当前位置： SCI文献检索 > Genome Biology and Evolution期刊下所有文献 > Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels.

Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels.

Abstract：

:Multicopy 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 polymerase chain reaction, combined these estimates with published data for human and gorilla, and produced genome-wide testis gene expression data for great apes. Analyzing this comprehensive data set within an evolutionary framework, we, first, found high inter- and intraspecific variation in gene family size, with larger families exhibiting higher variation as compared with smaller families, a pattern consistent with random genetic drift. Second, for four gene families, we observed significant interspecific size differences, sometimes even between sister species-chimpanzee and bonobo. Third, despite substantial variation in copy number, Y ampliconic gene families' expression levels did not differ significantly among species, suggesting dosage regulation. Fourth, for three gene families, size was positively correlated with gene expression levels across species, suggesting that, given sufficient evolutionary time, copy number influences gene expression. Our results indicate high variability in size but conservation in gene expression levels in Y ampliconic gene families, significantly advancing our understanding of Y-chromosome evolution in great apes.

journal_name

Genome Biol Evol

journal_title

Genome biology and evolution

authors

Vegesna R,Tomaszkiewicz M,Ryder OA,Campos-Sánchez R,Medvedev P,DeGiorgio M,Makova KD

doi

10.1093/gbe/evaa088

subject

Has Abstract

pub_date

2020-06-01 00:00:00

pages

842-859

issue

6

issn

1759-6653

pii

5831295

journal_volume

12

pub_type

杂志文章

相关文献

Genome Biology and Evolution文献大全
  • Evolutionary rate heterogeneity of core and attachment proteins in yeast protein complexes.

    abstract：:In general, proteins do not work alone; they form macromolecular complexes to play fundamental roles in diverse cellular functions. On the basis of their iterative clustering procedure and frequency of occurrence in the macromolecular complexes, the protein subunits have been categorized as core and attachment. Core p...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evt096

    authors： Chakraborty S,Ghosh TC

    更新日期：2013-01-01 00:00:00

  • Evaluating the fitness cost of protein expression in Saccharomyces cerevisiae.

    abstract：:Protein metabolism is one of the most costly processes in the cell and is therefore expected to be under the effective control of natural selection. We stimulated yeast strains to overexpress each single gene product to approximately 1% of the total protein content. Consistent with previous reports, we found that exce...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evt154

    authors： Tomala K,Korona R

    更新日期：2013-01-01 00:00:00

  • Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds.

    abstract：:The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effect...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evt083

    authors： Nabholz B,Uwimana N,Lartillot N

    更新日期：2013-01-01 00:00:00

  • Multiple Rounds of Artificial Selection Promote Microbe Secondary Domestication-The Case of Cachaça Yeasts.

    abstract：:The study of microbe domestication has witnessed major advances that contribute to a better understanding of the emergence of artificially selected phenotypes and set the foundations of their rational improvement for biotechnology. Several features make Saccharomyces cerevisiae an ideal model for such a study, notably...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy132

    authors： Barbosa R,Pontes A,Santos RO,Montandon GG,de Ponzzes-Gomes CM,Morais PB,Gonçalves P,Rosa CA,Sampaio JP

    更新日期：2018-08-01 00:00:00

  • High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups.

    abstract：:Because of its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconi...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy086

    authors： Ye D,Zaidi AA,Tomaszkiewicz M,Anthony K,Liebowitz C,DeGiorgio M,Shriver MD,Makova KD

    更新日期：2018-05-01 00:00:00

  • Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids.

    abstract：:Discoba (Excavata) is an evolutionarily important group of eukaryotes that includes Jakobida, with the most bacterial-like mitochondrial genomes known, and Euglenozoa, many of which have extensively fragmented mitochondrial genomes. However, little is known about the mitochondrial genomes of Heterolobosea, the third m...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evx086

    authors： Yang J,Harding T,Kamikawa R,Simpson AGB,Roger AJ

    更新日期：2017-05-01 00:00:00

  • OASes and STING: adaptive evolution in concert.

    abstract：:OAS (2'-5'-oligoadenylate synthases) proteins and cyclic GMP-AMP synthase (cGAS, gene symbol: MB21D1) patrol the cytoplasm for the presence of foreign nucleic acids. Upon binding to double-stranded RNA or double-stranded DNA, OAS proteins and cGAS produce nucleotide second messengers to activate RNase L and STING (sti...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv046

    authors： Mozzi A,Pontremoli C,Forni D,Clerici M,Pozzoli U,Bresolin N,Cagliani R,Sironi M

    更新日期：2015-03-09 00:00:00

  • Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.

