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https://www.readbyqxmd.com/read/30256937/high-order-formation-and-evolution-of-hornerin-in-primates
#1
Vanessa Romero, Hirofumi Nakaoka, Kazuyoshi Hosomichi, Ituro Inoue
Genomic duplication or loss can accelerate evolution because the number of repeats could affect molecular pathways and phenotypes. We have previously reported that the repeated region of filaggrin (FLG), a crucial component of the outer layers of mammalian skin, had high levels of nucleotide diversity with species-specific divergence and expansion and that it evolved under the birth-and-death model. We focused on hornerin (HRNR), a member of the same gene family that harbor similar tandem repeats as FLG, and examined the formation process of repeated regions and the evolutional model that best fit the HRNR repeated region in the crab-eating macaque (Macaca fascicularis), orangutan (Pongo abelii), gorilla (Gorilla gorilla), and chimpanzee (Pan troglodytes) and compared them with the human (Homo sapiens) sequence...
September 26, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/30237828/phylogenomic-analysis-reveals-splicing-as-a-mechanism-of-parallel-evolution-of-non-canonical-svas-in-hominine-primates
#2
Annette Damert
SVA (SINE-R-VNTR- Alu ) elements are non-autonomous non-LTR (Long Terminal Repeat) retrotransposons. They are found in all hominoid primates but did not amplify to appreciable numbers in gibbons. Recently, phylogenetic networks of hominid (orangutan, gorilla, chimpanzee, human) SVA elements based on comparison of overall sequence identity have been reported. Here I present a detailed phylogeny of SVA_D elements in gorilla, chimpanzee and humans based on sorting of co-segregating substitutions. Complementary comparative genomics analysis revealed that the majority (1763 out of 1826-97%) of SVA_D elements in gorilla represent species-specific insertions - indicating very low activity of the subfamily before the gorilla/chimpanzee-human split...
2018: Mobile DNA
https://www.readbyqxmd.com/read/30127015/evolutionary-history-of-human-plasmodium-vivax-revealed-by-genome-wide-analyses-of-related-ape-parasites
#3
Dorothy E Loy, Lindsey J Plenderleith, Sesh A Sundararaman, Weimin Liu, Jakub Gruszczyk, Yi-Jun Chen, Stephanie Trimboli, Gerald H Learn, Oscar A MacLean, Alex L K Morgan, Yingying Li, Alexa N Avitto, Jasmin Giles, Sébastien Calvignac-Spencer, Andreas Sachse, Fabian H Leendertz, Sheri Speede, Ahidjo Ayouba, Martine Peeters, Julian C Rayner, Wai-Hong Tham, Paul M Sharp, Beatrice H Hahn
Wild-living African apes are endemically infected with parasites that are closely related to human Plasmodium vivax , a leading cause of malaria outside Africa. This finding suggests that the origin of P. vivax was in Africa, even though the parasite is now rare in humans there. To elucidate the emergence of human P. vivax and its relationship to the ape parasites, we analyzed genome sequence data of P. vivax strains infecting six chimpanzees and one gorilla from Cameroon, Gabon, and Côte d'Ivoire. We found that ape and human parasites share nearly identical core genomes, differing by only 2% of coding sequences...
September 4, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30126415/promoter-expression-of-herv-k-hml-2-provirus-derived-sequences-is-related-to-ltr-sequence-variation-and-polymorphic-transcription-factor-binding-sites
#4
Meagan Montesion, Zachary H Williams, Ravi P Subramanian, Charlotte Kuperwasser, John M Coffin
BACKGROUND: Increased transcription of the human endogenous retrovirus group HERV-K (HML-2) is often seen during disease. Although the mechanism of its tissue-specific activation is unclear, research shows that LTR CpG hypomethylation alone is not sufficient to induce its promoter activity and that the transcriptional milieu of a malignant cell contributes, at least partly, to differential HML-2 expression. RESULTS: We analyzed the relationship between LTR sequence variation and promoter expression patterns in human breast cancer cell lines, finding them to be positively correlated...
