Abstract:
:Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced the genomes of Dictyostelium fasciculatum (DF) and Polysphondylium pallidum (PP), which represent the early diverging groups 1 and 2, respectively. In contrast to DD, PP and DF have conventional telomere organization and strongly reduced numbers of transposable elements. The number of protein-coding genes is similar between species, but only half of them comprise an identifiable set of orthologous genes. In general, genes involved in primary metabolism, cytoskeletal functions and signal transduction are conserved, while genes involved in secondary metabolism, export, and signal perception underwent large differential gene family expansions. This most likely signifies involvement of the conserved set in core cell and developmental mechanisms, and of the diverged set in niche- and species-specific adaptations for defense and food, mate, and kin selection. Phylogenetic dating using a concatenated data set and extensive loss of synteny indicate that DF, PP, and DD split from their last common ancestor at least 0.6 billion years ago.
journal_name
Genome Resjournal_title
Genome researchauthors
Heidel AJ,Lawal HM,Felder M,Schilde C,Helps NR,Tunggal B,Rivero F,John U,Schleicher M,Eichinger L,Platzer M,Noegel AA,Schaap P,Glöckner Gdoi
10.1101/gr.121137.111subject
Has Abstractpub_date
2011-11-01 00:00:00pages
1882-91issue
11eissn
1088-9051issn
1549-5469pii
gr.121137.111journal_volume
21pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.128652.111
更新日期:2012-03-01 00:00:00
abstract::The remarkable olfactory power of insect species is thought to be generated by a combinatorial action of two large protein families, G protein-coupled olfactory receptors (ORs) and odorant binding proteins (OBPs). In olfactory sensilla, OBPs deliver hydrophobic airborne molecules to ORs, but their expression in nonolf...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5075706
更新日期:2006-11-01 00:00:00
abstract::In an attempt to understand the origin of CpG islands (CGIs) in mammalian genomes, we have studied their location and structure according to the expression pattern of genes and to the G + C content of isochores in which they are embedded. We show that CGIs located over the transcription start site (named start CGIs) a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.174501
更新日期:2001-11-01 00:00:00
abstract::Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health o...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.171439.113
更新日期:2014-07-01 00:00:00
abstract::X inactivation equalizes the dosage of gene expression between the sexes, but some genes escape silencing and are thus expressed from both alleles in females. To survey X inactivation and escape in mouse, we performed RNA sequencing in Mus musculus x Mus spretus cells with complete skewing of X inactivation, relying o...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.103200.109
更新日期:2010-05-01 00:00:00
abstract::DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of approximately 70-mer probes, and used these arrays to analyze gene expression i...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1048803
更新日期:2003-07-01 00:00:00
abstract::Paternal X chromosome inactivation occurs in rodent extraembryonic membranes and in all tissues of marsupials. Methylation of CpG islands occurs on the inactive X in eutherians and is considered to be a stabilizing mechanism. The only previous study of a marsupial X-linked CpG island was of the G6PD gene of the Virgin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.2.114
更新日期:1996-02-01 00:00:00
abstract::To gauge the complexity of gene regulation in yeast, it is essential to know how much promoter sequence is functional. Conservation across species can be a sensitive means of detecting functional sequences, provided that the significance of conservation can be accurately calibrated with the local neutral mutation rate...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3243305
更新日期:2005-02-01 00:00:00
abstract::The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical m...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1555203
更新日期:2003-08-01 00:00:00
abstract::Alternative splicing is a major mechanism for gene product regulation in many multicellular organisms. By using different exon combinations, some coding regions can encode amino acids in multiple reading frames in different transcripts. Here we performed a systematic search through a set of high-quality human transcri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4246506
更新日期:2006-02-01 00:00:00
abstract::The recent publication of the FANTOM mouse transcriptome has provided a unique opportunity to study the diversity of transcripts arising from a single gene locus. We have focused on the Gnas complex, as imprinting loci themselves provide unique insights into transcriptional regulation. Thirteen full-length cDNAs from ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.955503
更新日期:2003-06-01 00:00:00
abstract::RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and c...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.189621.115
更新日期:2015-09-01 00:00:00
