The Experts below are selected from a list of 720 Experts worldwide ranked by ideXlab platform

Enzo Tramontano - One of the best experts on this subject based on the ideXlab platform.

  • identification and characterization of erv w like sequences in platyrrhini species provides new insights into the evolutionary history of erv w in primates
    Mobile Dna, 2020
    Co-Authors: Nicole Grandi, Maria Paola Pisano, Martina Demurtas, Jonas Blomberg, Gkikas Magiorkinis, Jens Mayer, Enzo Tramontano
    Abstract:

    Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W (HERV-W) sequences is investigated for a pathological role in various human diseases. We previously characterized ERV-W group genomic sequences in human and non-human Catarrhini species. We now investigated ERV-W-like sequences in the parvorder Platyrrhini, especially regarding two species with complete genome assemblies, namely marmoset (Callithrix jacchus) and squirrel monkey (Saimiri boliviensis). We identified in both species proviral sequences, annotated as ERV1–1 in respective genome assemblies, sharing high sequence similarities with Catarrhini ERV-W. A total of 130 relatively intact proviruses from the genomes of marmoset and squirrel monkey were characterized regarding their structural and evolutionarily relationships with Catarrhini ERV-W elements. Platyrrhini ERV-W sequences share several structural features with Catarrhini ERV-W elements and are closely related phylogenetically with the latter as well as with other ERV-W-related gammaretrovirus-like ERVs. The ERV-W group colonized Platyrrhini primates of both Callitrichidae and Atelidae lineages, with provirus formations having occurred mostly between 25 and 15 mya. Two LTR subgroups were associated with monophyletic proviral bodies. A pre-gag region appears to be a sequence feature common to the ERV-W group: it harbors a putative intron sequence that is missing in some ERV-W loci, holding a putative ORF as well. The presence of a long pre-gag portion was confirmed among all gammaretroviral ERV analyzed, suggesting a role in the latter biology. It is noteworthy that, contrary to Catarrhini ERV-W, there was no evidence of L1-mediated mobilization for Platyrrhini ERV-W sequences. Our data establish that ERV-W is not exclusive to Catarrhini primates but colonized both parvorders of Simiiformes, providing further insight into the evolution of ERV-W and the colonization of primate genomes.

  • HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini
    BMC Evolutionary Biology, 2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    Background The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. Results We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini ), Tarsiiformes and to the most primitive Prosimians . Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae , Platyrrhini parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae , representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians . Conclusions Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.

  • HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini.
    BMC Evolutionary Biology, 2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini), Tarsiiformes and to the most primitive Prosimians. Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae, Platyrrhini parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae, representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians. Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.

  • Additional file 1: Table S1. of HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini
    2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    HERV-W loci in the human reference genome sequence and ERV-W orthologous sequences in non-human Catarrhini primates reference genome sequences. Table S2: ERV-W loci in non-human Catarrhini primate reference genome sequences with a solitary HERV-W LTR at the orthologous human genome position. Table S3: ERV-W loci in non-human Catarrhini primates corresponding to HERV-W-like elements with lesser similarities to HERV17. Table S4: ERV-W loci in non-human Catarrhini primate genome sequences lacking an ortholog in the human reference genome sequence. (XLSX 85 kb

Nicole Grandi - One of the best experts on this subject based on the ideXlab platform.

  • identification and characterization of erv w like sequences in platyrrhini species provides new insights into the evolutionary history of erv w in primates
    Mobile Dna, 2020
    Co-Authors: Nicole Grandi, Maria Paola Pisano, Martina Demurtas, Jonas Blomberg, Gkikas Magiorkinis, Jens Mayer, Enzo Tramontano
    Abstract:

    Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W (HERV-W) sequences is investigated for a pathological role in various human diseases. We previously characterized ERV-W group genomic sequences in human and non-human Catarrhini species. We now investigated ERV-W-like sequences in the parvorder Platyrrhini, especially regarding two species with complete genome assemblies, namely marmoset (Callithrix jacchus) and squirrel monkey (Saimiri boliviensis). We identified in both species proviral sequences, annotated as ERV1–1 in respective genome assemblies, sharing high sequence similarities with Catarrhini ERV-W. A total of 130 relatively intact proviruses from the genomes of marmoset and squirrel monkey were characterized regarding their structural and evolutionarily relationships with Catarrhini ERV-W elements. Platyrrhini ERV-W sequences share several structural features with Catarrhini ERV-W elements and are closely related phylogenetically with the latter as well as with other ERV-W-related gammaretrovirus-like ERVs. The ERV-W group colonized Platyrrhini primates of both Callitrichidae and Atelidae lineages, with provirus formations having occurred mostly between 25 and 15 mya. Two LTR subgroups were associated with monophyletic proviral bodies. A pre-gag region appears to be a sequence feature common to the ERV-W group: it harbors a putative intron sequence that is missing in some ERV-W loci, holding a putative ORF as well. The presence of a long pre-gag portion was confirmed among all gammaretroviral ERV analyzed, suggesting a role in the latter biology. It is noteworthy that, contrary to Catarrhini ERV-W, there was no evidence of L1-mediated mobilization for Platyrrhini ERV-W sequences. Our data establish that ERV-W is not exclusive to Catarrhini primates but colonized both parvorders of Simiiformes, providing further insight into the evolution of ERV-W and the colonization of primate genomes.

  • HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini
    BMC Evolutionary Biology, 2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    Background The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. Results We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini ), Tarsiiformes and to the most primitive Prosimians . Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae , Platyrrhini parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae , representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians . Conclusions Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.

  • HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini.
    BMC Evolutionary Biology, 2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini), Tarsiiformes and to the most primitive Prosimians. Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae, Platyrrhini parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae, representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians. Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.

  • Additional file 1: Table S1. of HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini
    2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    HERV-W loci in the human reference genome sequence and ERV-W orthologous sequences in non-human Catarrhini primates reference genome sequences. Table S2: ERV-W loci in non-human Catarrhini primate reference genome sequences with a solitary HERV-W LTR at the orthologous human genome position. Table S3: ERV-W loci in non-human Catarrhini primates corresponding to HERV-W-like elements with lesser similarities to HERV17. Table S4: ERV-W loci in non-human Catarrhini primate genome sequences lacking an ortholog in the human reference genome sequence. (XLSX 85 kb

Jonas Blomberg - One of the best experts on this subject based on the ideXlab platform.

  • identification and characterization of erv w like sequences in platyrrhini species provides new insights into the evolutionary history of erv w in primates
    Mobile Dna, 2020
    Co-Authors: Nicole Grandi, Maria Paola Pisano, Martina Demurtas, Jonas Blomberg, Gkikas Magiorkinis, Jens Mayer, Enzo Tramontano
    Abstract:

    Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W (HERV-W) sequences is investigated for a pathological role in various human diseases. We previously characterized ERV-W group genomic sequences in human and non-human Catarrhini species. We now investigated ERV-W-like sequences in the parvorder Platyrrhini, especially regarding two species with complete genome assemblies, namely marmoset (Callithrix jacchus) and squirrel monkey (Saimiri boliviensis). We identified in both species proviral sequences, annotated as ERV1–1 in respective genome assemblies, sharing high sequence similarities with Catarrhini ERV-W. A total of 130 relatively intact proviruses from the genomes of marmoset and squirrel monkey were characterized regarding their structural and evolutionarily relationships with Catarrhini ERV-W elements. Platyrrhini ERV-W sequences share several structural features with Catarrhini ERV-W elements and are closely related phylogenetically with the latter as well as with other ERV-W-related gammaretrovirus-like ERVs. The ERV-W group colonized Platyrrhini primates of both Callitrichidae and Atelidae lineages, with provirus formations having occurred mostly between 25 and 15 mya. Two LTR subgroups were associated with monophyletic proviral bodies. A pre-gag region appears to be a sequence feature common to the ERV-W group: it harbors a putative intron sequence that is missing in some ERV-W loci, holding a putative ORF as well. The presence of a long pre-gag portion was confirmed among all gammaretroviral ERV analyzed, suggesting a role in the latter biology. It is noteworthy that, contrary to Catarrhini ERV-W, there was no evidence of L1-mediated mobilization for Platyrrhini ERV-W sequences. Our data establish that ERV-W is not exclusive to Catarrhini primates but colonized both parvorders of Simiiformes, providing further insight into the evolution of ERV-W and the colonization of primate genomes.

  • HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini
    BMC Evolutionary Biology, 2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    Background The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. Results We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini ), Tarsiiformes and to the most primitive Prosimians . Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae , Platyrrhini parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae , representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians . Conclusions Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.

  • HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini.
    BMC Evolutionary Biology, 2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini), Tarsiiformes and to the most primitive Prosimians. Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae, Platyrrhini parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae, representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians. Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.

  • Additional file 1: Table S1. of HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini
    2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    HERV-W loci in the human reference genome sequence and ERV-W orthologous sequences in non-human Catarrhini primates reference genome sequences. Table S2: ERV-W loci in non-human Catarrhini primate reference genome sequences with a solitary HERV-W LTR at the orthologous human genome position. Table S3: ERV-W loci in non-human Catarrhini primates corresponding to HERV-W-like elements with lesser similarities to HERV17. Table S4: ERV-W loci in non-human Catarrhini primate genome sequences lacking an ortholog in the human reference genome sequence. (XLSX 85 kb

Jens Mayer - One of the best experts on this subject based on the ideXlab platform.

  • identification and characterization of erv w like sequences in platyrrhini species provides new insights into the evolutionary history of erv w in primates
    Mobile Dna, 2020
    Co-Authors: Nicole Grandi, Maria Paola Pisano, Martina Demurtas, Jonas Blomberg, Gkikas Magiorkinis, Jens Mayer, Enzo Tramontano
    Abstract:

    Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W (HERV-W) sequences is investigated for a pathological role in various human diseases. We previously characterized ERV-W group genomic sequences in human and non-human Catarrhini species. We now investigated ERV-W-like sequences in the parvorder Platyrrhini, especially regarding two species with complete genome assemblies, namely marmoset (Callithrix jacchus) and squirrel monkey (Saimiri boliviensis). We identified in both species proviral sequences, annotated as ERV1–1 in respective genome assemblies, sharing high sequence similarities with Catarrhini ERV-W. A total of 130 relatively intact proviruses from the genomes of marmoset and squirrel monkey were characterized regarding their structural and evolutionarily relationships with Catarrhini ERV-W elements. Platyrrhini ERV-W sequences share several structural features with Catarrhini ERV-W elements and are closely related phylogenetically with the latter as well as with other ERV-W-related gammaretrovirus-like ERVs. The ERV-W group colonized Platyrrhini primates of both Callitrichidae and Atelidae lineages, with provirus formations having occurred mostly between 25 and 15 mya. Two LTR subgroups were associated with monophyletic proviral bodies. A pre-gag region appears to be a sequence feature common to the ERV-W group: it harbors a putative intron sequence that is missing in some ERV-W loci, holding a putative ORF as well. The presence of a long pre-gag portion was confirmed among all gammaretroviral ERV analyzed, suggesting a role in the latter biology. It is noteworthy that, contrary to Catarrhini ERV-W, there was no evidence of L1-mediated mobilization for Platyrrhini ERV-W sequences. Our data establish that ERV-W is not exclusive to Catarrhini primates but colonized both parvorders of Simiiformes, providing further insight into the evolution of ERV-W and the colonization of primate genomes.

  • HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini
    BMC Evolutionary Biology, 2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    Background The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. Results We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini ), Tarsiiformes and to the most primitive Prosimians . Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae , Platyrrhini parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae , representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians . Conclusions Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.

  • HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini.
    BMC Evolutionary Biology, 2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini), Tarsiiformes and to the most primitive Prosimians. Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae, Platyrrhini parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae, representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians. Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.

