Comparative Functional Genomics of Amino Acid Metabolism ...
Functional genomics: A comparative success
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8 | JANUARY 2005 | VOLUME 6 www.nature.com/reviews/genetics RESEARCH HIGHLIGHTS approaches. Dario Boffelli and colleagues have now succesfully risen to this challenge: by using the sea squirt Ciona intestinalis, they show that intraspecies sequence comparisons can be effec- tive for identifying functional sequences — and that other organisms, including humans, might also benefit from the same strategy. The most effective means of annotating genomes has been to compare the sequences among organisms at varying evolutionary dis- tances, on the premise that less divergent sequences will be functionally important. However, using different species restricts the analysis to genes that are common to the species compared. Intraspecies comparisons have always posed a theoretical way out of this limi- tation, but until now, the high costs of sequenc- ing many individuals prevented this method from being put into practice. However, with resequencing costs now becoming ever cheaper, it remains only to decide where to start. Boffelli and colleagues settled on C. intesti- nalis, an excellent experimental system that also benefits from a high level of allelic polymor- phism and a sequenced genome. The authors collected 140 individuals from 4 locations around the world, then using PCR, they amplified 4 defined stretches of coding and 5′ upstream sequences (a total of ~16 kb) from each organism. Although sequences were not obtained from all individuals, those that were available were used to infer the phylogenetic relationships, both among the four geographi- cal populations and within the individuals collected at each location. Crucially, the same intra-population sequ- ence comparisons also told the authors which nucleotide sites were mutating more slowly than others, and these were then used to detect func- tional DNA regions. Several exons of collagen and patched were predicted in this way. 5′ gene- control elements — five for the forkhead and two for the snail developmental genes — were also predicted computationally, and then veri- fied by using in vivo reporter studies. Intraspecies comparisons are unlikely to sup- plant the more conventional interspecies appr- oaches. However, they come into their own when investigating species-specific sequences (including those that occur in humans), new species or those that lack relatives at a convenient phylogenetic distance. Tanita Casci References and links ORIGINAL RESEARCH PAPER Boffelli, D. et al. Intraspecies sequence comparisons for annotating genomes. Genome Res. 15 November 2004 (doi:10.1101/gr.3199704) WEB SITE Eddy Rubin’s laboratory: http://www-gsd.lbl.gov/rubin Assigning a biological function to a string of DNA bases is the hardest and arguably the most important part of any genome-sequencing effort, as without knowing where genes are, we cannot say anything about their biological importance and evolutionary history. Tried and tested meth- ods for genome annotation have their merits, but there is ample scope for developing new However choosy you are about who you mate with, it is unlikely that any mistake will have an appreciable impact on the course of human evolution. In the same situation, a female Drosophila pseudoobscura has a more onerous decision to take. Because this species coexists in some regions with the related Drosophila persimilis, and mating between the two gives rise to sterile males, the female’s decision makes the difference between propagating the line and an evolutionary dead end. The genetics of reproductive isolation between the two species is well known; now, Daniel Ortiz-Barrientos and colleagues reveal how this behavioural discrimination is strengthened by natural selection. Their high-resolution genetic analysis is the first to examine the nitty gritty of the final stages of speciation, so filling one of several experimental gaps in the study of adaptation. D. persimilis and D. pseudoobscura mate in the wild but, because of the sterility of the male offspring, females of both species (but not males) select mates primarily from their own species. How is this behaviour reinforced by natural selection, such that the discriminatory mating behaviour survives in the face of gene flow? D. pseudoobscura females sampled from regions in which the two fly species overlap (in ‘sympatry’) are much choosier than those that do not live alongside D. persimilis (in ‘allopatry’), and the authors show that this ‘reinforced mating discrimination’ trait is inherited from the female in a dominant manner. Backcrossing the progeny of a sympatric × allopatric cross into an allopatric background identified strong candidate regions for the trait on the X and fourth chromosomes, which were mapped in more detail to three QTL intervals by using 70 microsatellite markers. One of the candidate regions contains as few as five genes, and both the D. pseudoobscura genome sequence and information from Drosophila melanogaster mutants indicate the involvement of the olfactory response. As with many studies of adaptation, theories abound over experiments. An exciting aspect of the work was to find that the genetic architecture of reinforcement traits within species differs from the basal level of mating discrimination seen between species, which is what some theories would predict. Tanita Casci References and links ORIGINAL RESEARCH PAPER Ortiz-Barrientos, D. et al. The genetics of speciation by reinforcement. PLoS Biol. 2, e416 (2004) FURTHER READING Coyne, J. A. & Orr, H. A. Speciation (Sinauer Associates Inc., Sunderland, Massachusetts, 2004) WEB SITE Mohamed Noor’s laboratory: http://www.biology.lsu.edu/webfac/mnoor/Noorlab.html Together apart SPECIATION A comparative success FUNCTIONAL GENOMICS © 2005 Nature Publishing Group
Transcript of Functional genomics: A comparative success
8 | JANUARY 2005 | VOLUME 6 www.nature.com/reviews/genetics
R E S E A R C H H I G H L I G H T S
approaches. Dario Boffelli and colleagues havenow succesfully risen to this challenge: by usingthe sea squirt Ciona intestinalis, they show thatintraspecies sequence comparisons can be effec-tive for identifying functional sequences — andthat other organisms, including humans, mightalso benefit from the same strategy.
