Genome size diversity in the family Drosophilidae

Gregory, T. Ryan; Johnston, J. Spencer

doi:10.1038/hdy.2008.49

Cited by 129 publications

(137 citation statements)

References 74 publications

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“…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.…”

Section: Resultsmentioning

confidence: 87%

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

et al. 2011

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The genus Drosophila has been the subject of intense comparative phylogenomics characterization to provide insights into genome evolution under diverse biological and ecological contexts and to functionally annotate the Drosophila melanogaster genome, a model system for animal and insect genetics. Recent sequencing of 11 additional Drosophila species from various divergence points of the genus is a first step in this direction. However, to fully reap the benefits of this resource, the Drosophila community is faced with two critical needs: i.e., the expansion of genomic resources from a much broader range of phylogenetic diversity and the development of additional resources to aid in finishing the existing draft genomes. To address these needs, we report the first synthesis of a comprehensive set of bacterial artificial chromosome (BAC) resources for 19 Drosophila species from all three subgenera. Ten libraries were derived from the exact source used to generate 10 of the 12 draft genomes, while the rest were generated from a strategically selected set of species on the basis of salient ecological and life history features and their phylogenetic positions. The majority of the new species have at least one sequenced reference genome for immediate comparative benefit. This 19-BAC library set was rigorously characterized and shown to have large insert sizes (125-168 kb), low nonrecombinant clone content (0.3-5.3%), and deep coverage (9.1-42.93). Further, we demonstrated the utility of this BAC resource for generating physical maps of targeted loci, refining draft sequence assemblies and identifying potential genomic rearrangements across the phylogeny.

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Section: Resultsmentioning

confidence: 87%

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

et al. 2011

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“…Genome sizes of C. fuscipes, P. cinerea, C. albipunctata, and C. riparius were estimated using brain nuclei and a propidium iodide flow cytometry protocol (Bennett et al 2003;DeSalle et al 2005;Gregory and Johnston 2008). Briefly, sample and standard were ground together and passed through a 50-µm filter, stained with 50 ppm of propidium iodide and run (after 30 min in the cold and dark) in a Beckman Coulter Elite flow cytometer with the laser emitting 25 mW of exciting light at 488 nm.…”

Section: Flow Cytometrymentioning

confidence: 99%

“…A recent study surveying the genome sizes of 67 drosophilid species provided evidence for a significant positive correlation between genome size and developmental time, which suggests that, as a rule, species with smaller genome sizes develop more quickly than those with larger genomes (Gregory and Johnston 2008). Another developmental factor, egg size, might influence the genome size of dipteran insects as well.…”

Section: Introductionmentioning

confidence: 99%

Extremely small genomes in two unrelated dipteran insects with shared early developmental traits

et al. 2009

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We discovered extremely small genomes (1C~100 Mb) in the dipteran insects Coboldia fuscipes (Scatopsidae) and Psychoda cinerea (Psychodidae). The small genomes of these species cannot be explained by a fast developmental rate, which has been shown to correlate with small genome sizes in animals and plants but might accommodate the combined effects of other developmental traits, including small egg size, thin blastoderm layer, and long-germ development.

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“…SatDNAs often represent more than 30% of total genomic DNA (Pons et al, 2004). In Drosophila, changes in satDNA copy number during evolution positively correlate with genome sizes, which in turn might affect organismal traits of selective value, such as developmental rate, body size and/or sperm size (Gregory and Johnston, 2008).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species

et al. 2009

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Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM Â DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.

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Genome size diversity in the family Drosophilidae

Cited by 129 publications

References 74 publications

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

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

Extremely small genomes in two unrelated dipteran insects with shared early developmental traits

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species

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