August 20, 2018: Retrovirology
https://www.readbyqxmd.com/read/29897475/developmental-loci-harbor-clusters-of-accelerated-regions-that-evolved-independently-in-ape-lineages
#5
Dennis Kostka, Alisha K Holloway, Katherine S Pollard
Some of the fastest evolving regions of the human genome are conserved noncoding elements with many human-specific DNA substitutions. These human accelerated regions (HARs) are enriched nearby regulatory genes, and several HARs function as developmental enhancers. To investigate if this evolutionary signature is unique to humans, we quantified evidence of accelerated substitutions in conserved genomic elements across multiple lineages and applied this approach simultaneously to the genomes of five apes: human, chimpanzee, gorilla, orangutan, and gibbon...
August 1, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29880660/high-resolution-comparative-analysis-of-great-ape-genomes
#6
COMPARATIVE STUDY
Zev N Kronenberg, Ian T Fiddes, David Gordon, Shwetha Murali, Stuart Cantsilieris, Olivia S Meyerson, Jason G Underwood, Bradley J Nelson, Mark J P Chaisson, Max L Dougherty, Katherine M Munson, Alex R Hastie, Mark Diekhans, Fereydoun Hormozdiari, Nicola Lorusso, Kendra Hoekzema, Ruolan Qiu, Karen Clark, Archana Raja, AnneMarie E Welch, Melanie Sorensen, Carl Baker, Robert S Fulton, Joel Armstrong, Tina A Graves-Lindsay, Ahmet M Denli, Emma R Hoppe, PingHsun Hsieh, Christopher M Hill, Andy Wing Chun Pang, Joyce Lee, Ernest T Lam, Susan K Dutcher, Fred H Gage, Wesley C Warren, Jay Shendure, David Haussler, Valerie A Schneider, Han Cao, Mario Ventura, Richard K Wilson, Benedict Paten, Alex Pollen, Evan E Eichler
Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants...
June 8, 2018: Science
https://www.readbyqxmd.com/read/29784978/genomes-of-all-known-members-of-a-plasmodium-subgenus-reveal-paths-to-virulent-human-malaria
#7
Thomas D Otto, Aude Gilabert, Thomas Crellen, Ulrike Böhme, Céline Arnathau, Mandy Sanders, Samuel O Oyola, Alain Prince Okouga, Larson Boundenga, Eric Willaume, Barthélémy Ngoubangoye, Nancy Diamella Moukodoum, Christophe Paupy, Patrick Durand, Virginie Rougeron, Benjamin Ollomo, François Renaud, Chris Newbold, Matthew Berriman, Franck Prugnolle
Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite Plasmodium praefalciparum. Little is known about the other gorilla- and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum, but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species...
June 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29563166/repeat-associated-mechanisms-of-genome-evolution-and-function-revealed-by-the-mus-caroli-and-mus-pahari-genomes
#8
David Thybert, Maša Roller, Fábio C P Navarro, Ian Fiddes, Ian Streeter, Christine Feig, David Martin-Galvez, Mikhail Kolmogorov, Václav Janoušek, Wasiu Akanni, Bronwen Aken, Sarah Aldridge, Varshith Chakrapani, William Chow, Laura Clarke, Carla Cummins, Anthony Doran, Matthew Dunn, Leo Goodstadt, Kerstin Howe, Matthew Howell, Ambre-Aurore Josselin, Robert C Karn, Christina M Laukaitis, Lilue Jingtao, Fergal Martin, Matthieu Muffato, Stefanie Nachtweide, Michael A Quail, Cristina Sisu, Mario Stanke, Klara Stefflova, Cock Van Oosterhout, Frederic Veyrunes, Ben Ward, Fengtang Yang, Golbahar Yazdanifar, Amonida Zadissa, David J Adams, Alvis Brazma, Mark Gerstein, Benedict Paten, Son Pham, Thomas M Keane, Duncan T Odom, Paul Flicek
Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae...
