SMAL: A resource of spontaneous mutation accumulation lines

Molecular Biology and Evolution

Volumn 31, Issue 5, 2014, Pages 1302-1308

  Wei, Wen ^a   Ning, Lu Wen ^a   Ye, Yuan Nong ^a   Li, Shi Jie ^a   Zhou, Hui Qi ^a   Huang, Jian ^a   Guo, Feng Biao ^a  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Database; Mutation; SMAL

Indexed keywords

ARTICLE; DATA BASE; GENETIC VARIABILITY; GENOME; HIGH THROUGHPUT SEQUENCING; INCIDENCE; MOLECULAR EVOLUTION; NONHUMAN; SPONTANEOUS MUTATION; THEORETICAL STUDY;

DATABASE; MUTATION; SMAL;

ANIMALS; DATABASES, GENETIC; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; FEMALE; GENETIC DRIFT; GENETIC FITNESS; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MODELS, GENETIC; MUTATION; SALMONELLA TYPHIMURIUM;

EID: 84899556282     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu073     Document Type: Article

References (39)

1. Berglund J, Pollard KS, Webster MT. 2009. Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 7:e26.
2. Birky CW Jr. 2001. The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models. Annu Rev Genet. 35: 125-148.
3. Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. 2013. Amodel-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet. 9:e1003684.
4. Chen X, Chen Z, Chen H, Su Z, Yang J, Lin F, Shi S, He X. 2012. Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes. Science 335:1235-1238.
5. Chen X, Zhang J. 2013. No gene-specific optimization of mutation rate in Escherichia coli. Mol Biol Evol. 30:1559-1562.
6. Denver DR, Dolan PC, Wilhelm LJ, Sung W, Lucas-Lledo JI, Howe DK, Lewis SC, Okamoto K, Thomas WK, Lynch M, et al. 2009. A genomewide view of Caenorhabditis elegans base-substitutionmutation processes. Proc Natl Acad Sci U S A. 106:16310-16314.
7. Denver DR, Wilhelm LJ, Howe DK, Gafner K, Dolan PC, Baer CF. 2012. Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes. Genome Biol Evol. 4:513-522.
8. Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, et al. 2011. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet. 43: 482-486.
9. Gao F, Luo H, Zhang CT. 2013. DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Res. 41:D90-D93.
10. Haag-Liautard C, Coffey N, Houle D, LynchM, Charlesworth B, Keightley PD. 2008. Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS Biol. 6:e204.
11. Hall DW, Mahmoudizad R, Hurd AW, Joseph SB. 2008. Spontaneous mutations in diploid Saccharomyces cerevisiae: another thousand cell generations. Genet Res. 90:229-241.
12. Hershberg R, Petrov DA. 2010. Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet. 6:e1001115.
13. Hodgkinson A, Eyre-Walker A. 2011. Variation in the mutation rate across mammalian genomes. Nat Rev Genet. 12:756-766.
14. Houle D, Nuzhdin SV. 2004. Mutation accumulation and the effect of copia insertions in Drosophila melanogaster. Genet Res. 83:7-18.
15. Hurst LD, Ellegren H. 1998. Sex biases in themutation rate. Trends Genet. 14:446-452.
16. Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, Blaxter ML. 2009. Analysis of the genome sequences of three Drosophila melanogaster spontaneousmutation accumulation lines. Genome Res. 19: 1195-1201.
17. Lee H, Popodi E, Tang H, Foster PL. 2012. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc Natl Acad Sci U S A. 109:E2774-E2783.
18. Lind PA, Andersson DI. 2008. Whole-genome mutational biases in bacteria. Proc Natl Acad Sci U S A. 105:17878-17883.
19. Long HA, Paixao T, Azevedo RB, Zufall RA. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics 195:527-540.
20. Lynch M. 2010. Evolution of the mutation rate. Trends Genet. 26: 345-352.
21. Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, et al. 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A. 105:9272-9277.
22. McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B. 2013. Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res. 41:e140.
23. Meiklejohn CD, Montooth KL, Rand DM. 2007. Positive and negative selection on the mitochondrial genome. Trends Genet. 23: 259-263.
24. Neiman M, Hehman G, Miller JT, Logsdon JM Jr, Taylor DR. 2010. Accelerated mutation accumulation in asexual lineages of a freshwater snail. Mol Biol Evol. 27:954-963.
25. Ness RW, Morgan AD, Colegrave N, Keightley PD. 2012. Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii. Genetics 192:1447-1454.
26. Ossowski S, Schneeberger K, Lucas-Lledo JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M. 2010. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
27. Park C, Qian W, Zhang J. 2012. Genomic evidence for elevated mutation rates in highly expressed genes. EMBO Rep. 13:1123-1129.
28. Paul S, Million-Weaver S, Chattopadhyay S, Sokurenko E, Merrikh H. 2013. Accelerated gene evolution through replication-transcription conflicts. Nature 495:512-515.
29. Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, et al. 2006. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2: e168.
30. Rocha EP, Danchin A. 2004. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol Biol Evol. 21:108-116.
31. Schrider DR, Houle D, Lynch M, Hahn MW. 2013. Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster. Genetics 194:937-954.
32. Shen YY, Liang L, Zhu ZH, Zhou WP, Irwin DM, Zhang YP. 2010. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci U S A. 107:8666-8671.
33. Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M. 2012. Drift-barrier hypothesis and mutation-rate evolution. Proc Natl Acad Sci U S A. 109:18488-18492.
34. Sung W, Tucker AE, Doak TG, Choi E, Thomas WK, Lynch M. 2012. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc Natl Acad Sci U S A. 109:19339-19344.
35. Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD. 2006. Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison. Mol Biol Evol. 23:565-573.
36. Wei W, Zhang T, Lin D, Yang ZJ, Guo FB. 2013. Transcriptional abundance is not the single force driving the evolution of bacterial proteins. BMC Evol Biol. 13:162.
37. Xu S, Schaack S, Seyfert A, Choi E, Lynch M, Cristescu ME. 2012. High mutation rates in the mitochondrial genomes of Daphnia pulex. Mol Biol Evol. 29:763-769.
38. Xue Y,Wang Q, Long Q, Ng BL, Swerdlow H, Burton J, Skuce C, Taylor R, Abdellah Z, Zhao Y, et al. 2009. Human Y chromosome basesubstitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol. 19:1453-1457.
39. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.