abstract::Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5016106
更新日期:2006-07-01 00:00:00
abstract::Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly un...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.384802
更新日期:2002-09-01 00:00:00
abstract::A benchmark problem is described for the reconstruction and analysis of biochemical networks given sampled experimental data. The growth of the organisms is described in a bioreactor in which one substrate is fed into the reactor with a given feed rate and feed concentration. Measurements for some intracellular compon...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1226004
更新日期:2004-09-01 00:00:00
abstract::Recent studies have analyzed large-scale data sets of gene expression to identify genes associated with interindividual variation in phenotypes ranging from cancer subtypes to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.227066.117
更新日期:2018-08-01 00:00:00
abstract::We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap bet...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.5.404
更新日期:1996-05-01 00:00:00
abstract::Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.166439.113
更新日期:2014-04-01 00:00:00
abstract::Coevolution maintains interactions between phenotypic traits through the process of reciprocal natural selection. Detecting molecular coevolution can expose functional interactions between molecules in the cell, generating insights into biological processes, pathways, and the networks of interactions important for cel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.092452.109
更新日期:2009-10-01 00:00:00
abstract::Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace. The resulting ambiguity sequence is aligned to the genome, identifying one template sequence. A second template se...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5661407
更新日期:2007-02-01 00:00:00
abstract::A detailed comparative map of Brassica oleracea and Arabidopsis thaliana has been established based largely on mapping of Arabidopsis ESTs in two Arabidopsis and four Brassica populations. Based on conservative criteria for inferring synteny, "one to one correspondence" between Brassica and Arabidopsis chromosomes acc...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.6.776
更新日期:2000-06-01 00:00:00
abstract::Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 indivi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.148718.112
更新日期:2013-05-01 00:00:00
abstract::The representation and discovery of transcription factor (TF) sequence binding specificities is critical for understanding gene regulatory networks and interpreting the impact of disease-associated noncoding genetic variants. We present a novel TF binding motif representation, the k-mer set memory (KSM), which consist...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.226852.117
更新日期:2018-06-01 00:00:00
abstract::We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spannin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.240739.118
更新日期:2019-04-01 00:00:00
abstract::Since complete redundancy between extant duplicates (paralogs) is evolutionarily unfavorable, some degree of functional congruency is eventually lost. However, in budding yeast, experimental evidence collected for duplicated metabolic enzymes and in global physical interaction surveys had suggested widespread function...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.076174.108
更新日期:2008-07-01 00:00:00
abstract::The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.132811.111
更新日期:2012-10-01 00:00:00
abstract::It appears that, for many genes, the two alleles possessed by an individual may produce different amounts of transcript. When such allelic differences in transcription are observed for some individuals but not others, a plausible explanation is genetic variation in the cis-acting elements that regulate the gene in que...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5663007
更新日期:2007-01-01 00:00:00
abstract::DNA methylation is found in many eukaryotes, but its function is still controversial. We have studied the methylation of plant and animal genomes using a PCR-based technique amenable for high throughput. Repetitive elements are methylated in both organisms, but whereas most mammalian exons are methylated, plant exons ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1784803
更新日期:2003-12-01 00:00:00
abstract::The Polycomb group (PcG) and Trithorax group (TrxG) of proteins are required for stable and heritable maintenance of repressed and active gene expression states. Their antagonistic function on gene control, repression for PcG and activity for TrxG, is mediated by binding to chromatin and subsequent epigenetic modifica...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.114348.110
更新日期:2011-02-01 00:00:00
abstract::Analysis procedures are needed to extract useful information from the large amount of gene expression data that is becoming available. This work describes a set of analytical tools and their application to yeast cell cycle data. The components of our approach are (1) a similarity measure that reduces the number of fal...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.9.11.1106
更新日期:1999-11-01 00:00:00