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Storer JM, Walker JA, Beckstrom TO, Batzer MA. Extensive Independent Amplification of Platy-1 Retroposons in Tamarins, Genus Saguinus. Genes (Basel) 2023; 14:1436. [PMID: 37510341 PMCID: PMC10378772 DOI: 10.3390/genes14071436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Platy-1 retroposons are short interspersed elements (SINEs) unique to platyrrhine primates. Discovered in the common marmoset (Callithrix jacchus) genome in 2016, these 100 bp mobile element insertions (MEIs) appeared to be novel drivers of platyrrhine evolution, with over 2200 full-length members across 62 different subfamilies, and strong evidence of ongoing proliferation in C. jacchus. Subsequent characterization of Platy-1 elements in Aotus, Saimiri and Cebus genera, suggested that the widespread mobilization detected in marmoset (family Callithrichidae) was perhaps an anomaly. Two additional Callithrichidae genomes are now available, a scaffold level genome assembly for Saguinus imperator (tamarin; SagImp_v1) and a chromosome-level assembly for Saguinus midas (Midas tamarin; ASM2_v1). Here, we report that each tamarin genome contains over 11,000 full-length Platy-1 insertions, about 1150 are shared by both Saguinus tamarins, 7511 are unique to S. imperator, and another 8187 are unique to S. midas. Roughly 325 are shared among the three callithrichids. We identified six new Platy-1 subfamilies derived from Platy-1-8, with the youngest new subfamily, Platy-1-8c_Saguinus, being the primary source of the Saguinus amplification burst. This constitutes the largest expansion of Platy-1 MEIs reported to date and the most extensive independent SINE amplification between two closely related species.
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Affiliation(s)
- Jessica M. Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Thomas O. Beckstrom
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- Department of Oral and Maxillofacial Surgery, University of Washington, 1959 NE Pacific Street, Health Sciences Building B-241, Seattle, WA 98195, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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Storer JM, Walker JA, Rewerts LC, Brown MA, Beckstrom TO, Herke SW, Roos C, Batzer MA. Owl Monkey Alu Insertion Polymorphisms and Aotus Phylogenetics. Genes (Basel) 2022; 13:2069. [PMID: 36360306 PMCID: PMC9691001 DOI: 10.3390/genes13112069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 07/30/2023] Open
Abstract
Owl monkeys (genus Aotus), or "night monkeys" are platyrrhine primates in the Aotidae family. Early taxonomy only recognized one species, Aotus trivirgatus, until 1983, when Hershkovitz proposed nine unique species designations, classified into red-necked and gray-necked species groups based predominately on pelage coloration. Recent studies questioned this conventional separation of the genus and proposed designations based on the geographical location of wild populations. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. A scaffold-level genome assembly for one Aotus species, Aotus nancymaae [Anan_2.0], facilitated large-scale ascertainment of nearly 2000 young lineage-specific Alu insertions. This study provides candidate oligonucleotides for locus-specific PCR assays for over 1350 of these elements. For 314 Alu elements across four taxa with multiple specimens, PCR analyses identified 159 insertion polymorphisms, including 21 grouping A. nancymaae and Aotus azarae (red-necked species) as sister taxa, with Aotus vociferans and A. trivirgatus (gray-necked) being more basal. DNA sequencing identified five novel Alu elements from three different taxa. The Alu datasets reported in this study will assist in species identification and provide a valuable resource for Aotus phylogenetics, population genetics and conservation strategies when applied to wild populations.
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Affiliation(s)
- Jessica M. Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Lydia C. Rewerts
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Morgan A. Brown
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Thomas O. Beckstrom
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- Department of Oral and Maxillofacial Surgery, University of Washington, 1959 NE Pacific Street, Health Sciences Building B-241, Seattle, WA 98195, USA
| | - Scott W. Herke
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/ Sapajus Genomics. Genes (Basel) 2022; 13:genes13040572. [PMID: 35456378 PMCID: PMC9030454 DOI: 10.3390/genes13040572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.