    abstract：:The selective pressures acting on viruses that replicate under enhanced mutation rates are largely unknown. Here, we describe resistance of foot-and-mouth disease virus to the mutagen 5-fluorouracil (FU) through a single polymerase substitution that prevents an excess of A to G and U to C transitions evoked by FU on t...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evx075

    authors： de la Higuera I,Ferrer-Orta C,de Ávila AI,Perales C,Sierra M,Singh K,Sarafianos SG,Dehouck Y,Bastolla U,Verdaguer N,Domingo E

    更新日期：2017-05-01 00:00:00

  • Transcriptional Mutagenesis Prevents Ribosomal DNA Deterioration: The Role of Duplications and Deletions.

    abstract：:Clashes between transcription and replication complexes can cause point mutations and chromosome rearrangements on heavily transcribed genes. In eukaryotic ribosomal RNA genes, the system that prevents transcription-replication conflicts also causes frequent copy number variation. Such fast mutational dynamics do not ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz235

    authors： Colizzi ES,Hogeweg P

    更新日期：2019-11-01 00:00:00

  • Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure.

    abstract：:It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34-41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a compa...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv209

    authors： Sillo F,Garbelotto M,Friedman M,Gonthier P

    更新日期：2015-11-01 00:00:00

  • Genome of the Parasitoid Wasp Diachasma alloeum, an Emerging Model for Ecological Speciation and Transitions to Asexual Reproduction.

    abstract：:Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model fo...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz205

    authors： Tvedte ES,Walden KKO,McElroy KE,Werren JH,Forbes AA,Hood GR,Logsdon JM,Feder JL,Robertson HM

    更新日期：2019-10-01 00:00:00

  • Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta).

    abstract：:We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene cont...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy103

    authors： Guillory WX,Onyshchenko A,Ruck EC,Parks M,Nakov T,Wickett NJ,Alverson AJ

    更新日期：2018-06-01 00:00:00

  • Multiple Roots of Fruiting Body Formation in Amoebozoa.

    abstract：:Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy011

    authors： Hillmann F,Forbes G,Novohradská S,Ferling I,Riege K,Groth M,Westermann M,Marz M,Spaller T,Winckler T,Schaap P,Glöckner G

    更新日期：2018-02-01 00:00:00

  • Metabolic Determinants of Enzyme Evolution in a Genome-Scale Bacterial Metabolic Network.

    abstract：:Different genes and proteins evolve at very different rates. To identify the factors that explain these differences is an important aspect of research in molecular evolution. One such factor is the role a protein plays in a large molecular network. Here, we analyze the evolutionary rates of enzyme-coding genes in the ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy234

    authors： Aguilar-Rodríguez J,Wagner A

    更新日期：2018-11-01 00:00:00

  • Sex Chromosome Evolution: So Many Exceptions to the Rules.

    abstract：:Genomic analysis of many nonmodel species has uncovered an incredible diversity of sex chromosome systems, making it possible to empirically test the rich body of evolutionary theory that describes each stage of sex chromosome evolution. Classic theory predicts that sex chromosomes originate from a pair of homologous ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evaa081

    authors： Furman BLS,Metzger DCH,Darolti I,Wright AE,Sandkam BA,Almeida P,Shu JJ,Mank JE

    更新日期：2020-06-01 00:00:00

  • On the Function of Trans-Splicing: No Evidence for Widespread Proteome Diversification in Trypanosomes.

    abstract：:A long-standing mystery of genomic/transcriptomic structure involves spliced leader trans-splicing (SLTS), in which short RNA "tags" transcribed from a distinct genomic locus is added near the 5' end of RNA transcripts by the spliceosome. SLTS has been observed in diverse eukaryotes in a phylogenetic pattern implying ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz217

    authors： Soulette CM,Oliverio O,Roy SW

    更新日期：2019-10-01 00:00:00

  • The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV).

    abstract：:The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this perio...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv231

    authors： Brito AF,Braconi CT,Weidmann M,Dilcher M,Alves JM,Gruber A,Zanotto PM

    更新日期：2015-11-27 00:00:00

  • Early Metazoan Origin and Multiple Losses of a Novel Clade of RIM Presynaptic Calcium Channel Scaffolding Protein Homologs.

    abstract：:The precise localization of CaV2 voltage-gated calcium channels at the synapse active zone requires various interacting proteins, of which, Rab3-interacting molecule or RIM is considered particularly important. In vertebrates, RIM interacts with CaV2 channels in vitro via a PDZ domain that binds to the extreme C-termi...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evaa097

    authors： Piekut T,Wong YY,Walker SE,Smith CL,Gauberg J,Harracksingh AN,Lowden C,Novogradac BB,Cheng HM,Spencer GE,Senatore A

    更新日期：2020-08-01 00:00:00

  • Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation.