  • Additional file 1: Table S1. of HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini
    2018
    Co-Authors: Nicole Grandi, Jonas Blomberg, Jens Mayer, Marta Cadeddu, Enzo Tramontano
    Abstract:

    HERV-W loci in the human reference genome sequence and ERV-W orthologous sequences in non-human Catarrhini primates reference genome sequences. Table S2: ERV-W loci in non-human Catarrhini primate reference genome sequences with a solitary HERV-W LTR at the orthologous human genome position. Table S3: ERV-W loci in non-human Catarrhini primates corresponding to HERV-W-like elements with lesser similarities to HERV17. Table S4: ERV-W loci in non-human Catarrhini primate genome sequences lacking an ortholog in the human reference genome sequence. (XLSX 85 kb

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  • Implicacions filogenètiques i adaptatives de la variabilitat morfològica de la dentició dels primats Catarrhini actuals i fòssils
    'Edicions de la Universitat de Barcelona', 2015
    Co-Authors: Gamarra Rubio Beatriz
    Abstract:

    [cat]La present Tesi Doctoral tracta de l’estudi de la morfologia dental, concretament de la primera (M1) i segona (M2) molars inferiors d’un ampli grup de primats catarrins. En general, la morfologia dental és el reflex del compromís entre les influències filogenètiques i funcionals. L’objectiu principal del present estudi és analitzar quines són aquestes influències en les molars dels catarrins per tal de relacionar filogenèticament o ecològicament els espècimens fòssils del Miocè i Pliocè amb les espècies actuals. Aquest treball es divideix en dos clars apartats: una part d’exploració de la metodologia per analitzar la forma dental i una altra que analitza la morfologia i la topografia dental de la mostra de catarrins. L’exploració de la metodologia consisteix en trobar aquella tècnica que millor s’adeqüi a la mostra de primats catarrins. Existeixen vàries metodologies per analitzar la morfologia dental, entre les quals trobem les anàlisis de Fourier i la Morfometria Geomètrica (MG). Els resultats de l’anàlisi de Fourier indiquen que aquesta tècnica és útil per diferenciar espècies de primats hominoïdeus. No obstant, aquesta tècnica només permet caracteritzar el contorn de les estructures estudiades, en aquest cas les molars, de tal manera que no permet incloure altres trets de la cara oclusal de les dents biològicament més informatius. Les tècniques de MG han permeten caracteritzar trets tant del contorn dental com de la cara oclusal de les molars en una mateixa anàlisi. Els resultats obtinguts de la comparació d’una mateixa submostra d’hominoïdeus indiquen que, amb la tècnica de landmarks, s’obtenen millors resultats en l’estudi de la variabilitat morfològica de la M1,respecte les tècniques de sliding semilandmarks i sèries el·líptiques de Fourier. És per això que es va decidir analitzar la variabilitat morfològica dental d’una mostra molt més àmplia de catarrins a partir d’aquesta tècnica. Per determinar si una estructura biològica és útil per inferir filogenèticament les relacions entre les espècies, s’ha de comprovar prèviament si aquesta presenta una senyal filogenètica. Els resultats del present treball indiquen que la morfologia de les molars inferiors de catarrins presenten senyal filogenètica i que permet agrupar les espècies de catarrins per categories taxonòmiques a nivell de Família en els hominoïdeus i a nivell de Subfamília en els cercopitecoïdeus per ambdues molars. No obstant, la M2 presentava una forta influència de la dieta. Un cop determinat aquestes influències, es van incloure espècimens fòssils, concretament, les espècies d’hominoïdeus euroasiàtics del Miocè (Dryopithecus fontani, Hispanopithecus