RESUMO
BACKGROUND: Gene copy-number variation (CNVs), which provides the raw material for the evolution of novel genes, is widespread in natural populations. We investigated whether CNVs constitute a common mechanism of genetic change during adaptation in experimental Caenorhabditis elegans populations. Outcrossing C. elegans populations with low fitness were evolved for >200 generations. The frequencies of CNVs in these populations were analyzed by oligonucleotide array comparative genome hybridization, quantitative PCR, PCR, DNA sequencing across breakpoints, and single-worm PCR. RESULTS: Multiple duplications and deletions rose to intermediate or high frequencies in independent populations. Several lines of evidence suggest that these changes were adaptive: (i) copy-number changes reached high frequency or were fixed in a short time, (ii) many independent populations harbored CNVs spanning the same genes, and (iii) larger average size of CNVs in adapting populations relative to spontaneous CNVs. The latter is expected if larger CNVs are more likely to encompass genes under selection for a change in gene dosage. Several convergent CNVs originated in populations descended from different low fitness ancestors as well as high fitness controls. CONCLUSIONS: We show that gene copy-number changes are a common class of adaptive genetic change. Due to the high rates of origin of spontaneous duplications and deletions, copy-number changes containing the same genes arose readily in independent populations. Duplications that reached high frequencies in these adapting populations were significantly larger in span. Many convergent CNVs may be general adaptations to laboratory conditions. These results demonstrate the great potential borne by CNVs for evolutionary adaptation.
Assuntos
Caenorhabditis elegans/genética , Variações do Número de Cópias de DNA , Evolução Molecular , Dosagem de Genes , Adaptação Biológica/genética , Animais , Cruzamentos Genéticos , Deleção de Genes , Duplicação Gênica , Aptidão Genética , Variação Genética , Genética Populacional , Mutação , Sequências Repetitivas de Ácido NucleicoRESUMO
Gene and genome duplications are the primary source of new genes and novel functions and have played a pivotal role in the evolution of genomic and organismal complexity. The spontaneous rate of gene duplication is a critical parameter for understanding the evolutionary dynamics of gene duplicates; yet few direct empirical estimates exist and differ widely. The presence of a large population of recently derived gene duplicates in sequenced genomes suggests a high rate of spontaneous origin, also evidenced by population genomic studies reporting rampant copy-number polymorphism at the intraspecific level. An analysis of long-term mutation accumulation lines of Caenorhabditis elegans for gene copy-number changes with array comparative genomic hybridization yields the first direct estimate of the genome-wide rate of gene duplication in a multicellular eukaryote. The gene duplication rate in C. elegans is quite high, on the order of 10(-7) duplications/gene/generation. This rate is two orders of magnitude greater than the spontaneous rate of point mutation per nucleotide site in this species and also greatly exceeds an earlier estimate derived from the frequency distribution of extant gene duplicates in the sequenced C. elegans genome.
Assuntos
Caenorhabditis elegans/genética , Duplicação Gênica/genética , Animais , Evolução Biológica , Mapeamento Cromossômico , Deleção de Genes , Regulação da Expressão Gênica , Genes DuplicadosRESUMO
The fungal loop model of semiarid ecosystems integrates microtopographic structures and pulse dynamics with key microbial processes. However limited data exist about the composition and structure of fungal communities in these ecosystems. The goal of this study was to characterize diversity and structure of soil fungal communities in a semiarid grassland. The effect of long-term nitrogen fertilization on fungi also was evaluated. Samples of rhizosphere (soil surrounding plant roots) and biological soil crust (BSC) were collected in central New Mexico, USA. DNA was amplified from the samples with fungal specific primers. Twelve clone libraries were generated with a total of 307 (78 operational taxonomic units, OTUs) and 324 sequences (67 OTUs) for BSC and rhizosphere respectively. Approximately 40% of soil OTUs were considered novel (less than 97% identity when compared to other sequences in NCBI using BLAST). The dominant organisms were dark-septate (melanized fungi) ascomycetes belonging to Pleosporales. Effects of N enrichment on fungi were not evident at the community level; however the abundance of unique sequences, sampling intensity and temporal variations may be uncovering the effect of N in composition and diversity of fungal communities. The fungal communities of rhizosphere soil and BSC overlapped substantially in composition, with a Jaccard abundance similarity index of 0.75. Further analyses are required to explore possible functions of the dominant species colonizing zones of semiarid grassland soils.
Assuntos
Ecossistema , Fungos/isolamento & purificação , Poaceae/microbiologia , Microbiologia do Solo , Sequência de Bases , DNA Fúngico/química , DNA Fúngico/genética , DNA Espaçador Ribossômico/química , DNA Espaçador Ribossômico/genética , Fungos/classificação , Fungos/genética , Variação Genética , Dados de Sequência Molecular , New Mexico , Filogenia , Reação em Cadeia da Polimerase , Análise de Componente Principal , RNA Ribossômico 18S/química , RNA Ribossômico 18S/genética , Distribuição Aleatória , Rizosfera , Alinhamento de SequênciaRESUMO
Caenorhabditis elegans primarily reproduces as a hermaphrodite. Independent gene conversion events in mutant obligately outcrossing populations of C. elegans [fog-2(lf)] spontaneously repaired the loss-of-function mutation in the fog-2 locus, thereby reestablishing hermaphroditism as the primary means of reproduction for the populations.