For Genomes, Repetition Breeds Diversity 英文参考文献.docVIP

Synopsis ForGenomes,RepetitionBreedsDiversity RichardRobinson* FreelanceScienceWriter,Sherborn,Massachusetts,UnitedStatesofAmerica A long-time observation in genomes frombacteriatohumansisthatthelevelof nucleotide diversity varies from region to region within the genome. The sequence at some spots is virtually identical among all individuals in a population, while at other spots, variation abounds. What accounts for this differential variability from place to place within the genome? In this issue of PloS Biology, Michael McDonald, Jun-Yi Leu, and colleagues provide evidence that one prominent hypothesis doesn’t explain all the facts, whileanother,lesspopularonedoes. genicindelhypothesisreliesonthisevent, there should be little opportunity for nucleotide diversity to accumulate over timeasitdoesindiploideukaryotes.Thus, younger indels should have accumulated justasmanysubstitutionsaroundthemas older ones. Instead, the authors found, older E. coli indels were surrounded by many more substitutions, suggesting that, despite the absence of diploidy and its associated repair mechanisms, substitu- tions continue to accumulate around indelsovertime. A second test was to compare nucleo- tide diversity in regions without indels to comparable regions with indels. If indels promote substitutions (and therefore di- versity), the region surrounding the indel should be more diverse, and the region withoutitshouldbenomorediversethan expected from the background rate of sequence change. This comparison is trickier than it sounds, since it requires knowing ahead of time which of two similar sequences contains an indel. The authors proceeded by comparing similar regions in two different bacterial strains, andusingthesequencefromathirdstrain to infer the ancestral sequence. Contrary to the mutagenic indel hypothesis, they foundthatdiversityinbothsequenceswas elevated above the background, but that thesequencewithouttheindelwasjustas diverseasthesequencewiththeindel. Further