The most effective means of annotatinggenomes has been to compare the sequencesamong organisms at varying evolutionary dis-tances, on the premise that less divergentsequences will be functionally important.However, using different species restricts theanalysis to genes that are common to the speciescompared. Intraspecies comparisons havealways posed a theoretical way out of this limi-tation, but until now, the high costs of sequenc-ing many individuals prevented this methodfrom being put into practice. However, withresequencing costs now becoming ever cheaper,it remains only to decide where to start.
Boffelli and colleagues settled on C. intesti-nalis, an excellent experimental system that alsobenefits from a high level of allelic polymor-phism and a sequenced genome. The authorscollected 140 individuals from 4 locationsaround the world, then using PCR, theyamplified 4 defined stretches of coding and 5′ upstream sequences (a total of ~16 kb) from
each organism. Although sequences were notobtained from all individuals, those that wereavailable were used to infer the phylogeneticrelationships, both among the four geographi-cal populations and within the individualscollected at each location.
Crucially, the same intra-population sequ-ence comparisons also told the authors whichnucleotide sites were mutating more slowly thanothers, and these were then used to detect func-tional DNA regions. Several exons of collagenand patched were predicted in this way. 5′ gene-control elements — five for the forkhead andtwo for the snail developmental genes — werealso predicted computationally, and then veri-fied by using in vivo reporter studies.
Intraspecies comparisons are unlikely to sup-plant the more conventional interspecies appr-oaches. However, they come into their ownwhen investigating species-specific sequences(including those that occur in humans), newspecies or those that lack relatives at a convenientphylogenetic distance.
Tanita Casci
References and linksORIGINAL RESEARCH PAPER Boffelli, D. et al. Intraspeciessequence comparisons for annotating genomes. Genome Res.15 November 2004 (doi:10.1101/gr.3199704)WEB SITE
Eddy Rubin’s laboratory: http://www-gsd.lbl.gov/rubin
Assigning a biological function to a string ofDNA bases is the hardest and arguably the mostimportant part of any genome-sequencing effort,as without knowing where genes are, we cannotsay anything about their biological importanceand evolutionary history. Tried and tested meth-ods for genome annotation have their merits,but there is ample scope for developing new
However choosy you are about who you matewith, it is unlikely that any mistake will havean appreciable impact on the course ofhuman evolution. In the same situation, afemale Drosophila pseudoobscura has a moreonerous decision to take. Because this speciescoexists in some regions with the relatedDrosophila persimilis, and mating betweenthe two gives rise to sterile males, the female’sdecision makes the difference betweenpropagating the line and an evolutionarydead end. The genetics of reproductiveisolation between the two species is wellknown; now, Daniel Ortiz-Barrientos andcolleagues reveal how this behaviouraldiscrimination is strengthened by naturalselection. Their high-resolution geneticanalysis is the first to examine the nitty grittyof the final stages of speciation, so filling oneof several experimental gaps in the study ofadaptation.
D. persimilis and D. pseudoobscura mate inthe wild but, because of the sterility of themale offspring, females of both species (butnot males) select mates primarily from theirown species. How is this behaviour
reinforced by natural selection, such that thediscriminatory mating behaviour survivesin the face of gene flow? D. pseudoobscurafemales sampled from regions in which thetwo fly species overlap (in ‘sympatry’) aremuch choosier than those that do not livealongside D. persimilis (in ‘allopatry’), andthe authors show that this ‘reinforcedmating discrimination’ trait is inheritedfrom the female in a dominant manner.Backcrossing the progeny of a sympatric ×allopatric cross into an allopatricbackground identified strong candidateregions for the trait on the X and fourthchromosomes, which were mapped in moredetail to three QTL intervals by using 70microsatellite markers. One of the candidateregions contains as few as five genes, andboth the D. pseudoobscura genome sequenceand information from Drosophilamelanogaster mutants indicate theinvolvement of the olfactory response.
As with many studies of adaptation,theories abound over experiments. Anexciting aspect of the work was to find thatthe genetic architecture of reinforcementtraits within species differs from the basallevel of mating discrimination seen betweenspecies, which is what some theories wouldpredict.
Tanita Casci
References and linksORIGINAL RESEARCH PAPER Ortiz-Barrientos, D. et al. The genetics of speciation by reinforcement. PLoS Biol. 2, e416 (2004) FURTHER READING Coyne, J. A. & Orr, H. A. Speciation (Sinauer Associates Inc.,Sunderland, Massachusetts, 2004)WEB SITEMohamed Noor’s laboratory:http://www.biology.lsu.edu/webfac/mnoor/Noorlab.html
Together apart
S P E C I AT I O N
A comparative success
F U N C T I O N A L G E N O M I C S
© 2005 Nature Publishing Group
