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Chimpanzee OR gorilla AND genome

Bret M Boyd, Julie M Allen, Nam-Phuong Nguyen, Pranjal Vachaspati, Zach 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...
April 14, 2017: Molecular Biology and Evolution
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
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...
March 22, 2017: Immunogenetics
Peter Rotwein
Insulin-like growth factor 1 (IGF1) is a multifunctional peptide that is involved in a wide range of physiological and pathophysiological processes in many animal species, ranging from somatic growth in children to metabolism and tissue regeneration and repair in adults. The IGF1 gene is under multifactorial regulation in the few species in which it has been studied, with major control being exerted by growth hormone through a gene expression pathway involving inducible binding of the STAT5b transcription factor to dispersed enhancer elements...
April 1, 2017: Endocrinology
Pille Hallast, Mark A Jobling
The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome...
March 6, 2017: Human Genetics
Zhongbo Chen, Kuang Lin, Jeffrey D Macklis, Ammar Al-Chalabi
OBJECTIVE: Amyotrophic lateral sclerosis (ALS) is a fatal disease caused by motor neuron and sub-cerebral projection neuron degeneration. We sought to explore the particular susceptibility of humans to neurodegeneration and whether any characteristic human features might predispose to selective vulnerability of the critical motor circuitry in ALS. The pathophysiology of the C9orf72 repeat is not yet understood, despite its role as a common cause of ALS and frontotemporal dementia. METHODS: We examined the development of the monosynaptic cortico-motoneuronal system, key to skilled hand movements, measured by the thumb opposability index, and its relationship to the C9orf72 hexanucleotide repeat expansion, a strong predisposing factor for neurodegeneration, using the genomic tool BLAST...
December 23, 2016: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration
Martin Kuhlwilm, Marc de Manuel, Alexander Nater, Maja P Greminger, Michael Krützen, Tomas Marques-Bonet
The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics...
December 2016: Current Opinion in Genetics & Development
Kym S Antonation, Kim Grützmacher, Susann Dupke, Philip Mabon, Fee Zimmermann, Felix Lankester, Tianna Peller, Anna Feistner, Angelique Todd, Ilka Herbinger, Hélène M de Nys, Jean-Jacques Muyembe-Tamfun, Stomy Karhemere, Roman M Wittig, Emmanuel Couacy-Hymann, Roland Grunow, Sébastien Calvignac-Spencer, Cindi R Corbett, Silke R Klee, Fabian H Leendertz
Through full genome analyses of four atypical Bacillus cereus isolates, designated B. cereus biovar anthracis, we describe a distinct clade within the B. cereus group that presents with anthrax-like disease, carrying virulence plasmids similar to those of classic Bacillus anthracis. We have isolated members of this clade from different mammals (wild chimpanzees, gorillas, an elephant and goats) in West and Central Africa (Côte d'Ivoire, Cameroon, Central African Republic and Democratic Republic of Congo). The isolates shared several phenotypic features of both B...
September 2016: PLoS Neglected Tropical Diseases
Priya Moorjani, Carlos Eduardo G Amorim, Peter F Arndt, Molly Przeworski
Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites...
September 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
Andrew H Moeller, Alejandro Caro-Quintero, Deus Mjungu, Alexander V Georgiev, Elizabeth V Lonsdorf, Martin N Muller, Anne E Pusey, Martine Peeters, Beatrice H Hahn, Howard Ochman
The evolutionary origins of the bacterial lineages that populate the human gut are unknown. Here we show that multiple lineages of the predominant bacterial taxa in the gut arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over the past 15 million years. Analyses of strain-level bacterial diversity within hominid gut microbiomes revealed that clades of Bacteroidaceae and Bifidobacteriaceae have been maintained exclusively within host lineages across hundreds of thousands of host generations...
July 22, 2016: Science
Igor Rodrigues Costa, Francisco Prosdocimi, W Bryan Jennings
The increasing availability of complete genome data is facilitating the acquisition of phylogenomic data sets, but the process of obtaining orthologous sequences from other genomes and assembling multiple sequence alignments remains piecemeal and arduous. We designed software that performs these tasks and outputs anonymous loci (AL) or anchored enrichment/ultraconserved element loci (AE/UCE) data sets in ready-to-analyze formats. We demonstrate our program by applying it to the hominoids. Starting with human, chimpanzee, gorilla, and orangutan genomes, our software generated an exhaustive data set of 292 ALs (∼1 kb each) in ∼3 h...
September 2016: Genome Research
Dorothy E Loy, Weimin Liu, Yingying Li, Gerald H Learn, Lindsey J Plenderleith, Sesh A Sundararaman, Paul M Sharp, Beatrice H Hahn
Plasmodium falciparum and Plasmodium vivax account for more than 95% of all human malaria infections, and thus pose a serious public health challenge. To control and potentially eliminate these pathogens, it is important to understand their origins and evolutionary history. Until recently, it was widely believed that P. falciparum had co-evolved with humans (and our ancestors) over millions of years, whilst P. vivax was assumed to have emerged in southeastern Asia following the cross-species transmission of a parasite from a macaque...
