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Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity.

Ellis LL, Huang W, Quinn AM, Ahuja A, Alfrejd B, Gomez FE, Hjelmen CE, Moore KL, Mackay TF, Johnston JS, Tarone AM - PLoS Genet. (2014)

Bottom Line: We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates.Expression data implicate differences in metabolism that correspond to genome size variation.These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, Texas A&M University, College Station, Texas, United States of America.

ABSTRACT
We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions.

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Genome size-associated changes in gene expression.Box plots highlight the most up-regulated and down-regulated genes based on comparisons between small (red), average (green), and large (blue) genome strains. (A) MetallothioneB (MtnB) (B) Related to the N terminus of tre oncogene (RN-tre). (C) CG4415. (D) Cyp12d1-d. (E) CG17192. (F) AttacinA (AttA).
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pgen-1004522-g004: Genome size-associated changes in gene expression.Box plots highlight the most up-regulated and down-regulated genes based on comparisons between small (red), average (green), and large (blue) genome strains. (A) MetallothioneB (MtnB) (B) Related to the N terminus of tre oncogene (RN-tre). (C) CG4415. (D) Cyp12d1-d. (E) CG17192. (F) AttacinA (AttA).

Mentions: Genome wide variation in gene expression has been evaluated using microarrays for a subset of the DGRP strains [37]. We assessed whether there is variation in gene expression between lines with small and large genomes. These observations can be used to guide further efforts to dissect mechanisms by which genome size can lead to phenotypic differences. Comparisons between microarray results of adult females of small genome (DGRP_208, DGRP_307, DGRP_313, DGRP_335, DGRP_360, DGRP_379, DGRP_555, DGRP_786, and DGRP_820), large genome (DGRP_362, DGRP_391, DGRP_517, DGRP_705), and more species-typical genome (DGRP_301, DGRP_303, DGRP_304, DGRP_306, DGRP_315, DGRP_324, DGRP_357, DGRP_358, DGRP_365, DGRP_375, DGRP_380, DGRP_399, DGRP_427, DGRP_437, DGRP_486, DGRP_514, DGRP_639, DGRP_707, DGRP_712, DGRP_714, DGRP_730, DGRP_732, DGRP_765, DGRP_774, DGRP_799, DGRP_852, DGRP_859) strains revealed 562 differentially expressed genes (Figure 4, Tables S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13). One hundred forty-nine genes were up-regulated in strains with small genomes (Figure 4; Table S3); 227 genes were up-regulated in strains with large genomes (Figure 4; Table S4). Strains with small genomes down-regulated 91 genes (Figure 4, Table S5) while strains with large genomes down-regulated 95 genes (Figure 4, Table S6). Gene ontology enrichment analyses revealed that strains with small genomes up-regulated genes related to metabolism, mitosis, egg development, translation, and salt transport (Tables S7, S9) and down-regulated genes related to development and enzymatic activity (Table S11). The up-regulated genes included ion binding genes that appear to be differentially regulated during exposure to thermal and chemical environments that affect oxidative stress [38]. Strains with large genomes up-regulated genes involved with development, metabolism, TOR signaling, and heme and ion binding (Tables S8, S10) while down-regulating primarily genes affecting gametogenesis (Tables S12, S13). Many of the enriched genes were expressed in the digestive system. This suggests, (in combination with the increased expression of metabolism and TOR signaling genes in strains with large genomes), that nutritional ecology plays an important role in these responses.


Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity.

Ellis LL, Huang W, Quinn AM, Ahuja A, Alfrejd B, Gomez FE, Hjelmen CE, Moore KL, Mackay TF, Johnston JS, Tarone AM - PLoS Genet. (2014)

Genome size-associated changes in gene expression.Box plots highlight the most up-regulated and down-regulated genes based on comparisons between small (red), average (green), and large (blue) genome strains. (A) MetallothioneB (MtnB) (B) Related to the N terminus of tre oncogene (RN-tre). (C) CG4415. (D) Cyp12d1-d. (E) CG17192. (F) AttacinA (AttA).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109859&req=5

pgen-1004522-g004: Genome size-associated changes in gene expression.Box plots highlight the most up-regulated and down-regulated genes based on comparisons between small (red), average (green), and large (blue) genome strains. (A) MetallothioneB (MtnB) (B) Related to the N terminus of tre oncogene (RN-tre). (C) CG4415. (D) Cyp12d1-d. (E) CG17192. (F) AttacinA (AttA).
Mentions: Genome wide variation in gene expression has been evaluated using microarrays for a subset of the DGRP strains [37]. We assessed whether there is variation in gene expression between lines with small and large genomes. These observations can be used to guide further efforts to dissect mechanisms by which genome size can lead to phenotypic differences. Comparisons between microarray results of adult females of small genome (DGRP_208, DGRP_307, DGRP_313, DGRP_335, DGRP_360, DGRP_379, DGRP_555, DGRP_786, and DGRP_820), large genome (DGRP_362, DGRP_391, DGRP_517, DGRP_705), and more species-typical genome (DGRP_301, DGRP_303, DGRP_304, DGRP_306, DGRP_315, DGRP_324, DGRP_357, DGRP_358, DGRP_365, DGRP_375, DGRP_380, DGRP_399, DGRP_427, DGRP_437, DGRP_486, DGRP_514, DGRP_639, DGRP_707, DGRP_712, DGRP_714, DGRP_730, DGRP_732, DGRP_765, DGRP_774, DGRP_799, DGRP_852, DGRP_859) strains revealed 562 differentially expressed genes (Figure 4, Tables S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13). One hundred forty-nine genes were up-regulated in strains with small genomes (Figure 4; Table S3); 227 genes were up-regulated in strains with large genomes (Figure 4; Table S4). Strains with small genomes down-regulated 91 genes (Figure 4, Table S5) while strains with large genomes down-regulated 95 genes (Figure 4, Table S6). Gene ontology enrichment analyses revealed that strains with small genomes up-regulated genes related to metabolism, mitosis, egg development, translation, and salt transport (Tables S7, S9) and down-regulated genes related to development and enzymatic activity (Table S11). The up-regulated genes included ion binding genes that appear to be differentially regulated during exposure to thermal and chemical environments that affect oxidative stress [38]. Strains with large genomes up-regulated genes involved with development, metabolism, TOR signaling, and heme and ion binding (Tables S8, S10) while down-regulating primarily genes affecting gametogenesis (Tables S12, S13). Many of the enriched genes were expressed in the digestive system. This suggests, (in combination with the increased expression of metabolism and TOR signaling genes in strains with large genomes), that nutritional ecology plays an important role in these responses.

Bottom Line: We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates.Expression data implicate differences in metabolism that correspond to genome size variation.These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, Texas A&M University, College Station, Texas, United States of America.

ABSTRACT
We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions.

Show MeSH
Related in: MedlinePlus