Limits...
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes.

Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, Cutter AD, Phillips PC - PLoS Genet. (2015)

Bottom Line: Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size.Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes.Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.

View Article: PubMed Central - PubMed

Affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America.

ABSTRACT
The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.

No MeSH data available.


Differences in total gene size (introns and exons) versus protein coding size (exons) in C. elegans, C. briggsae and C. remanei.(a-b) Gene Size differs between autosomes and the X chromosome in C. briggsae (Kruskal-Wallis χ2 = 24.63, df = 1, p < 6.96x10−7), C. elegans (Kruskal-Wallis χ2 = 58.04, df = 1, p < 2.56x10−14) and C. remanei (Kruskal-Wallis χ2 = 99.10, df = 1, p < 2x10−16) but protein size does not (C. briggsae Kruskal-Wallis χ2 = 0.94, df = 1, p = 0.66; C. elegans Kruskal-Wallis χ2 = 0.29, df = 1, p = 1; C. remanei Kruskal-Wallis χ2 = 4.3096, df = 1, p = 0.08). Gene size differs significantly among the species on autosomes (Kruskal-Wallis χ2 = 152.86; df = 2, p < 2x10−16; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp < 2x10−16, C. remanei:C. briggsaep < 2x10−16; C. briggsae:C. elegansp < 6x10−5) and between C. remanei and the self-fertile hermaprodites on the X chromsome (Kruskal-Wallis χ2 = 64.39; df = 2, p < 1x10−14; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp < 2x10−10, C. remanei:C. briggsaep < 1.8x10−11; C. briggsae:C.elegansp = 1). (c-d) Protein size differs significantly between C. briggsae and C. elegans and C. briggsae and C. remanei on both the autosomes (Kruskal-Wallis χ2 = 91.32; df = 2, p < 2x10−16; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp = 1, C. remanei:C. briggsaep < 2x10−16; C. briggsae:C.elegansp < 1.5x10−11) and X chromosome (Kruskal-Wallis χ2 = 40.36; df = 2, p < 1.7x10−9; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp = 0.92, C. remanei:C. briggsaep < 4x10−9; C. briggsae:C.elegansp < 2x10−5).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4482642&req=5

pgen.1005323.g004: Differences in total gene size (introns and exons) versus protein coding size (exons) in C. elegans, C. briggsae and C. remanei.(a-b) Gene Size differs between autosomes and the X chromosome in C. briggsae (Kruskal-Wallis χ2 = 24.63, df = 1, p < 6.96x10−7), C. elegans (Kruskal-Wallis χ2 = 58.04, df = 1, p < 2.56x10−14) and C. remanei (Kruskal-Wallis χ2 = 99.10, df = 1, p < 2x10−16) but protein size does not (C. briggsae Kruskal-Wallis χ2 = 0.94, df = 1, p = 0.66; C. elegans Kruskal-Wallis χ2 = 0.29, df = 1, p = 1; C. remanei Kruskal-Wallis χ2 = 4.3096, df = 1, p = 0.08). Gene size differs significantly among the species on autosomes (Kruskal-Wallis χ2 = 152.86; df = 2, p < 2x10−16; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp < 2x10−16, C. remanei:C. briggsaep < 2x10−16; C. briggsae:C. elegansp < 6x10−5) and between C. remanei and the self-fertile hermaprodites on the X chromsome (Kruskal-Wallis χ2 = 64.39; df = 2, p < 1x10−14; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp < 2x10−10, C. remanei:C. briggsaep < 1.8x10−11; C. briggsae:C.elegansp = 1). (c-d) Protein size differs significantly between C. briggsae and C. elegans and C. briggsae and C. remanei on both the autosomes (Kruskal-Wallis χ2 = 91.32; df = 2, p < 2x10−16; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp = 1, C. remanei:C. briggsaep < 2x10−16; C. briggsae:C.elegansp < 1.5x10−11) and X chromosome (Kruskal-Wallis χ2 = 40.36; df = 2, p < 1.7x10−9; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp = 0.92, C. remanei:C. briggsaep < 4x10−9; C. briggsae:C.elegansp < 2x10−5).

Mentions: In order to analyze gene structure, we identified a set of co-orthologs conserved as pairs between C. remanei, C. briggsae and C. elegans (Fig 4). We found that among our co-ortholog coding sequences the average number (6) and length (~200bp) of exons per gene was similar for the three species. The total length of gene transcripts was longer on autosomes in C. remanei than in C. briggsae or C. elegans but smaller on the X chromosome in C. remanei than in C. briggsae or C. elegans (Fig 4, Table 2). The protein sequences were not significantly different between the X chromosome and autosomes in any of the three species and among the species only C. briggsae had protein sizes that differed significantly from the other species.


Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes.

Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, Cutter AD, Phillips PC - PLoS Genet. (2015)

Differences in total gene size (introns and exons) versus protein coding size (exons) in C. elegans, C. briggsae and C. remanei.(a-b) Gene Size differs between autosomes and the X chromosome in C. briggsae (Kruskal-Wallis χ2 = 24.63, df = 1, p < 6.96x10−7), C. elegans (Kruskal-Wallis χ2 = 58.04, df = 1, p < 2.56x10−14) and C. remanei (Kruskal-Wallis χ2 = 99.10, df = 1, p < 2x10−16) but protein size does not (C. briggsae Kruskal-Wallis χ2 = 0.94, df = 1, p = 0.66; C. elegans Kruskal-Wallis χ2 = 0.29, df = 1, p = 1; C. remanei Kruskal-Wallis χ2 = 4.3096, df = 1, p = 0.08). Gene size differs significantly among the species on autosomes (Kruskal-Wallis χ2 = 152.86; df = 2, p < 2x10−16; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp < 2x10−16, C. remanei:C. briggsaep < 2x10−16; C. briggsae:C. elegansp < 6x10−5) and between C. remanei and the self-fertile hermaprodites on the X chromsome (Kruskal-Wallis χ2 = 64.39; df = 2, p < 1x10−14; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp < 2x10−10, C. remanei:C. briggsaep < 1.8x10−11; C. briggsae:C.elegansp = 1). (c-d) Protein size differs significantly between C. briggsae and C. elegans and C. briggsae and C. remanei on both the autosomes (Kruskal-Wallis χ2 = 91.32; df = 2, p < 2x10−16; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp = 1, C. remanei:C. briggsaep < 2x10−16; C. briggsae:C.elegansp < 1.5x10−11) and X chromosome (Kruskal-Wallis χ2 = 40.36; df = 2, p < 1.7x10−9; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp = 0.92, C. remanei:C. briggsaep < 4x10−9; C. briggsae:C.elegansp < 2x10−5).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482642&req=5

pgen.1005323.g004: Differences in total gene size (introns and exons) versus protein coding size (exons) in C. elegans, C. briggsae and C. remanei.(a-b) Gene Size differs between autosomes and the X chromosome in C. briggsae (Kruskal-Wallis χ2 = 24.63, df = 1, p < 6.96x10−7), C. elegans (Kruskal-Wallis χ2 = 58.04, df = 1, p < 2.56x10−14) and C. remanei (Kruskal-Wallis χ2 = 99.10, df = 1, p < 2x10−16) but protein size does not (C. briggsae Kruskal-Wallis χ2 = 0.94, df = 1, p = 0.66; C. elegans Kruskal-Wallis χ2 = 0.29, df = 1, p = 1; C. remanei Kruskal-Wallis χ2 = 4.3096, df = 1, p = 0.08). Gene size differs significantly among the species on autosomes (Kruskal-Wallis χ2 = 152.86; df = 2, p < 2x10−16; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp < 2x10−16, C. remanei:C. briggsaep < 2x10−16; C. briggsae:C. elegansp < 6x10−5) and between C. remanei and the self-fertile hermaprodites on the X chromsome (Kruskal-Wallis χ2 = 64.39; df = 2, p < 1x10−14; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp < 2x10−10, C. remanei:C. briggsaep < 1.8x10−11; C. briggsae:C.elegansp = 1). (c-d) Protein size differs significantly between C. briggsae and C. elegans and C. briggsae and C. remanei on both the autosomes (Kruskal-Wallis χ2 = 91.32; df = 2, p < 2x10−16; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp = 1, C. remanei:C. briggsaep < 2x10−16; C. briggsae:C.elegansp < 1.5x10−11) and X chromosome (Kruskal-Wallis χ2 = 40.36; df = 2, p < 1.7x10−9; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum C. remanei:C. elegansp = 0.92, C. remanei:C. briggsaep < 4x10−9; C. briggsae:C.elegansp < 2x10−5).
Mentions: In order to analyze gene structure, we identified a set of co-orthologs conserved as pairs between C. remanei, C. briggsae and C. elegans (Fig 4). We found that among our co-ortholog coding sequences the average number (6) and length (~200bp) of exons per gene was similar for the three species. The total length of gene transcripts was longer on autosomes in C. remanei than in C. briggsae or C. elegans but smaller on the X chromosome in C. remanei than in C. briggsae or C. elegans (Fig 4, Table 2). The protein sequences were not significantly different between the X chromosome and autosomes in any of the three species and among the species only C. briggsae had protein sizes that differed significantly from the other species.

Bottom Line: Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size.Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes.Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.

View Article: PubMed Central - PubMed

Affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America.

ABSTRACT
The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.

No MeSH data available.