keyword
https://read.qxmd.com/read/34542594/frequent-lineage-specific-substitution-rate-changes-support-an-episodic-model-for-protein-evolution
#21
JOURNAL ARTICLE
Neel Prabh, Diethard Tautz
Since the inception of the molecular clock model for sequence evolution, the investigation of protein divergence has revolved around the question of a more or less constant change of amino acid sequences, with specific overall rates for each family. Although anomalies in clock-like divergence are well known, the assumption of a constant decay rate for a given protein family is usually taken as the null model for protein evolution. However, systematic tests of this null model at a genome-wide scale have lagged behind, despite the databases' enormous growth...
December 8, 2021: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/34456962/current-progress-in-evolutionary-comparative-genomics-of-great-apes
#22
REVIEW
Aisha Yousaf, Junfeng Liu, Sicheng Ye, Hua Chen
The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.
2021: Frontiers in Genetics
https://read.qxmd.com/read/34406591/a-comprehensive-analysis-of-gorilla-specific-line-1-retrotransposons
#23
JOURNAL ARTICLE
Soyeon Jeon, Songmi Kim, Man Hwan Oh, Ping Liang, Wanxiangfu Tang, Kyudong Han
BACKGROUND: Long interspersed element-1 (LINE-1 or L1) is the most abundant retrotransposons in the primate genome. They have approximately 520,000 copies and make up ~ 17% of the primate genome. Full-length L1s can mobilize to a new genomic location using their enzymatic machinery. Gorilla is the second closest species to humans after the chimpanzee, and human-gorilla split 7-12 million years ago. The gorilla genome provides an opportunity to explore primate origins and evolution...
October 2021: Genes & Genomics
https://read.qxmd.com/read/34328525/spectrum-of-protein-location-in-proteomes-captures-evolutionary-relationship-between-species
#24
JOURNAL ARTICLE
Valérie Marot-Lassauzaie, Tatyana Goldberg, Jose Juan Almagro Armenteros, Henrik Nielsen, Burkhard Rost
The native subcellular location (also referred to as localization or cellular compartment) of a protein is the one in which it acts most frequently; it is one aspect of protein function. Do ten eukaryotic model organisms differ in their location spectrum, i.e., the fraction of its proteome in each of seven major cellular compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data...
October 2021: Journal of Molecular Evolution
https://read.qxmd.com/read/34081117/population-dynamics-of-gc-changing-mutations-in-humans-and-great-apes
#25
JOURNAL ARTICLE
Juraj Bergman, Mikkel Heide Schierup
The nucleotide composition of the genome is a balance between the origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms...
July 14, 2021: Genetics
https://read.qxmd.com/read/34035253/epigenomic-profiling-of-primate-lymphoblastoid-cell-lines-reveals-the-evolutionary-patterns-of-epigenetic-activities-in-gene-regulatory-architectures
#26
JOURNAL ARTICLE
Raquel García-Pérez, Paula Esteller-Cucala, Glòria Mas, Irene Lobón, Valerio Di Carlo, Meritxell Riera, Martin Kuhlwilm, Arcadi Navarro, Antoine Blancher, Luciano Di Croce, José Luis Gómez-Skarmeta, David Juan, Tomàs Marquès-Bonet
Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ChIP-seq for five histone marks, ATAC-seq and RNA-seq, further complemented with whole genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS). We annotated regulatory elements (RE) and integrated chromatin contact maps to define gene regulatory architectures, creating the largest catalog of RE in primates to date...
May 25, 2021: Nature Communications
https://read.qxmd.com/read/33953399/a-high-quality-bonobo-genome-refines-the-analysis-of-hominid-evolution
#27
COMPARATIVE STUDY
Yafei Mao, Claudia R Catacchio, LaDeana W Hillier, David Porubsky, Ruiyang Li, Arvis Sulovari, Jason D Fernandes, Francesco Montinaro, David S Gordon, Jessica M Storer, Marina Haukness, Ian T Fiddes, Shwetha Canchi Murali, Philip C Dishuck, PingHsun Hsieh, William T Harvey, Peter A Audano, Ludovica Mercuri, Ilaria Piccolo, Francesca Antonacci, Katherine M Munson, Alexandra P Lewis, Carl Baker, Jason G Underwood, Kendra Hoekzema, Tzu-Hsueh Huang, Melanie Sorensen, Jerilyn A Walker, Jinna Hoffman, Françoise Thibaud-Nissen, Sofie R Salama, Andy W C Pang, Joyce Lee, Alex R Hastie, Benedict Paten, Mark A Batzer, Mark Diekhans, Mario Ventura, Evan E Eichler
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2 . Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements...