April 2018: Genome Research
https://www.readbyqxmd.com/read/29518153/species-specific-vulnerability-of-ranbp2-shaped-the-evolution-of-siv-as-it-transmitted-in-african-apes
#9
Nicholas R Meyerson, Cody J Warren, Daniel A S A Vieira, Felipe Diaz-Griferro, Sara L Sawyer
HIV-1 arose as the result of spillover of simian immunodeficiency viruses (SIVs) from great apes in Africa, namely from chimpanzees and gorillas. Chimpanzees and gorillas were, themselves, infected with SIV after virus spillover from African monkeys. During spillover events, SIV is thought to require adaptation to the new host species. The host barriers that drive viral adaptation have predominantly been attributed to restriction factors, rather than cofactors (host proteins exploited to promote viral replication)...
March 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29351742/herv-w-group-evolutionary-history-in-non-human-primates-characterization-of-erv-w-orthologs-in-catarrhini-and-related-erv-groups-in-platyrrhini
#10
Nicole Grandi, Marta Cadeddu, Jonas Blomberg, Jens Mayer, Enzo Tramontano
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...
January 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29259021/evolutionary-expansion-of-dna-hypomethylation-in-the-mammalian-germline-genome
#11
Jianghan Qu, Emily Hodges, Antoine Molaro, Pascal Gagneux, Matthew D Dean, Gregory J Hannon, Andrew D Smith
DNA methylation in the germline is among the most important factors influencing the evolution of mammalian genomes. Yet little is known about its evolutionary rate or the fraction of the methylome that has undergone change. We compared whole-genome, single-CpG DNA methylation profiles in sperm of seven species-human, chimpanzee, gorilla, rhesus macaque, mouse, rat, and dog-to investigate epigenomic evolution. We developed a phylo-epigenetic model for DNA methylation that accommodates the correlation of states at neighboring sites and allows for inference of ancestral states...
February 2018: Genome Research
https://www.readbyqxmd.com/read/29103940/morphometric-behavioral-and-genomic-evidence-for-a-new-orangutan-species
#12
Alexander Nater, Maja P Mattle-Greminger, Anton Nurcahyo, Matthew G Nowak, Marc de Manuel, Tariq Desai, Colin Groves, Marc Pybus, Tugce Bilgin Sonay, Christian Roos, Adriano R Lameira, Serge A Wich, James Askew, Marina Davila-Ross, Gabriella Fredriksson, Guillem de Valles, Ferran Casals, Javier Prado-Martinez, Benoit Goossens, Ernst J Verschoor, Kristin S Warren, Ian Singleton, David A Marques, Joko Pamungkas, Dyah Perwitasari-Farajallah, Puji Rianti, Augustine Tuuga, Ivo G Gut, Marta Gut, Pablo Orozco-terWengel, Carel P van Schaik, Jaume Bertranpetit, Maria Anisimova, Aylwyn Scally, Tomas Marques-Bonet, Erik Meijaard, Michael Krützen
Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P...
November 20, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29101448/discovery-of-gorilla-mhc-c-expressing-c1-ligand-for-kir
#13
Jörg B Hans, Linda Vigilant
In comparison to humans and chimpanzees, gorillas show low diversity at MHC class I genes (Gogo), as reflected by an overall reduced level of allelic variation as well as the absence of a functionally important sequence motif that interacts with killer cell immunoglobulin-like receptors (KIR). Here, we use recently generated large-scale genomic sequence data for a reassessment of allelic diversity at Gogo-C, the gorilla orthologue of HLA-C. Through the combination of long-range amplifications and long-read sequencing technology, we obtained, among the 35 gorillas reanalyzed, three novel full-length genomic sequences including a coding region sequence that has not been previously described...
