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Identification and characterization of diverse groups of endogenous retroviruses in felids.

Mata H, Gongora J, Eizirik E, Alves BM, Soares MA, Ravazzolo AP - Retrovirology (2015)

Bottom Line: We also compared them with publicly available genomic sequences of Felis catus and Panthera tigris, as well as with representatives of other vertebrate groups, and performed phylogenetic and molecular dating analyses to investigate the pattern and timing of diversification of these retroviral elements.Finally, our phylogenetic analyses indicate the presence of a genetically divergent group of sequences whose position in our phylogenetic tree was difficult to establish confidently relative to known retroviruses, and another lineage identified as ERVs belonging to class II.Our findings highlight the importance of additional studies on the role of ERVs in the genome landscaping of other carnivore species.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Endogenous retroviruses (ERVs) are genetic elements with a retroviral origin that are integrated into vertebrate genomes. In felids (Mammalia, Carnivora, Felidae), ERVs have been described mostly in the domestic cat, and only rarely in wild species. To gain insight into the origins and evolutionary dynamics of endogenous retroviruses in felids, we have identified and characterized partial pro/pol ERV sequences from eight Neotropical wild cat species, belonging to three distinct lineages of Felidae. We also compared them with publicly available genomic sequences of Felis catus and Panthera tigris, as well as with representatives of other vertebrate groups, and performed phylogenetic and molecular dating analyses to investigate the pattern and timing of diversification of these retroviral elements.

Results: We identified a high diversity of ERVs in the sampled felids, with a predominance of Gammaretrovirus-related sequences, including class I ERVs. Our data indicate that the identified ERVs arose from at least eleven horizontal interordinal transmissions from other mammals. Furthermore, we estimated that the majority of the Gamma-like integrations took place during the diversification of modern felids. Finally, our phylogenetic analyses indicate the presence of a genetically divergent group of sequences whose position in our phylogenetic tree was difficult to establish confidently relative to known retroviruses, and another lineage identified as ERVs belonging to class II.

Conclusions: Retroviruses have circulated in felids along with their evolution. The majority of the deep clades of ERVs exist since the primary divergence of felids' base and cluster with retroviruses of divergent mammalian lineages, suggesting horizontal interordinal transmission. Our findings highlight the importance of additional studies on the role of ERVs in the genome landscaping of other carnivore species.

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Phylogenetic tree showing the relationships of class II ERV sequences. A maximum likelihood tree was based on deduced amino acids of Pro-Pol fragments (Dataset 4; 236 codons). Bootstrap values >70% are indicated. Felid illustrations are shown to designate their clades. The three ERV clades mentioned in the text are highlighted by showing sequences from four of the major felid lineages: blue (from tiger belonging to the Panthera lineage), red (cat, domestic cat lineage), green (PYEM13001, from P. yagouaroundi and Puma concolor, both from the Puma lineage) and pink (L. geoffroyi, ocelot lineage). The scale bar at the bottom of the Figure represents distance in amino acid substitutions per site. Sequences retrieved from GenBank are listed in Additional file 1: Table S1.
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Fig4: Phylogenetic tree showing the relationships of class II ERV sequences. A maximum likelihood tree was based on deduced amino acids of Pro-Pol fragments (Dataset 4; 236 codons). Bootstrap values >70% are indicated. Felid illustrations are shown to designate their clades. The three ERV clades mentioned in the text are highlighted by showing sequences from four of the major felid lineages: blue (from tiger belonging to the Panthera lineage), red (cat, domestic cat lineage), green (PYEM13001, from P. yagouaroundi and Puma concolor, both from the Puma lineage) and pink (L. geoffroyi, ocelot lineage). The scale bar at the bottom of the Figure represents distance in amino acid substitutions per site. Sequences retrieved from GenBank are listed in Additional file 1: Table S1.

Mentions: We have also identified ERVs belonging to class II (Dataset 4; Figure 4), by using our sequences and others previously described as queries in Blast searches. This group seems to be less diverse than class I (Gamma-like) sequences. We found 12 Megablast hits with score > 200 using LgEM10003 as query against Felidae (taxid: 9681) and the same number of hits by using PyEM13001. This contrasted, for example, with the use of Gamma-like PyJO10001 sequence as query, when we found almost a two-fold number of Megablast hits (20 with score > 200).Figure 4


Identification and characterization of diverse groups of endogenous retroviruses in felids.

