Frequent birth-and-death events throughout perforin-1 evolution
Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large...
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| Format: | Article |
| Language: | English |
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BMC
2020-10-01
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| Series: | BMC Evolutionary Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12862-020-01698-1 |
| _version_ | 1819130968735219712 |
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| author | Miguel Araujo-Voces Víctor Quesada |
| author_facet | Miguel Araujo-Voces Víctor Quesada |
| author_sort | Miguel Araujo-Voces |
| collection | DOAJ |
| description | Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes. |
| first_indexed | 2024-12-22T09:08:03Z |
| format | Article |
| id | doaj.art-dcae38f6f4254d56b8ae1e811dedfdae |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-22T09:08:03Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-dcae38f6f4254d56b8ae1e811dedfdae2022-12-21T18:31:33ZengBMCBMC Evolutionary Biology1471-21482020-10-0120111110.1186/s12862-020-01698-1Frequent birth-and-death events throughout perforin-1 evolutionMiguel Araujo-Voces0Víctor Quesada1Departamento de Bioquímica y Biología Molecular - IUOPA, Universidad de OviedoDepartamento de Bioquímica y Biología Molecular - IUOPA, Universidad de OviedoAbstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.http://link.springer.com/article/10.1186/s12862-020-01698-1Perforin-1Assisted annotationImmuneBirth-and-deathTandem duplication |
| spellingShingle | Miguel Araujo-Voces Víctor Quesada Frequent birth-and-death events throughout perforin-1 evolution BMC Evolutionary Biology Perforin-1 Assisted annotation Immune Birth-and-death Tandem duplication |
| title | Frequent birth-and-death events throughout perforin-1 evolution |
| title_full | Frequent birth-and-death events throughout perforin-1 evolution |
| title_fullStr | Frequent birth-and-death events throughout perforin-1 evolution |
| title_full_unstemmed | Frequent birth-and-death events throughout perforin-1 evolution |
| title_short | Frequent birth-and-death events throughout perforin-1 evolution |
| title_sort | frequent birth and death events throughout perforin 1 evolution |
| topic | Perforin-1 Assisted annotation Immune Birth-and-death Tandem duplication |
| url | http://link.springer.com/article/10.1186/s12862-020-01698-1 |
| work_keys_str_mv | AT miguelaraujovoces frequentbirthanddeatheventsthroughoutperforin1evolution AT victorquesada frequentbirthanddeatheventsthroughoutperforin1evolution |