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

PCA results summarizing differences in TE landscape across four species. Phylogenetic relationships are (Batrachoseps nigriventris, Eurycea tynerensis), (Aneides flavipunctatus, Desmognathus ochrophaeus).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

fig5: PCA results summarizing differences in TE landscape across four species. Phylogenetic relationships are (Batrachoseps nigriventris, Eurycea tynerensis), (Aneides flavipunctatus, Desmognathus ochrophaeus).

Mentions: Our PCA analyses summarize the main differences in TE landscape among four of our six focal taxa. All three PC axes are composed of TEs from all three classes (LTR retrotransposons, non-LTR retrotransposons, and DNA transposons), indicating that differences in genome content among taxa are not limited to differences in a specific type of TE (fig. 5). More generally, these results allow us to test whether genome content is similar among taxa with more recent shared ancestry, similar genome sizes, or neither. Species show no clustering based on phylogenetic relationships, indicating that species are sufficiently diverged from one another (≥25 Myr) that their TE landscapes retain no pattern of shared ancestry. Finally, no PC scores for any axis were related to genome size, indicating that groups of different TEs that vary in a correlated fashion do not explain genome size variation among these four species.


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)

PCA results summarizing differences in TE landscape across four species. Phylogenetic relationships are (Batrachoseps nigriventris, Eurycea tynerensis), (Aneides flavipunctatus, Desmognathus ochrophaeus).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

fig5: PCA results summarizing differences in TE landscape across four species. Phylogenetic relationships are (Batrachoseps nigriventris, Eurycea tynerensis), (Aneides flavipunctatus, Desmognathus ochrophaeus).
Mentions: Our PCA analyses summarize the main differences in TE landscape among four of our six focal taxa. All three PC axes are composed of TEs from all three classes (LTR retrotransposons, non-LTR retrotransposons, and DNA transposons), indicating that differences in genome content among taxa are not limited to differences in a specific type of TE (fig. 5). More generally, these results allow us to test whether genome content is similar among taxa with more recent shared ancestry, similar genome sizes, or neither. Species show no clustering based on phylogenetic relationships, indicating that species are sufficiently diverged from one another (≥25 Myr) that their TE landscapes retain no pattern of shared ancestry. Finally, no PC scores for any axis were related to genome size, indicating that groups of different TEs that vary in a correlated fashion do not explain genome size variation among these four species.

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