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Chimpanzee OR gorilla AND genome

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...
October 4, 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...
July 2, 2016: 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...
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...
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...
March 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 2016: Cold Spring Harbor Perspectives in Medicine
Laurie S Stevison, August E Woerner, Jeffrey M Kidd, Joanna L Kelley, Krishna R Veeramah, Kimberly F McManus, Carlos D Bustamante, Michael F Hammer, Jeffrey D Wall
We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths...
April 2016: Molecular Biology and Evolution
Kristýna Brožová, Kristýna Hrazdilová, Eva Slaninková, David Modrý, Jiří Černý, Vladimír Celer
Primate bocaparvoviruses were first described in 2005, since then further human and gorilla bocaparvoviruses have been identified. To uncover diversity of non-human primates' bocaparvoviruses, their phylogenetic relationship and potential to cross the host species barrier, we tested 153 fecal samples from 17 captive primate species. The only one captive female of central chimpanzee (coded CPZh2) has been identified as bocaparvovirus positive. Based on the full genome phylogenetic analyses, CPZh2 strain shows close relationship to HBoV3 and GBoV...
January 2016: Infection, Genetics and Evolution
Kristýna Hrazdilová, Eva Slaninková, Kristýna Brožová, David Modrý, Roman Vodička, Vladimír Celer
Anelloviridae family is comprised of small, non-enveloped viruses of various genome lengths, high sequence diversity, sharing the same genome organization. Infections and co-infections by different genotypes in humans are ubiquitous. Related viruses were described in number of mammalian hosts, but very limited data are available from the closest human relatives - great apes and non-human primates. Here we report the 100% prevalence determined by semi-nested PCR from fecal samples of 16 captive primate species...
January 2016: Virology
Daiki Okada, Fumihiko Ino, Kenichi Hagihara
BACKGROUND: The Smith-Waterman algorithm is known to be a more sensitive approach than heuristic algorithms for local sequence alignment algorithms. Despite its sensitivity, a greater time complexity associated with the Smith-Waterman algorithm prevents its application to the all-pairs comparisons of base sequences, which aids in the construction of accurate phylogenetic trees. The aim of this study is to achieve greater acceleration using the Smith-Waterman algorithm (by realizing interpair block pruning and band optimization) compared with that achieved using a previous method that performs intrapair block pruning on graphics processing units (GPUs)...
2015: BMC Bioinformatics
Jessica L Joganic
OBJECTIVES: Non-human primate growth trajectories are often used to estimate the age and life history traits of fossil taxa. The exclusive use of chimpanzee growth patterns to estimate developmental stages for the earliest hominins is problematic because incomplete lineage sorting in the hominoid clade has produced a mosaic human genome that contains different regions shared with any one of the great apes. The accidental death of a sub-adult male western lowland gorilla (Gorilla gorilla gorilla) provides not only an opportunity to compare the degree of dentoskeletal maturation in this individual with published data from conspecifics, but also insight into gorilla growth and development as it applies to modeling that of early hominins...
January 2016: American Journal of Physical Anthropology
Eileen Hoppe, Maude Pauly, Martha Robbins, Maryke Gray, Deo Kujirakwinja, Radar Nishuli, Dieu-Donné Boji Mungu-Akonkwa, Fabian H Leendertz, Bernhard Ehlers
Human adenoviruses (HAdVs) of species Human mastadenovirus B (HAdV-B) are genetically highly diverse and comprise several pathogenic types. AdVs closely related to members of HAdV-B infect African great apes and the evolutionary origin of HAdV-B has recently been determined in ancient gorillas. Genetic evidence for intra- and inter-species recombination has been obtained for AdVs of humans and captive great apes, but evidence from wild great apes is lacking. In this study, potential HAdV-B members of wild Eastern gorillas were analysed for evidence of recombination...
October 2015: Journal of General Virology
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