February 2017: International Journal for Parasitology
Weimin Liu, Sesh A Sundararaman, Dorothy E Loy, Gerald H Learn, Yingying Li, Lindsey J Plenderleith, Jean-Bosco N Ndjango, Sheri Speede, Rebeca Atencia, Debby Cox, George M Shaw, Ahidjo Ayouba, Martine Peeters, Julian C Rayner, Beatrice H Hahn, Paul M Sharp
Plasmodium falciparum, the major cause of malaria morbidity and mortality worldwide, is only distantly related to other human malaria parasites and has thus been placed in a separate subgenus, termed Laverania Parasites morphologically similar to P. falciparum have been identified in African apes, but only one other Laverania species, Plasmodium reichenowi from chimpanzees, has been formally described. Although recent studies have pointed to the existence of additional Laverania species, their precise number and host associations remain uncertain, primarily because of limited sampling and a paucity of parasite sequences other than from mitochondrial DNA...
July 2, 2016: Genome Biology and Evolution
Alicia Gallego, Marta Melé, Ingrid Balcells, Eva García-Ramallo, Ignasi Torruella-Loran, Hugo Fernández-Bellon, Teresa Abelló, Ivanela Kondova, Ronald Bontrop, Christina Hvilsom, Arcadi Navarro, Tomàs Marquès-Bonet, Yolanda Espinosa-Parrilla
microRNAs are crucial post-transcriptional regulators of gene expression involved in a wide range of biological processes. Although microRNAs are highly conserved among species, the functional implications of existing lineage-specific changes and their role in determining differences between humans and other great apes have not been specifically addressed. We analyzed the recent evolutionary history of 1,595 human microRNAs by looking at their intra- and inter-species variation in great apes using high-coverage sequenced genomes of 82 individuals including gorillas, orangutans, bonobos, chimpanzees and humans...
2016: PloS One
Daniele Guerzoni, Aoife McLysaght
De novo protein-coding gene origination is increasingly recognized as an important evolutionary mechanism. However, there remains a large amount of uncertainty regarding the frequency of these events and the mechanisms and speed of gene establishment. Here, we describe a rigorous search for cases of de novo gene origination in the great apes. We analyzed annotated proteomes as well as full genomic DNA and transcriptional and translational evidence. It is notable that results vary between database updates due to the fluctuating annotation of these genes...
April 25, 2016: Genome Biology and Evolution
Marta Tomaszkiewicz, Samarth Rangavittal, Monika Cechova, Rebeca Campos Sanchez, Howard W Fescemyer, Robert Harris, Danling Ye, Patricia C M O'Brien, Rayan Chikhi, Oliver A Ryder, Malcolm A Ferguson-Smith, Paul Medvedev, Kateryna D Makova
The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications...
April 2016: Genome Research
Kyoungwoo Nam, Heesu Jeong, Jin-Wu Nam
High-throughput RNA sequencing (RNA-seq) provides a comprehensive picture of the transcriptome, including the identity, structure, quantity, and variability of expressed transcripts in cells, through the assembly of sequenced short RNA-seq reads. Although the reference-based approach guarantees the high quality of the resulting transcriptome, this approach is only applicable when the relevant reference genome is present. Here, we developed a pseudo-reference-based assembly (PRA) that reconstructs a transcriptome based on a linear regression function of the optimized mapping parameters and genetic distances of the closest species...
2016: Genes
Pille Hallast, Pierpaolo Maisano Delser, Chiara Batini, Daniel Zadik, Mariano Rocchi, Werner Schempp, Chris Tyler-Smith, Mark A Jobling
The distribution of genetic diversity in great ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2...
April 2016: Genome Research
Takashi Kitano, Choong-Gon Kim, Antoine Blancher, Naruya Saitou
On human (Homo sapiens) chromosome 1, there is a tandem duplication encompassing Rh blood group genes (Hosa_RHD and Hosa_RHCE). This duplication occurred in the common ancestor of humans, chimpanzees (Pan troglodytes), and gorillas, after splitting from their common ancestor with orangutans. Although several studies have been conducted on ape Rh blood group genes, the clear genome structures of the gene clusters remain unknown. Here, we determined the genome structure of the gene cluster of chimpanzee Rh genes by sequencing five BAC (Bacterial Artificial Chromosome) clones derived from chimpanzees...
February 12, 2016: Genome Biology and Evolution
Margaret Littlejohn, Stephen Locarnini, Lilly Yuen
Members of the family Hepadnaviridae fall into two subgroups: mammalian and avian. The detection of endogenous avian hepadnavirus DNA integrated into the genomes of zebra finches has revealed a deep evolutionary origin of hepadnaviruses that was not previously recognized, dating back at least 40 million and possibly >80 million years ago. The nonprimate mammalian members of the Hepadnaviridae include the woodchuck hepatitis virus (WHV), the ground squirrel hepatitis virus, and arctic squirrel hepatitis virus, as well as a number of members of the recently described bat hepatitis virus...
January 4, 2016: Cold Spring Harbor Perspectives in Medicine
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