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Storer JM, Walker JA, Jordan VE, Batzer MA. Sensitivity of the polyDetect computational pipeline for phylogenetic analyses. Anal Biochem 2020; 593:113516. [PMID: 31794702 DOI: 10.1016/j.ab.2019.113516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 01/16/2023]
Abstract
Alu elements are powerful phylogenetic markers. The combination of a recently-developed computational pipeline, polyDetect, with high copy number Alu insertions has previously been utilized to help resolve the Papio baboon phylogeny with high statistical support. Here, the polyDetect method was applied to the highly contentious Cebidae phylogeny within New World monkeys (NWM). The polyDetect method relies on conserved homology/identity of short read sequence data among the species being compared to accurately map predicted shared Alu insertions to each unique flanking sequence. The results of this comprehensive assessment indicate that there were insufficient sequence homology/identity stretches in non-repeated DNA sequences among the four Cebidae genera analyzed in this study to make this strategy phylogenetically viable. The ~20 million years of evolutionary divergence of the Cebidae genera has resulted in random sequence decay within the short read data, obscuring potentially orthologous elements in the species tested. These analyses suggest that the polyDetect pipeline is best suited to resolving phylogenies of more recently diverged lineages when high-quality assembled genomes are not available for the taxa of interest.
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Affiliation(s)
- Jessica M Storer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Vallmer E Jordan
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA.
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Walker JA, Jordan VE, Storer JM, Steely CJ, Gonzalez-Quiroga P, Beckstrom TO, Rewerts LC, St Romain CP, Rockwell CE, Rogers J, Jolly CJ, Konkel MK, Batzer MA. Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry. Mob DNA 2019; 10:46. [PMID: 31788036 PMCID: PMC6880559 DOI: 10.1186/s13100-019-0187-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022] Open
Abstract
Background Baboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-throughput "poly-Detect" method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data. Results We identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings. Conclusions Our discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting.
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Affiliation(s)
- Jerilyn A Walker
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Vallmer E Jordan
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Jessica M Storer
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Cody J Steely
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Paulina Gonzalez-Quiroga
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Thomas O Beckstrom
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Lydia C Rewerts
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Corey P St Romain
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Catherine E Rockwell
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
| | - Jeffrey Rogers
- 2Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Clifford J Jolly
- 4Department of Anthropology, New York University, New York, NY 10003 USA
| | - Miriam K Konkel
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA.,Department of Genetics & Biochemistry, Clemson Center for Human Genetics, Clemson, SC 29634 USA
| | | | - Mark A Batzer
- 1Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana, 70803 USA
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Doronina L, Reising O, Clawson H, Ray DA, Schmitz J. True Homoplasy of Retrotransposon Insertions in Primates. Syst Biol 2019; 68:482-493. [PMID: 30445649 DOI: 10.1093/sysbio/syy076] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 01/24/2023] Open
Abstract
How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, which were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multigenome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages and twelve incidences of precise deletions of previously established SINEs. Correspondingly, eight precise parallel insertions and no exact deletions were detected in a comparison of lemuriform primate and human insertions spanning the range of primate diversity. With an overall frequency of homoplasious Alu insertions of only 0.01% (for human-chimpanzee-rhesus macaque) and 0.02-0.04% (for human-bushbaby-lemurs) and precise Alu deletions of 0.001-0.002% (for human-chimpanzee-rhesus macaque), real homoplasy is not considered to be a quantitatively relevant source of evolutionary noise. Thus, presence/absence patterns of Alu retrotransposons and, presumably, all LINE1-mobilized elements represent indeed the virtually homoplasy-free markers they are considered to be. Therefore, ancestral incomplete lineage sorting and hybridization remain the only serious sources of conflicting presence/absence patterns of retrotransposon insertions, and as such are detectable and quantifiable. [Homoplasy; precise deletions; precise parallel insertions; primates; retrotransposons.].
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Olga Reising
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, 2901 Main Street, Lubbock, TX, USA
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
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