Mata H, Gongora J, Eizirik E, Alves BM, Soares MA, Ravazzolo AP - Retrovirology (2015)

Phylogenetic tree showing the relationships of class II ERV sequences. A maximum likelihood tree was based on deduced amino acids of Pro-Pol fragments (Dataset 4; 236 codons). Bootstrap values >70% are indicated. Felid illustrations are shown to designate their clades. The three ERV clades mentioned in the text are highlighted by showing sequences from four of the major felid lineages: blue (from tiger belonging to the Panthera lineage), red (cat, domestic cat lineage), green (PYEM13001, from P. yagouaroundi and Puma concolor, both from the Puma lineage) and pink (L. geoffroyi, ocelot lineage). The scale bar at the bottom of the Figure represents distance in amino acid substitutions per site. Sequences retrieved from GenBank are listed in Additional file 1: Table S1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373062&req=5

Fig4: Phylogenetic tree showing the relationships of class II ERV sequences. A maximum likelihood tree was based on deduced amino acids of Pro-Pol fragments (Dataset 4; 236 codons). Bootstrap values >70% are indicated. Felid illustrations are shown to designate their clades. The three ERV clades mentioned in the text are highlighted by showing sequences from four of the major felid lineages: blue (from tiger belonging to the Panthera lineage), red (cat, domestic cat lineage), green (PYEM13001, from P. yagouaroundi and Puma concolor, both from the Puma lineage) and pink (L. geoffroyi, ocelot lineage). The scale bar at the bottom of the Figure represents distance in amino acid substitutions per site. Sequences retrieved from GenBank are listed in Additional file 1: Table S1.
Mentions: We have also identified ERVs belonging to class II (Dataset 4; Figure 4), by using our sequences and others previously described as queries in Blast searches. This group seems to be less diverse than class I (Gamma-like) sequences. We found 12 Megablast hits with score > 200 using LgEM10003 as query against Felidae (taxid: 9681) and the same number of hits by using PyEM13001. This contrasted, for example, with the use of Gamma-like PyJO10001 sequence as query, when we found almost a two-fold number of Megablast hits (20 with score > 200).Figure 4

Bottom Line: We also compared them with publicly available genomic sequences of Felis catus and Panthera tigris, as well as with representatives of other vertebrate groups, and performed phylogenetic and molecular dating analyses to investigate the pattern and timing of diversification of these retroviral elements.Finally, our phylogenetic analyses indicate the presence of a genetically divergent group of sequences whose position in our phylogenetic tree was difficult to establish confidently relative to known retroviruses, and another lineage identified as ERVs belonging to class II.Our findings highlight the importance of additional studies on the role of ERVs in the genome landscaping of other carnivore species.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Endogenous retroviruses (ERVs) are genetic elements with a retroviral origin that are integrated into vertebrate genomes. In felids (Mammalia, Carnivora, Felidae), ERVs have been described mostly in the domestic cat, and only rarely in wild species. To gain insight into the origins and evolutionary dynamics of endogenous retroviruses in felids, we have identified and characterized partial pro/pol ERV sequences from eight Neotropical wild cat species, belonging to three distinct lineages of Felidae. We also compared them with publicly available genomic sequences of Felis catus and Panthera tigris, as well as with representatives of other vertebrate groups, and performed phylogenetic and molecular dating analyses to investigate the pattern and timing of diversification of these retroviral elements.

Results: We identified a high diversity of ERVs in the sampled felids, with a predominance of Gammaretrovirus-related sequences, including class I ERVs. Our data indicate that the identified ERVs arose from at least eleven horizontal interordinal transmissions from other mammals. Furthermore, we estimated that the majority of the Gamma-like integrations took place during the diversification of modern felids. Finally, our phylogenetic analyses indicate the presence of a genetically divergent group of sequences whose position in our phylogenetic tree was difficult to establish confidently relative to known retroviruses, and another lineage identified as ERVs belonging to class II.

Conclusions: Retroviruses have circulated in felids along with their evolution. The majority of the deep clades of ERVs exist since the primary divergence of felids' base and cluster with retroviruses of divergent mammalian lineages, suggesting horizontal interordinal transmission. Our findings highlight the importance of additional studies on the role of ERVs in the genome landscaping of other carnivore species.

Show MeSH
Related in: MedlinePlus