June 2021: Nature
https://read.qxmd.com/read/33753927/hovlinc-is-a-recently-evolved-class-of-ribozyme-found-in-human-lncrna
#28
JOURNAL ARTICLE
Yue Chen, Fei Qi, Fan Gao, Huifen Cao, Dongyang Xu, Kourosh Salehi-Ashtiani, Philipp Kapranov
Although naturally occurring catalytic RNA molecules-ribozymes-have attracted a great deal of research interest, very few have been identified in humans. Here, we developed a genome-wide approach to discovering self-cleaving ribozymes and identified a naturally occurring ribozyme in humans. The secondary structure and biochemical properties of this ribozyme indicate that it belongs to an unidentified class of small, self-cleaving ribozymes. The sequence of the ribozyme exhibits a clear evolutionary path, from its appearance between ~130 and ~65 million years ago (Ma), to acquiring self-cleavage activity very recently, ~13-10 Ma, in the common ancestors of humans, chimpanzees and gorillas...
May 2021: Nature Chemical Biology
https://read.qxmd.com/read/33681998/higher-rates-of-processed-pseudogene-acquisition-in-humans-and-three-great-apes-revealed-by-long-read-assemblies
#29
JOURNAL ARTICLE
Xiaowen Feng, Heng Li
LINE-1-mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes. Prior works that surveyed human data mostly relied on detecting discordant mappings of paired-end short reads, or exon junctions contained in short reads. Moreover, there have been few genome-wide comparisons between gene retrocopies in great apes and humans. In this study, we introduced a more sensitive and accurate method to identify processed pseudogenes. Our method utilizes long-read assemblies, and more importantly, is able to provide full-length retrocopy sequences as well as flanking regions which are missed by short-read based methods...
June 25, 2021: Molecular Biology and Evolution
https://read.qxmd.com/read/33575633/characterization-of-nuclear-mitochondrial-insertions-in-the-whole-genomes-of-primates
#30
JOURNAL ARTICLE
Gargi Dayama, Weichen Zhou, Javier Prado-Martinez, Tomas Marques-Bonet, Ryan E Mills
The transfer and integration of whole and partial mitochondrial genomes into the nuclear genomes of eukaryotes is an ongoing process that has facilitated the transfer of genes and contributed to the evolution of various cellular pathways. Many previous studies have explored the impact of these insertions, referred to as NumtS, but have focused primarily on older events that have become fixed and are therefore present in all individual genomes for a given species. We previously developed an approach to identify novel Numt polymorphisms from next-generation sequence data and applied it to thousands of human genomes...
December 2020: NAR genomics and bioinformatics
https://read.qxmd.com/read/33454958/elevated-diversity-in-loci-linked-to-facial-morphology-is-consistent-with-the-hypothesis-that-individual-facial-recognition-is-important-across-hominoids
#31
JOURNAL ARTICLE
Michael E Steiper, Natalia T Grube, Christian M Gagnon
OBJECTIVES: The ability to use visual signals to identify individuals is an important feature of primate social groups, including humans. Sheehan and Nachman (2014) showed that loci linked to facial morphology had elevated levels of diversity and interpreted this as evidence that the human face is under frequency-dependent selection to enhance individual recognition (Nature Communications 5). In our study, we tested whether this pattern is found in non-human ape species, to help understand whether individual recognition might also play a role in species other than humans...
April 2021: American Journal of Physical Anthropology
https://read.qxmd.com/read/33207801/site-specific-evolutionary-rate-shifts-in-hiv-1-and-siv
#32
JOURNAL ARTICLE
Maoz Gelbart, Adi Stern
Site-specific evolutionary rate shifts are defined as protein sites, where the rate of substitution has changed dramatically across the phylogeny. With respect to a given clade, sites may either undergo a rate acceleration or a rate deceleration, reflecting a site that was conserved and became variable, or vice-versa, respectively. Sites displaying such a dramatic evolutionary change may point to a loss or gain of function at the protein site, reflecting adaptation, or they may indicate epistatic interactions among sites...
November 16, 2020: Viruses
https://read.qxmd.com/read/33202777/enteroviruses-from-humans-and-great-apes-in-the-republic-of-congo-recombination-within-enterovirus-c-serotypes
#33
JOURNAL ARTICLE
Inestin Amona, Hacène Medkour, Jean Akiana, Bernard Davoust, Mamadou Lamine Tall, Clio Grimaldier, Celine Gazin, Christine Zandotti, Anthony Levasseur, Bernard La Scola, Didier Raoult, Florence Fenollar, Henri Banga-Mboko, Oleg Mediannikov
Enteroviruses (EVs) are viruses of the family Picornaviridae that cause mild to severe infections in humans and in several animal species, including non-human primates (NHPs). We conducted a survey and characterization of enteroviruses circulating between humans and great apes in the Congo. Fecal samples (N = 24) of gorillas and chimpanzees living close to or distant from humans in three Congolese parks were collected, as well as from healthy humans (N = 38) living around and within these parks. Enteroviruses were detected in 29...
November 13, 2020: Microorganisms
https://read.qxmd.com/read/33020265/dynamic-evolution-of-great-ape-y-chromosomes
#34
JOURNAL ARTICLE
Monika Cechova, Rahulsimham Vegesna, Marta Tomaszkiewicz, Robert S Harris, Di Chen, Samarth Rangavittal, Paul Medvedev, Kateryna D Makova
The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee share a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera...
