Analysis of Drosophila Species Genome Size and Satellite DNA Content Reveals Significant Differences Among Strains as Well as Between Species

Abstract

The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although ''whole''-genome sequences, such as those now available for 12 Drosophila species, provide information about euchromatic DNA content, they cannot give an accurate estimate of genome sizes that include heterochromatin or repetitive DNA content. Moreover, genome sequences typically represent only one strain or isolate of a single species that does not reflect intraspecies variation. To more accurately estimate whole-genome DNA content and compare these estimates to newly assembled genomes, we used flow cytometry to measure the 2C genome values, relative to Drosophila melanogaster. We estimated genome sizes for the 12 sequenced Drosophila species as well as 91 different strains of 38 species of Drosophilidae. Significant differences in intra-and interspecific 2C genome values exist within the Drosophilidae. Furthermore, by measuring polyploid 16C ovarian follicle cell underreplication we estimated the amount of satellite DNA in each of these species. We found a strong correlation between genome size and amount of satellite underreplication. Addition and loss of heterochromatin satellite repeat elements appear to have made major contributions to the large differences in genome size observed in the Drosophilidae.

The 19 Genomes of Drosophila: A BAC Library Resource for Genus-Wide and Genome-Scale Comparative Evolutionary Research

“…Nine of the Drosophila species strains were not the same as the strains analyzed by Bosco et al (2007). An important finding to consider, as reported by Bosco et al (2007) and Gregory and Johnston (2008), is that DAPI may overestimate genome size, which could affect the estimated genome coverage of these four libraries.…”

“…Previously determined genome sizes (Bosco et al 2007) were used in this study for estimating the coverage of the BAC libraries for different Drosophila species. Bosco et al (2007) employed two nucleic-acid-binding fluorescent dyes, propidium iodide (PI) and 49,6-diamidino-2-phenylindole (DAPI), in conjunction with flow cytometry to determine genome sizes of 38 species of Drosophilidae, including the 12 sequenced Drosophila species (Drosophila 12 Genomes Consortium 2007).…”

Genome size evolution: Within-species variation in genome size

“…However, we do not have to throw the baby out with the bath water as all these confounding factors can be taken into account by using appropriate protocols and statistical methods, which take different levels of sampling and replicates into account, for determining within-and between-species variation. A recent study of genome size in various Drosophila species (Bosco et al, 2007) concludes that there is a significant statistical difference in genome size between species, and some significant differences between strains in some species. Vieira et al (1999Vieira et al ( , 2002 have also identified genome-size differences between populations of both Drosophila melanogaster and D. simulans, but no differences between replicates of batches of flies reared in the same vial.…”

“…Vieira et al (1999Vieira et al ( , 2002 have also identified genome-size differences between populations of both Drosophila melanogaster and D. simulans, but no differences between replicates of batches of flies reared in the same vial. In the Bosco et al (2007) paper, the variation in genome size was related to variation in heterochromatin composition, mostly of satellite DNA, whereas TEs were mostly involved in the Vieira et al (1999Vieira et al ( , 2002 study. Such data give credibility to between-individual variations in the amount of heterochromatic TEs that have been estimated using dot blots and in situ hybridization in Drosophila (Charlesworth et al, 1994).…”

Conservation of Epigenetic Regulation, ORC Binding and Developmental Timing of DNA Replication Origins in the Genus Drosophila

“…Incorporation was mosaic among follicle cells in an egg chamber, and progressively fewer cells labeled with BrdU from stage 9 to late stage 10A, indicating that follicle cell endocycles are not synchronized with one another and arrest at different developmental times. Despite different times of endocycle completion among cells, a nuclear flow-sorting analysis indicates that, like D. melanogaster, most follicle cells in these other species achieve a final DNA content of 16C (G. Bosco, personal communication; Bosco et al 2007). These results reveal that the developmental timing of endocycles and endocycle exit is conserved among Drosophila species.…”