    abstract：:Conservation of function can be accompanied by obvious similarity of homologous sequences which may persist for billions of years (Iyer LM, Leipe DD, Koonin EV, Aravind L. 2004. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 146:11-31.). However, presumably homologous segments of ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evt023

    authors： Vakhrusheva OA,Bazykin GA,Kondrashov AS

    更新日期：2013-01-01 00:00:00

  • The potential role of sexual conflict and sexual selection in shaping the genomic distribution of Mito-nuclear genes.

    abstract：:Mitochondrial interactions with the nuclear genome represent one of life's most important co-evolved mutualisms. In many organisms, mitochondria are maternally inherited, and in these cases, co-transmission between the mitochondrial and nuclear genes differs across different parts of the nuclear genome, with genes on ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evu063

    authors： Dean R,Zimmer F,Mank JE

    更新日期：2014-05-01 00:00:00

  • Molecular Darwinism: the contingency of spontaneous genetic variation.

    abstract：:The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be ass...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evr035

    authors： Arber W

    更新日期：2011-01-01 00:00:00

  • Plastome-Wide Rearrangements and Gene Losses in Carnivorous Droseraceae.

    abstract：:The plastid genomes of four related carnivorous plants (Drosera regia, Drosera erythrorhiza, Aldrovanda vesiculosa, and Dionaea muscipula) were sequenced to examine changes potentially induced by the transition to carnivory. The plastid genomes of the Droseraceae show multiple rearrangements, gene losses, and large ex...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz005

    authors： Nevill PG,Howell KA,Cross AT,Williams AV,Zhong X,Tonti-Filippini J,Boykin LM,Dixon KW,Small I

    更新日期：2019-02-01 00:00:00

  • Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer.

    abstract：:Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evaa058

    authors： Coimbra NDR,Goes-Neto A,Azevedo V,Ouangraoua A

    更新日期：2020-04-01 00:00:00

  • A genomic survey of HECT ubiquitin ligases in eukaryotes reveals independent expansions of the HECT system in several lineages.

    abstract：:The posttranslational modification of proteins by the ubiquitination pathway is an important regulatory mechanism in eukaryotes. To date, however, studies on the evolutionary history of the proteins involved in this pathway have been restricted to E1 and E2 enzymes, whereas E3 studies have been focused mainly in metaz...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evt052

    authors： Grau-Bové X,Sebé-Pedrós A,Ruiz-Trillo I

    更新日期：2013-01-01 00:00:00

  • Regulation of Large Number of Weak Targets-New Insights from Twin-microRNAs.

    abstract：:Each animal microRNA (miRNA) targets many genes for repression. Down-regulation of most of these targets is weak and has no detectable individual phenotypic effect. Whether this extensive weak repression is biologically relevant is a central issue in the debate on miRNA functionality. In the "small (target) pool" view...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy079

    authors： Zhao Y,Lin P,Liufu Z,Yang H,Lyu Y,Shen X,Wu CI,Tang T

    更新日期：2018-04-01 00:00:00

  • Genetic Competence Drives Genome Diversity in Bacillus subtilis.

    abstract：:Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evx270

    authors： Brito PH,Chevreux B,Serra CR,Schyns G,Henriques AO,Pereira-Leal JB

    更新日期：2018-01-01 00:00:00

  • Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.

    abstract：:Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, howe...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evaa098

    authors： Naidoo T,Xu J,Vicente M,Malmström H,Soodyall H,Jakobsson M,Schlebusch CM

    更新日期：2020-07-01 00:00:00

  • Nucleomorph Genome Sequences of Two Chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata.

    abstract：:Many algal groups acquired complex plastids by the uptake of green and red algae through multiple secondary endosymbioses. As a result of gene loss and transfer during the endosymbiotic processes, algal endosymbiont nuclei disappeared in most cases. However, chlorarachniophytes and cryptophytes still possess a relict ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv096

    authors： Suzuki S,Shirato S,Hirakawa Y,Ishida K

    更新日期：2015-05-22 00:00:00

  • Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

    abstract：:The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv244

    authors： Jackman SD,Warren RL,Gibb EA,Vandervalk BP,Mohamadi H,Chu J,Raymond A,Pleasance S,Coope R,Wildung MR,Ritland CE,Bousquet J,Jones SJ,Bohlmann J,Birol I

    更新日期：2015-12-08 00:00:00

  • Comparative Transcriptomics across Nematode Life Cycles Reveal Gene Expression Conservation and Correlated Evolution in Adjacent Developmental Stages.

    abstract：:Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free living whereas others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. To determine the relationship between transcriptome evolut...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evaa110

    authors： Lu MR,Lai CK,Liao BY,Tsai IJ

    更新日期：2020-07-01 00:00:00