May 2018: Immunogenetics
https://www.readbyqxmd.com/read/28959963/parental-influence-on-human-germline-de-novo-mutations-in-1-548-trios-from-iceland
#14
Hákon Jónsson, Patrick Sulem, Birte Kehr, Snaedis Kristmundsdottir, Florian Zink, Eirikur Hjartarson, Marteinn T Hardarson, Kristjan E Hjorleifsson, Hannes P Eggertsson, Sigurjon Axel Gudjonsson, Lucas D Ward, Gudny A Arnadottir, Einar A Helgason, Hannes Helgason, Arnaldur Gylfason, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Thorunn Rafnar, Mike Frigge, Simon N Stacey, Olafur Th Magnusson, Unnur Thorsteinsdottir, Gisli Masson, Augustine Kong, Bjarni V Halldorsson, Agnar Helgason, Daniel F Gudbjartsson, Kari Stefansson
The characterization of mutational processes that generate sequence diversity in the human genome is of paramount importance both to medical genetics and to evolutionary studies. To understand how the age and sex of transmitting parents affect de novo mutations, here we sequence 1,548 Icelanders, their parents, and, for a subset of 225, at least one child, to 35× genome-wide coverage. We find 108,778 de novo mutations, both single nucleotide polymorphisms and indels, and determine the parent of origin of 42,961...
September 28, 2017: Nature
https://www.readbyqxmd.com/read/28675688/whole-mitochondrial-genome-capture-from-faecal-samples-and-museum-preserved-specimens
#15
Tom van der Valk, Frida Lona Durazo, Love Dalén, Katerina Guschanski
Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee...
November 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28672035/modern-day-siv-viral-diversity-generated-by-extensive-recombination-and-cross-species-transmission
#16
Sidney M Bell, Trevor Bedford
Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic approach to better understand the natural history of SIV recombination and CST...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28633494/silencing-effect-of-hominoid-highly-conserved-noncoding-sequences-on-embryonic-brain-development
#17
Morteza Mahmoudi Saber, Naruya Saitou
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes...
August 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28419279/primates-lice-and-bacteria-speciation-and-genome-evolution-in-the-symbionts-of-hominid-lice
#18
Bret M Boyd, Julie M Allen, Nam-Phuong Nguyen, Pranjal Vachaspati, Zachary S Quicksall, Tandy Warnow, Lawrence Mugisha, Kevin P Johnson, David L Reed
Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement...
July 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28348269/bonobos-maintain-immune-system-diversity-with-three-functional-types-of-mhc-b
#19
COMPARATIVE STUDY
Emily E Wroblewski, Lisbeth A Guethlein, Paul J Norman, Yingying Li, Christiana M Shaw, Alex S Han, Jean-Bosco N Ndjango, Steve Ahuka-Mundeke, Alexander V Georgiev, Martine Peeters, Beatrice H Hahn, Peter Parham
Fast-evolving MHC class I polymorphism serves to diversify NK cell and CD8 T cell responses in individuals, families, and populations. Because only chimpanzee and bonobo have strict orthologs of all HLA class I , their study gives unique perspectives on the human condition. We defined polymorphism of Papa-B , the bonobo ortholog of HLA-B , for six wild bonobo populations. Sequences for Papa-B exon 2 and 3 were determined from the genomic DNA in 255 fecal samples, minimally representing 110 individuals. Twenty-two Papa-B alleles were defined, each encoding a different Papa-B protein...
May 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28332079/gorilla-mhc-class-i-gene-and-sequence-variation-in-a-comparative-context
#20
COMPARATIVE STUDY
Jörg B Hans, Richard A Bergl, Linda Vigilant
Comparisons of MHC gene content and diversity among closely related species can provide insights into the evolutionary mechanisms shaping immune system variation. After chimpanzees and bonobos, gorillas are humans' closest living relatives; but in contrast, relatively little is known about the structure and variation of gorilla MHC class I genes (Gogo). Here, we combined long-range amplifications and long-read sequencing technology to analyze full-length MHC class I genes in 35 gorillas. We obtained 50 full-length genomic sequences corresponding to 15 Gogo-A alleles, 4 Gogo-Oko alleles, 21 Gogo-B alleles, and 10 Gogo-C alleles including 19 novel coding region sequences...
May 2017: Immunogenetics
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