TY - JOUR
T1 - Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera
AU - Lavoie, Christine A.
AU - Platt, Roy N.
AU - Novick, Peter A.
AU - Counterman, Brian A.
AU - Ray, David A.
N1 - Funding Information:
We thank Federico Hoffmann, Ananya Sharma, and Mike Vandewege for support and ideas. We thank Alex Suh for his help with TinT and Robert Hubley for providing help with COSEG. This work was supported by the National Science Foundation [MCB-0841821 and DEB-1020865 (DAR), NSF DEB-1257839 (BAC)]. Additional support was provided by the College of Agriculture and Life Sciences at Mississippi State University.
PY - 2013
Y1 - 2013
N2 - Abstract. Background: Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. Results: We determined that TEs comprise ∼25% of the genome. The predominant class of TEs (∼12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. Conclusions: Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group.
AB - Abstract. Background: Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. Results: We determined that TEs comprise ∼25% of the genome. The predominant class of TEs (∼12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. Conclusions: Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group.
KW - Butterfly
KW - Genomic deletions
KW - Heliconius melpomene
KW - Lepidopteran
KW - Transposable elements
UR - http://www.scopus.com/inward/record.url?scp=84884748768&partnerID=8YFLogxK
U2 - 10.1186/1759-8753-4-21
DO - 10.1186/1759-8753-4-21
M3 - Article
C2 - 24088337
AN - SCOPUS:84884748768
VL - 4
JO - Mobile DNA
JF - Mobile DNA
SN - 1759-8753
IS - 1
M1 - 21
ER -