Limits...
LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.

Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL - Genome Biol Evol (2011)

Bottom Line: The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size.However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements.These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Colorado State University, CO, USA.

ABSTRACT
Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

Show MeSH

Related in: MedlinePlus

Age distribution of Ty3/gypsy elements in four species of salamanders.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3318908&req=5

fig6: Age distribution of Ty3/gypsy elements in four species of salamanders.

Mentions: Sequence divergence distributions representing proliferation history of the most abundant superfamilies in each TE class are shown in figure 6 (Ty3/gypsy elements), supplementary file 5, Supplementary Material online (LINE/L2 elements), and supplementary file 6, Supplementary Material online (DNA/Harbinger). Under the assumption of a constant substitution rate, sequence divergence distributions are equivalent to age distributions. All distributions suggest ongoing TE proliferation, indicated by element copies with sequence divergence ≤1% from the consensus (Novick et al. 2010). Transcripts of all such superfamilies were detected in the Ambystoma mexicanum transcriptome database (http://www.ambystoma.org/genome-resources/21-blast [date last accessed 26 Sep 2011]), suggesting that they are also transcriptionally active in this ambystomatid salamander species. In addition, all distributions include copies with high (≤40%) sequence divergence, suggesting that elements reach fixation in salamander populations and are subsequently preserved in the genome for long periods of time; this pattern is consistent with a low negative impact of TE insertions on the host (Novick et al. 2009; Novick et al. 2010). However, we emphasize that this pattern may also reflect our inability to assemble consensus sequences representing all families/subfamilies within each superfamily from low-coverage shotgun data. Thus, additional data collection will be required to rigorously test this hypothesis.


LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.

Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL - Genome Biol Evol (2011)

Age distribution of Ty3/gypsy elements in four species of salamanders.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3318908&req=5

fig6: Age distribution of Ty3/gypsy elements in four species of salamanders.
Mentions: Sequence divergence distributions representing proliferation history of the most abundant superfamilies in each TE class are shown in figure 6 (Ty3/gypsy elements), supplementary file 5, Supplementary Material online (LINE/L2 elements), and supplementary file 6, Supplementary Material online (DNA/Harbinger). Under the assumption of a constant substitution rate, sequence divergence distributions are equivalent to age distributions. All distributions suggest ongoing TE proliferation, indicated by element copies with sequence divergence ≤1% from the consensus (Novick et al. 2010). Transcripts of all such superfamilies were detected in the Ambystoma mexicanum transcriptome database (http://www.ambystoma.org/genome-resources/21-blast [date last accessed 26 Sep 2011]), suggesting that they are also transcriptionally active in this ambystomatid salamander species. In addition, all distributions include copies with high (≤40%) sequence divergence, suggesting that elements reach fixation in salamander populations and are subsequently preserved in the genome for long periods of time; this pattern is consistent with a low negative impact of TE insertions on the host (Novick et al. 2009; Novick et al. 2010). However, we emphasize that this pattern may also reflect our inability to assemble consensus sequences representing all families/subfamilies within each superfamily from low-coverage shotgun data. Thus, additional data collection will be required to rigorously test this hypothesis.

Bottom Line: The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size.However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements.These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Colorado State University, CO, USA.

ABSTRACT
Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

Show MeSH
Related in: MedlinePlus