A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca)

Abstract

Transcriptome analysis of polar bears (Ursus maritimus) yielded sequences with highest similarity to the human endogenous retrovirus group HERV-K(HML-2). Further analysis of the polar bear draft genome identified an endogenous betaretrovirus group comprising 26 proviral copies and 231 solo LTRs. Molecular dating indicates the group originated before the divergence of bears from a common ancestor but is not present in all carnivores. Closely related sequences were identified in the giant panda (Ailuropoda melanoleuca) and characterized from its genome. We have designated the polar bear and giant panda sequences U. maritimus endogenous retrovirus (UmaERV) and A. melanoleuca endogenous retrovirus (AmeERV), respectively. Phylogenetic analysis demonstrated that the bear virus group is nested within the HERV-K supergroup among bovine and bat endogenous retroviruses suggesting a complex evolutionary history within the HERV-K group. All individual remnants of proviral sequences contain numerous frameshifts and stop codons and thus, the virus is likely non-infectious.

Figure 1. Consensus sequence of UmaERV provirus

The consensus provirus sequence of UmaERV is displayed in A. ORFs for proviral gag, pro, pol and env genes, resulting protein sequences and protein domains, the latter as predicted by NCBI Conserved Domain Search (Marchler-Bauer et al., 2013) and Retrotector (Sperber et al., 2009)(Sperber et al., 2007), are indicated. Starts and ends of ORF are further highlighted by colored arrows and lines ending in diamonds respectively. The generated consensus sequence did not result in complete ORFs for pol and env gene regions, and frameshifts are indicated. Proviral 5′ and 3′ LTRs are highlighted in light green. Note that the PBS predicted by Retrotector (Sperber et al., 2007) overlaps with the 5′LTR 3′ end by 5 nt. The Pustell matrix diagram in Figure 2 and the comparative alignment in Figure S1 demonstrates the near identity of the consensus sequences of UmaERV and AmeERV.

Figure 1. Consensus sequence of UmaERV provirus

The consensus provirus sequence of UmaERV is displayed in A. ORFs for proviral gag, pro, pol and env genes, resulting protein sequences and protein domains, the latter as predicted by NCBI Conserved Domain Search (Marchler-Bauer et al., 2013) and Retrotector (Sperber et al., 2009)(Sperber et al., 2007), are indicated. Starts and ends of ORF are further highlighted by colored arrows and lines ending in diamonds respectively. The generated consensus sequence did not result in complete ORFs for pol and env gene regions, and frameshifts are indicated. Proviral 5′ and 3′ LTRs are highlighted in light green. Note that the PBS predicted by Retrotector (Sperber et al., 2007) overlaps with the 5′LTR 3′ end by 5 nt. The Pustell matrix diagram in Figure 2 and the comparative alignment in Figure S1 demonstrates the near identity of the consensus sequences of UmaERV and AmeERV.

Figure 2. High sequence similarity between UmaERV and AmeERV proviral sequences

Shown is a Pustell matrix comparison of UmaERV and AmeERV proviral consensus sequences (window size=30; min. % score=90; jump=1). Note that the LTR1_Ame sequence, as provided by Repbase v17.08, in the AmeERV provirus sequence displays some sequence differences to the actual majority rule consensus sequence for AmeERV-associated LTRs, the latter of which is very similar to the consensus sequence of UmaERV-associated LTRs. A pairwise sequence comparison of both proviral sequences is shown in Figure S1.

Figure 3. Phylogenetic relationship of UmaERV and AmeERV within the Retroviridae

Bayesian phylogenetic trees are shown for the GAG, PRO, POL and ENV proteins. Posterior probabilities >50% are shown. All sequences from taxa represented in the trees are described in the Materials and Methods. The overall topology with respect to UmaERV and AMeERV was consistent regardless of the protein analyzed except for PRO where HML-6 was not basal to UmaERV and AMeERV.

Figure 4. Phylogenetic relationship of UmaERV and AmeERV LTR sequences

A neighbor joining tree is shown for the 261 UmaERV and 145 AmeERV proviral and solitary LTR sequences identified in the polar bear and panda draft genomes. Green circles represent UmaERV LTRs and blue circles AmeERV.