laietanus, Oreopithecus bambolii, Ouranopithecus macedoniensis, Rudapithecus hungaricus i Sivapithecu sivalenis), els pliopitecoïdeus Anapithecus heryaki, Barberopithecus huerzeleri i vàries espècies del gènere Pliopithecus, i el cercopitecoïdeu del Pliocè euroasiàtic Mesopithecus pentelicus, per determinar les relacions filogenètiques amb les espècies actuals. En general, les espècies de dryopitecins s’agrupen amb els grans simis actuals, sense cap afinitat clara entre les espècies actuals; els pliopitecoïdeus es confirmen com a grup monofilètic dins dels catarrins; i Mesopithecus amb els colobins actuals. Els resultats anteriors apuntaven a que a nivells taxonòmics inferiors existeixen altres factors que estan influint en la morfologia de les molars dels catarrins, com és per exemple la dieta. L’anàlisi de la topografia dental permet relacionar els trets oclusals de les molars amb la dieta dels individus. Els resultats de l’anàlisi de la topografia dental d’hominoïdeus actuals i Mandrillus sphinx indiquen que la M2 està relacionada amb el grau de folivorisme de la dieta d’aquests espècimens. L’anàlisi de la topografia dental dels hominoïdeus fòssils indiquen que aquests estaven adaptats a diferents graus de fruigivorisme i sobretot, a fer front als períodes d’escassetat de recursos d’aliments durs.[eng]The present Thesis deals about the phylogenetic and adaptive influences in the morphologic variability of lower molars of extinct and living Catarrhini species. The study is divided in three parts. The first one deals with the methodology employed in the morphometric analysis of lower molar. First analyses of M2 shape employing Fourier analysis indicate that the molar outline could be used to differentiate hominid species. Nevertheless, no occlusal dental traits could be analyzed using this technique, which may be informative for biological purposes. On the other hand, Geometric Morphometric (GM) methods allow studying both sources of information, occlusal and contour traits, in the same analysis. Comparative analyses show that employing only landmarks (GM method) for the description of Hominoidea molar morphology is the best technique that explains the variability of this group. The second part of the dissertation analyzes the factors that influence the molar morphology variability of a huge sample of catarrini primates employing landmark-technique. The results indicate that molar morphology of both first (M1) and second (M2) lower molars carry a strong phylogenetic signal, which allows grouping catarrini specimens at Family level in Hominoidea and Subfamily level in Cercopithecoidea. Besides, the diet also has an influence on the M2 morphology. When employing fossil specimens, they present taxonomic affinities with the expected groups: Miocene dryopithecins are grouped with great apes; pliopithecoidea species form a monophyletic group into the Infraordre of Catarrhini, while Mesopithecus (a Pliocene cercopithecid) present affinities with colobine species. Finally, the dental topography studies have shown the relationship between occlusal traits and diet. The topographic analysis employing some Hominoidea species indicates that only M2 has a significant correlation between folivory degree in the diet and occlusal complexity: species that rely more on cellulose aliments have high occlusal complexity and the ones that ingest more hard items, having lower values of occlusal complexity. This fact allows infer on the foraging ecology of fossil specimens. The dental topographic analyses of fossil hominids show that they were adapted to different degree of frugivory, and faced to periods of lower availability of preferred diet resources, in agreement with other studies

