Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes

被引:122
作者
Axelsson, E
Webster, MT
Smith, NGC
Burt, DW
Ellegren, H [1 ]
机构
[1] Uppsala Univ, Dept Evolut Biol, Evolut Biol Ctr, SE-75236 Uppsala, Sweden
[2] Univ Lancaster, Fylde Coll, Dept Math & Stat, Lancaster LA1 4YF, England
[3] Roslin Inst, Div Genom & Bioinformat, Roslin EH25 9PS, Midlothian, Scotland
关键词
D O I
10.1101/gr.3021305
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A distinctive feature of the avian genome is the large heterogeneity in the size of chromosomes, which are usually classified into a small number of macrochromosomes and numerous microchromosomes. These chromosome classes show characteristic differences in a number of interrelated features that Could potentially affect the rate of sequence evolution, such as GC content, gene density, and recombination rate. We studied the effects of these factors by analyzing patterns of nucleotide Substitution in two sets of chicken-turkey sequence alignments. First, in a set of 67 orthologous introns, divergence was significantly higher in microchromosomes (chromosomes 11-38; 11.7% divergence) than in both macrochromosomes (chromosomes 1-5; 9.9% divergence; P = 0.016) and intermediate-sized chromosomes (chromosomes 6-10; 9.5% divergence; P = 0.026). At least part of this difference was due to the higher incidence of CpG sites on microchromosomes. Second, using 155 orthologous coding sequences we noted a similar pattern, in which synonymous Substitution rates on microchromosomes (13.1%) were significantly higher than were rates on macrochromosomes (10.3%; P = 0.024). Broadly assuming neutrality of introns and synonymous sites, or constraints oil such sequences do not differ between chromosomal classes, these observations imply that microchromosomal genes are exposed to more germ line mutations than those on other chromosomes. We also find that dN/dS ratios for genes located on microchromosomes (average, 0.094) are significantly lower than those of macrochromosomes (average, 0.185; P = 0.025), suggesting that the proteins of genes oil microchromosomes are under greater evolutionary constraint.
引用
收藏
页码:120 / 125
页数:6
相关论文
共 55 条
[11]   Mutation rate variation in the mammalian genome [J].
Ellegren, H ;
Smith, NGC ;
Webster, MT .
CURRENT OPINION IN GENETICS & DEVELOPMENT, 2003, 13 (06) :562-568
[12]   The evolution of isochores [J].
Eyre-Walker, A ;
Hurst, LD .
NATURE REVIEWS GENETICS, 2001, 2 (07) :549-555
[13]   RECOMBINATION AND MAMMALIAN GENOME EVOLUTION [J].
EYREWALKER, A .
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 1993, 252 (1335) :237-243
[14]   A gradient of silent substitution rate in the human pseudoautosomal region [J].
Filatov, DA .
MOLECULAR BIOLOGY AND EVOLUTION, 2004, 21 (02) :410-417
[15]  
Galtier N, 2001, GENETICS, V159, P907
[16]  
GOLDMAN N, 1994, MOL BIOL EVOL, V11, P725
[17]   Chicken microchromosomes are hypermethylated and can be identified by specific painting probes [J].
Grützner, F ;
Zend-Ajusch, E ;
Stout, K ;
Munsche, S ;
Niveleau, A ;
Nanda, I ;
Schmid, M ;
Haaf, T .
CYTOGENETICS AND CELL GENETICS, 2001, 93 (3-4) :265-269
[18]   Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila [J].
Halligan, DL ;
Eyre-Walker, A ;
Andolfatto, P ;
Keightley, PD .
GENOME RESEARCH, 2004, 14 (02) :273-279
[19]   Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution [J].
Hardison, RC ;
Roskin, KM ;
Yang, S ;
Diekhans, M ;
Kent, WJ ;
Weber, R ;
Elnitski, L ;
Li, J ;
O'Connor, M ;
Kolbe, D ;
Schwartz, S ;
Furey, TS ;
Whelan, S ;
Goldman, N ;
Smit, A ;
Miller, W ;
Chiaromonte, F ;
Haussler, D .
GENOME RESEARCH, 2003, 13 (01) :13-26
[20]   High intron sequence conservation across three mammalian orders suggests functional constraints [J].
Hare, MP ;
Palumbi, SR .
MOLECULAR BIOLOGY AND EVOLUTION, 2003, 20 (06) :969-978