October 20, 2020: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/32939517/medical-genomic-and-evolutionary-aspects-of-the-peptide-sharing-between-pathogens-primates-and-humans
#35
JOURNAL ARTICLE
Darja Kanduc, Yehuda Shoenfeld
Comparing mammalian proteomes for molecular mimicry with infectious pathogens highlights the highest levels of heptapeptide sharing between pathogens and human, murine, and rat proteomes, while the peptide sharing level is minimal (or absent) with proteomes from nonhuman primates such as gorilla, chimpanzee, and rhesus macaque. From the medical point of view, the data might be useful to clinicians and vaccinologists to develop and evaluate immunomodulatory and immunotherapeutic approaches. As a matter of fact, primates seem to be unreliable animal models for revealing potential autoimmune events in preclinical testing of immunotherapies...
August 2020: Global medical genetics
https://read.qxmd.com/read/32570742/adenovirus-infections-in-african-humans-and-wild-non-human-primates-great-diversity-and-cross-species-transmission
#36
JOURNAL ARTICLE
Hacène Medkour, Inestin Amona, Jean Akiana, Bernard Davoust, Idir Bitam, Anthony Levasseur, Mamadou Lamine Tall, Georges Diatta, Cheikh Sokhna, Raquel Adriana Hernandez-Aguilar, Amanda Barciela, Slim Gorsane, Bernard La Scola, Didier Raoult, Florence Fenollar, Oleg Mediannikov
Non-human primates (NHPs) are known hosts for adenoviruses (AdVs), so there is the possibility of the zoonotic or cross-species transmission of AdVs. As with humans, AdV infections in animals can cause diseases that range from asymptomatic to fatal. The aim of this study was to investigate the occurrence and diversity of AdVs in: (i) fecal samples of apes and monkeys from different African countries (Republic of Congo, Senegal, Djibouti and Algeria), (ii) stool of humans living near gorillas in the Republic of Congo, in order to explore the potential zoonotic risks...
June 18, 2020: Viruses
https://read.qxmd.com/read/32374870/ampliconic-genes-on-the-great-ape-y-chromosomes-rapid-evolution-of-copy-number-but-conservation-of-expression-levels
#37
JOURNAL ARTICLE
Rahulsimham Vegesna, Marta Tomaszkiewicz, Oliver A Ryder, Rebeca Campos-Sánchez, Paul Medvedev, Michael DeGiorgio, Kateryna D Makova
Multi-copy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with droplet digital PCR, combined these estimates with published data for human and gorilla, and produced genome-wide testis gene expression data for great apes. Analyzing this comprehensive dataset within an evolutionary framework, we, first, found high inter- and intraspecific variation in gene family size, with larger families exhibiting higher variation as compared to smaller families, a pattern consistent with random genetic drift...
May 6, 2020: Genome Biology and Evolution
https://read.qxmd.com/read/32143403/identification-of-structural-variation-in-chimpanzees-using-optical-mapping-and-nanopore-sequencing
#38
JOURNAL ARTICLE
Daniela C Soto, Colin Shew, Mira Mastoras, Joshua M Schmidt, Ruta Sahasrabudhe, Gulhan Kaya, Aida M Andrés, Megan Y Dennis
Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two additional Pan troglodytes verus individuals, one of whom carries 13% admixture from Pan troglodytes troglodytes ...
March 4, 2020: Genes
https://read.qxmd.com/read/31975179/population-genomics-in-the-great-apes
#39
JOURNAL ARTICLE
David Castellano, Kasper Munch
The great apes play an important role as model organisms. They are our closest living relatives, allowing us to identify the genetic basis of phenotypic traits that we think of as characteristically human. However, the most significant asset of great apes as model organisms is that they share with humans most of their genetic makeup. This means that we can extend our vast knowledge of the human genome, its genes, and the associated phenotypes to these species. Comparative genomic studies of humans and apes thus reveal how very similar genomes react when exposed to different population genetic regimes...
2020: Methods in Molecular Biology
https://read.qxmd.com/read/31730374/a-catalogue-of-59-732-human-specific-regulatory-sequences-reveals-unique-to-human-regulatory-patterns-associated-with-virus-interacting-proteins-pluripotency-and-brain-development
#40
JOURNAL ARTICLE
Gennadi V Glinsky
Extensive searches for genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) identified thousands' HSRS using high-resolution next-generation sequencing technologies and methodologically diverse comparative analyses of human and nonhuman primates' (NHPs) reference genomes. In this study, a comprehensive catalogue of 59,732 genomic loci harboring candidate HSRS has been assembled to facilitate the systematic analyses of genomic sequences that were either inherited from extinct common ancestors (ECAs) or created de novo in human genomes...
November 15, 2019: DNA and Cell Biology
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