  • Implicacions filogenètiques i adaptatives de la variabilitat morfològica de la dentició dels primats Catarrhini actuals i fòssils
    'Edicions de la Universitat de Barcelona', 2014
    Co-Authors: Gamarra Rubio Beatriz
    Abstract:

    La present Tesi Doctoral tracta de l’estudi de la morfologia dental, concretament de la primera (M1) i segona (M2) molars inferiors d’un ampli grup de primats catarrins. En general, la morfologia dental és el reflex del compromís entre les influències filogenètiques i funcionals. L’objectiu principal del present estudi és analitzar quines són aquestes influències en les molars dels catarrins per tal de relacionar filogenèticament o ecològicament els espècimens fòssils del Miocè i Pliocè amb les espècies actuals. Aquest treball es divideix en dos clars apartats: una part d’exploració de la metodologia per analitzar la forma dental i una altra que analitza la morfologia i la topografia dental de la mostra de catarrins. L’exploració de la metodologia consisteix en trobar aquella tècnica que millor s’adeqüi a la mostra de primats catarrins. Existeixen vàries metodologies per analitzar la morfologia dental, entre les quals trobem les anàlisis de Fourier i la Morfometria Geomètrica (MG). Els resultats de l’anàlisi de Fourier indiquen que aquesta tècnica és útil per diferenciar espècies de primats hominoïdeus. No obstant, aquesta tècnica només permet caracteritzar el contorn de les estructures estudiades, en aquest cas les molars, de tal manera que no permet incloure altres trets de la cara oclusal de les dents biològicament més informatius. Les tècniques de MG han permeten caracteritzar trets tant del contorn dental com de la cara oclusal de les molars en una mateixa anàlisi. Els resultats obtinguts de la comparació d’una mateixa submostra d’hominoïdeus indiquen que, amb la tècnica de landmarks, s’obtenen millors resultats en l’estudi de la variabilitat morfològica de la M1,respecte les tècniques de sliding semilandmarks i sèries el·líptiques de Fourier. És per això que es va decidir analitzar la variabilitat morfològica dental d’una mostra molt més àmplia de catarrins a partir d’aquesta tècnica. Per determinar si una estructura biològica és útil per inferir filogenèticament les relacions entre les espècies, s’ha de comprovar prèviament si aquesta presenta una senyal filogenètica. Els resultats del present treball indiquen que la morfologia de les molars inferiors de catarrins presenten senyal filogenètica i que permet agrupar les espècies de catarrins per categories taxonòmiques a nivell de Família en els hominoïdeus i a nivell de Subfamília en els cercopitecoïdeus per ambdues molars. No obstant, la M2 presentava una forta influència de la dieta. Un cop determinat aquestes influències, es van incloure espècimens fòssils, concretament, les espècies d’hominoïdeus euroasiàtics del Miocè (Dryopithecus fontani, Hispanopithecus laietanus, Oreopithecus bambolii, Ouranopithecus macedoniensis, Rudapithecus hungaricus i Sivapithecu sivalenis), els pliopitecoïdeus Anapithecus heryaki, Barberopithecus huerzeleri i vàries espècies del gènere Pliopithecus, i el cercopitecoïdeu del Pliocè euroasiàtic Mesopithecus pentelicus, per determinar les relacions filogenètiques amb les espècies actuals. En general, les espècies de dryopitecins s’agrupen amb els grans simis actuals, sense cap afinitat clara entre les espècies actuals; els pliopitecoïdeus es confirmen com a grup monofilètic dins dels catarrins; i Mesopithecus amb els colobins actuals. Els resultats anteriors apuntaven a que a nivells taxonòmics inferiors existeixen altres factors que estan influint en la morfologia de les molars dels catarrins, com és per exemple la dieta. L’anàlisi de la topografia dental permet relacionar els trets oclusals de les molars amb la dieta dels individus. Els resultats de l’anàlisi de la topografia dental d’hominoïdeus actuals i Mandrillus sphinx indiquen que la M2 està relacionada amb el grau de folivorisme de la dieta d’aquests espècimens. L’anàlisi de la topografia dental dels hominoïdeus fòssils indiquen que aquests estaven adaptats a diferents graus de fruigivorisme i sobretot, a fer front als períodes d’escassetat de recursos d’aliments durs.The present Thesis deals about the phylogenetic and adaptive influences in the morphologic variability of lower molars of extinct and living Catarrhini species. The study is divided in three parts. The first one deals with the methodology employed in the morphometric analysis of lower molar. First analyses of M2 shape employing Fourier analysis indicate that the molar outline could be used to differentiate hominid species. Nevertheless, no occlusal dental traits could be analyzed using this technique, which may be informative for biological purposes. On the other hand, Geometric Morphometric (GM) methods allow studying both sources of information, occlusal and contour traits, in the same analysis. Comparative analyses show that employing only landmarks (GM method) for the description of Hominoidea molar morphology is the best technique that explains the variability of this group. The second part of the dissertation analyzes the factors that influence the molar morphology variability of a huge sample of catarrini primates employing landmark-technique. The results indicate that molar morphology of both first (M1) and second (M2) lower molars carry a strong phylogenetic signal, which allows grouping catarrini specimens at Family level in Hominoidea and Subfamily level in Cercopithecoidea. Besides, the diet also has an influence on the M2 morphology. When employing fossil specimens, they present taxonomic affinities with the expected groups: Miocene dryopithecins are grouped with great apes; pliopithecoidea species form a monophyletic group into the Infraordre of Catarrhini, while Mesopithecus (a Pliocene cercopithecid) present affinities with colobine species. Finally, the dental topography studies have shown the relationship between occlusal traits and diet. The topographic analysis employing some Hominoidea species indicates that only M2 has a significant correlation between folivory degree in the diet and occlusal complexity: species that rely more on cellulose aliments have high occlusal complexity and the ones that ingest more hard items, having lower values of occlusal complexity. This fact allows infer on the foraging ecology of fossil specimens. The dental topographic analyses of fossil hominids show that they were adapted to different degree of frugivory, and faced to periods of lower availability of preferred diet resources, in agreement with other studies