK/AY942404
  • GENBANK/AY942405
  • GENBANK/AY942406
  • GENBANK/AY942407
  • GENBANK/AY942408
  • GENBANK/AY942409
  • GENBANK/AY942410
  • GENBANK/AY942411
  • GENBANK/AY942412
  • GENBANK/AY942413
  • GENBANK/AY942414
  • GENBANK/AY942415
  • GENBANK/AY942416
  • GENBANK/AY942417
  • GENBANK/AY942418
  • GENBANK/AY942419
  • GENBANK/AY942420
  • GENBANK/AY942421
  • GENBANK/AY942422
  • GENBANK/AY942423
  • GENBANK/AY942424
  • GENBANK/AY942425
  • GENBANK/AY942426
  • GENBANK/AY942427
  • GENBANK/AY942428
  • GENBANK/AY942429
  • GENBANK/AY942430
  • GENBANK/AY942431
  • GENBANK/AY942432
  • GENBANK/AY942433
  • GENBANK/AY942434
  • GENBANK/AY942435
  • GENBANK/AY942436
  • GENBANK/AY942437
  • GENBANK/AY942438
  • GENBANK/AY942439
  • GENBANK/AY942440
  • GENBANK/AY942441
  • GENBANK/AY942442
  • GENBANK/AY942443
  • GENBANK/AY942444
  • GENBANK/AY942445
  • GENBANK/AY942446
  • GENBANK/AY942447
  • GENBANK/AY942448
  • GENBANK/AY942449
  • GENBANK/AY942450
  • GENBANK/AY942451
  • GENBANK/AY942452
  • GENBANK/AY942453
  • GENBANK/AY942454
  • GENBANK/AY942455
  • GENBANK/AY942456
  • GENBANK/AY942457
  • GENBANK/AY942458
  • GENBANK/AY942459
  • GENBANK/AY942460
  • GENBANK/AY942461
  • GENBANK/AY942462
  • GENBANK/AY942463
  • GENBANK/AY942464
  • GENBANK/AY942465
  • GENBANK/AY942466
  • GENBANK/AY942467
  • GENBANK/AY942468
  • GENBANK/AY942469
  • GENBANK/AY942470
  • GENBANK/AY942471
  • GENBANK/AY942472
  • GENBANK/AY942473
  • GENBANK/AY942474
  • GENBANK/AY942475
  • GENBANK/AY942476
  • GENBANK/AY942477
  • GENBANK/AY942478
  • GENBANK/AY942479
  • GENBANK/AY942480
  • GENBANK/AY942481
  • GENBANK/AY942482
  • GENBANK/AY942483
  • GENBANK/AY942484
  • GENBANK/AY942485
  • GENBANK/AY942486
  • GENBANK/AY942487
  • GENBANK/AY942488
  • GENBANK/AY942489
  • GENBANK/AY942490
  • GENBANK/AY942491
  • GENBANK/AY942492
  • GENBANK/AY942493
  • GENBANK/AY942494
  • GENBANK/AY942495
  • GENBANK/AY942496
  • GENBANK/AY942497
  • GENBANK/AY942498
  • GENBANK/AY942499
  • GENBANK/AY942500
  • GENBANK/AY942501
  • GENBANK/AY942502
  • GENBANK/AY942503
  • GENBANK/AY942504
  • GENBANK/AY942505
  • GENBANK/AY942506
  • GENBANK/AY942507
  • GENBANK/AY942508
  • GENBANK/AY942509
  • GENBANK/AY942510
  • GENBANK/AY942511
  • GENBANK/AY942512
  • GENBANK/AY942513
  • GENBANK/AY942514
  • GENBANK/AY942515
  • GENBANK/AY942516
  • GENBANK/AY942517
  • GENBANK/AY942518
  • GENBANK/AY942519
  • GENBANK/AY942520
  • GENBANK/AY942521
  • GENBANK/AY942522
  • GENBANK/AY942523
  • GENBANK/AY942524
  • GENBANK/AY942525
  • GENBANK/AY942526
  • GENBANK/AY942527
  • GENBANK/AY942528
  • GENBANK/AY942529
  • GENBANK/AY942530
  • GENBANK/AY942531
  • GENBANK/AY942532
  • GENBANK/AY942533
  • GENBANK/AY942534
  • GENBANK/AY942535
  • GENBANK/AY942536
  • GENBANK/AY942537
  • GENBANK/AY942538
  • GENBANK/AY942539
  • GENBANK/AY942540
  • GENBANK/AY942541
  • GENBANK/AY942542
  • GENBANK/AY942543
  • GENBANK/AY942544
  • GENBANK/AY942545
  • GENBANK/AY942546
  • GENBANK/AY942547
  • GENBANK/AY942548
  • GENBANK/AY942549
  • GENBANK/AY942550
  • GENBANK/AY942551
  • GENBANK/AY942552
  • GENBANK/AY942553
  • GENBANK/AY942554
  • GENBANK/AY942555
  • GENBANK/AY942556