A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates
Abstract Background The group XIV of C-type lectin domain-containing proteins (CTLDcps) is one of the seventeen groups of CTLDcps discovered in mammals and composed by four members: CD93, Clec14A, CD248 and Thrombomodulin, which have shown to be important players in cancer and vascular biology. Alth...
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08659-6 |
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| author | Stefano Barbera Claudio Cucini |
| author_facet | Stefano Barbera Claudio Cucini |
| author_sort | Stefano Barbera |
| collection | DOAJ |
| description | Abstract Background The group XIV of C-type lectin domain-containing proteins (CTLDcps) is one of the seventeen groups of CTLDcps discovered in mammals and composed by four members: CD93, Clec14A, CD248 and Thrombomodulin, which have shown to be important players in cancer and vascular biology. Although these proteins belong to the same family, their phylogenetic relationship has never been dissected. To resolve their evolution and characterize their protein domain composition we investigated CTLDcp genes in gnathostomes and cyclostomes and, by means of phylogenetic approaches as well as synteny analyses, we inferred an evolutionary scheme that attempts to unravel their evolution in modern vertebrates. Results Here, we evidenced the paralogy of the group XIV of CTLDcps in gnathostomes and discovered that a gene loss of CD248 and Clec14A occurred in different vertebrate groups, with CD248 being lost due to chromosome disruption in birds, while Clec14A loss in monotremes and marsupials did not involve chromosome rearrangements. Moreover, employing genome annotations of different lampreys as well as one hagfish species, we investigated the origin and evolution of modern group XIV of CTLDcps. Furthermore, we carefully retrieved and annotated gnathostome CTLDcp domains, pointed out important differences in domain composition between gnathostome classes, and assessed codon substitution rate of each domain by analyzing nonsynonymous (Ka) over synonymous (Ks) substitutions using one representative species per gnathostome order. Conclusions CTLDcps appeared with the advent of early vertebrates after a whole genome duplication followed by a sporadic tandem duplication. These duplication events gave rise to three CTLDcps in the ancestral vertebrate that underwent further duplications caused by the independent polyploidizations that characterized the evolution of cyclostomes and gnathostomes. Importantly, our analyses of CTLDcps in gnathostomes revealed critical inter-class differences in both extracellular and intracellular domains, which might help the interpretation of experimental results and the understanding of differences between animal models. |
| first_indexed | 2024-12-12T09:25:53Z |
| format | Article |
| id | doaj.art-6148eeab3f464a83842b30c04c9c0b05 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T09:25:53Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6148eeab3f464a83842b30c04c9c0b052022-12-22T00:29:03ZengBMCBMC Genomics1471-21642022-06-0123111510.1186/s12864-022-08659-6A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebratesStefano Barbera0Claudio Cucini1Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala UniversityDepartment of Life Sciences, University of SienaAbstract Background The group XIV of C-type lectin domain-containing proteins (CTLDcps) is one of the seventeen groups of CTLDcps discovered in mammals and composed by four members: CD93, Clec14A, CD248 and Thrombomodulin, which have shown to be important players in cancer and vascular biology. Although these proteins belong to the same family, their phylogenetic relationship has never been dissected. To resolve their evolution and characterize their protein domain composition we investigated CTLDcp genes in gnathostomes and cyclostomes and, by means of phylogenetic approaches as well as synteny analyses, we inferred an evolutionary scheme that attempts to unravel their evolution in modern vertebrates. Results Here, we evidenced the paralogy of the group XIV of CTLDcps in gnathostomes and discovered that a gene loss of CD248 and Clec14A occurred in different vertebrate groups, with CD248 being lost due to chromosome disruption in birds, while Clec14A loss in monotremes and marsupials did not involve chromosome rearrangements. Moreover, employing genome annotations of different lampreys as well as one hagfish species, we investigated the origin and evolution of modern group XIV of CTLDcps. Furthermore, we carefully retrieved and annotated gnathostome CTLDcp domains, pointed out important differences in domain composition between gnathostome classes, and assessed codon substitution rate of each domain by analyzing nonsynonymous (Ka) over synonymous (Ks) substitutions using one representative species per gnathostome order. Conclusions CTLDcps appeared with the advent of early vertebrates after a whole genome duplication followed by a sporadic tandem duplication. These duplication events gave rise to three CTLDcps in the ancestral vertebrate that underwent further duplications caused by the independent polyploidizations that characterized the evolution of cyclostomes and gnathostomes. Importantly, our analyses of CTLDcps in gnathostomes revealed critical inter-class differences in both extracellular and intracellular domains, which might help the interpretation of experimental results and the understanding of differences between animal models.https://doi.org/10.1186/s12864-022-08659-6C-type lectin evolutionCD93Clec14ACD248ThrombomodulinWhole genome duplications |
| spellingShingle | Stefano Barbera Claudio Cucini A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates BMC Genomics C-type lectin evolution CD93 Clec14A CD248 Thrombomodulin Whole genome duplications |
| title | A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates |
| title_full | A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates |
| title_fullStr | A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates |
| title_full_unstemmed | A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates |
| title_short | A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates |
| title_sort | glimpse into the past phylogenesis and protein domain analysis of the group xiv of c type lectins in vertebrates |
| topic | C-type lectin evolution CD93 Clec14A CD248 Thrombomodulin Whole genome duplications |
| url | https://doi.org/10.1186/s12864-022-08659-6 |
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