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Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.

Izutsu M, Zhou J, Sugiyama Y, Nishimura O, Aizu T, Toyoda A, Fujiyama A, Agata K, Fuse N - PLoS ONE (2012)

Bottom Line: We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness.We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome.Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan.

ABSTRACT
Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed "Dark-fly", which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.

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Related in: MedlinePlus

Survival curves of Dark-fly and Oregon-R-S.The viability of male flies (A) and female flies (B) reared together is plotted versus time (days). Dark-fly (red lines) and Oregon-R-S (blue lines) were reared under LD (dotted lines) and DD (solid lines) conditions. The viability of virgin females (C) was also measured in a similar manner. n = 92–100 flies. Oregon-R-S virgin females showed longer longevity than the mated ones, whereas Dark-fly virgin females showed shorter longevity than the mated ones.
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pone-0033288-g003: Survival curves of Dark-fly and Oregon-R-S.The viability of male flies (A) and female flies (B) reared together is plotted versus time (days). Dark-fly (red lines) and Oregon-R-S (blue lines) were reared under LD (dotted lines) and DD (solid lines) conditions. The viability of virgin females (C) was also measured in a similar manner. n = 92–100 flies. Oregon-R-S virgin females showed longer longevity than the mated ones, whereas Dark-fly virgin females showed shorter longevity than the mated ones.

Mentions: The decreased fecundity of Oregon-R-S in the dark appears to be partly due to decreased adult viability. When males and females were reared together, Oregon-R-S and Dark-fly males showed similar viability (Fig. 3A) but Dark-fly females survived longer than Oregon-R-S females in either the LD or DD condition (Fig. 3B). Females of both lines survived longer in the LD condition compared to the DD condition. However, remarkably, Oregon-R-S females gradually died in the DD condition (Fig. 3B, solid blue line), but Dark-fly females did not show such gradual death (Fig. 3B, solid red line). Consequently, the 50% survival period in the DD condition was 43 days for Dark-fly and 24 days for Oregon-R-S. It is unlikely that Dark-fly possesses extraordinary longevity, because Dark-fly virgin females showed shorter longevity than Oregon-R-S virgin females (Fig. 3C). Even more surprisingly, Dark-fly virgin females showed shorter longevity than the mated ones (Fig. 3B, 3C, red lines). It is generally considered that reproduction is a cost for longevity [20], as seen in Oregon-R-S (Fig. 3B, 3C, blue lines). Dark-fly females might not have the cost of reproduction. Thus, Dark-fly females produce offspring earlier and yet maintain longevity in dark conditions. These traits would contribute to the reproductive success in darkness.


Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment.

Izutsu M, Zhou J, Sugiyama Y, Nishimura O, Aizu T, Toyoda A, Fujiyama A, Agata K, Fuse N - PLoS ONE (2012)

Survival curves of Dark-fly and Oregon-R-S.The viability of male flies (A) and female flies (B) reared together is plotted versus time (days). Dark-fly (red lines) and Oregon-R-S (blue lines) were reared under LD (dotted lines) and DD (solid lines) conditions. The viability of virgin females (C) was also measured in a similar manner. n = 92–100 flies. Oregon-R-S virgin females showed longer longevity than the mated ones, whereas Dark-fly virgin females showed shorter longevity than the mated ones.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3303825&req=5

pone-0033288-g003: Survival curves of Dark-fly and Oregon-R-S.The viability of male flies (A) and female flies (B) reared together is plotted versus time (days). Dark-fly (red lines) and Oregon-R-S (blue lines) were reared under LD (dotted lines) and DD (solid lines) conditions. The viability of virgin females (C) was also measured in a similar manner. n = 92–100 flies. Oregon-R-S virgin females showed longer longevity than the mated ones, whereas Dark-fly virgin females showed shorter longevity than the mated ones.
Mentions: The decreased fecundity of Oregon-R-S in the dark appears to be partly due to decreased adult viability. When males and females were reared together, Oregon-R-S and Dark-fly males showed similar viability (Fig. 3A) but Dark-fly females survived longer than Oregon-R-S females in either the LD or DD condition (Fig. 3B). Females of both lines survived longer in the LD condition compared to the DD condition. However, remarkably, Oregon-R-S females gradually died in the DD condition (Fig. 3B, solid blue line), but Dark-fly females did not show such gradual death (Fig. 3B, solid red line). Consequently, the 50% survival period in the DD condition was 43 days for Dark-fly and 24 days for Oregon-R-S. It is unlikely that Dark-fly possesses extraordinary longevity, because Dark-fly virgin females showed shorter longevity than Oregon-R-S virgin females (Fig. 3C). Even more surprisingly, Dark-fly virgin females showed shorter longevity than the mated ones (Fig. 3B, 3C, red lines). It is generally considered that reproduction is a cost for longevity [20], as seen in Oregon-R-S (Fig. 3B, 3C, blue lines). Dark-fly females might not have the cost of reproduction. Thus, Dark-fly females produce offspring earlier and yet maintain longevity in dark conditions. These traits would contribute to the reproductive success in darkness.

Bottom Line: We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness.We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome.Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.

View Article: PubMed Central - PubMed

Affiliation: Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan.

ABSTRACT
Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed "Dark-fly", which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.

Show MeSH
Related in: MedlinePlus