Abstract:
:Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the AT- and DT-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.
journal_name
PLoS Genetjournal_title
PLoS geneticsauthors
Page JT,Liechty ZS,Alexander RH,Clemons K,Hulse-Kemp AM,Ashrafi H,Van Deynze A,Stelly DM,Udall JAdoi
10.1371/journal.pgen.1006012subject
Has Abstractpub_date
2016-05-11 00:00:00pages
e1006012issue
5eissn
1553-7390issn
1553-7404pii
PGENETICS-D-16-00057journal_volume
12pub_type
杂志文章相关文献
PLoS Genetics文献大全abstract::A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differenti...
journal_title:PLoS genetics
pub_type: 杂志文章,评审
doi:10.1371/journal.pgen.1004601
更新日期:2014-08-28 00:00:00
abstract::Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. But gene conversion i...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002968
更新日期:2012-01-01 00:00:00
abstract::Pre-mRNAs are often processed in complex patterns in tissue-specific manners to produce a variety of protein isoforms from single genes. However, mechanisms orchestrating the processing of the entire transcript are not well understood. Muscle-specific alternative pre-mRNA processing of the unc-60 gene in Caenorhabditi...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002991
更新日期:2012-01-01 00:00:00
abstract::UTX (KDM6A) and UTY are homologous X and Y chromosome members of the Histone H3 Lysine 27 (H3K27) demethylase gene family. UTX can demethylate H3K27; however, in vitro assays suggest that human UTY has lost enzymatic activity due to sequence divergence. We produced mouse mutations in both Utx and Uty. Homozygous Utx m...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002964
更新日期:2012-09-01 00:00:00
abstract::Although endocrine changes are known to modulate the timing of major developmental transitions, the genetic mechanisms underlying these changes remain poorly understood. In insects, two developmental hormones, juvenile hormone (JH) and ecdysteroids, are coordinated with each other to induce developmental changes assoc...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004425
更新日期:2014-06-19 00:00:00
abstract::Genotoxic agents that cause double-strand breaks (DSBs) often generate damage at the break termini. Processing enzymes, including nucleases and polymerases, must remove damaged bases and/or add new bases before completion of repair. Artemis is a nuclease involved in mammalian nonhomologous end joining (NHEJ), but in S...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000060
更新日期:2008-04-25 00:00:00
abstract::The neonatal intestine is a very complex and dynamic organ that must rapidly adapt and remodel in response to a barrage of environmental stimuli during the first few postnatal weeks. Recent studies demonstrate that the zinc finger transcriptional repressor Blimp1/Prdm1 plays an essential role governing postnatal repro...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005375
更新日期:2015-07-09 00:00:00
abstract::The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases, α, δ, and ε. Current evidence suggests that DNA polymerase ε (Pol ε) is the primary leading strand replicase, whereas Pols α and δ primarily perform lagging strand replication. The fact that these polymerases differ in...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1003016
更新日期:2012-01-01 00:00:00
abstract::Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000762
更新日期:2009-12-01 00:00:00
abstract::We have developed a powerful experimental framework that combines competitive selection and microarray-based genetic footprinting to comprehensively reveal the genetic basis of bacterial behaviors. Application of this method to Escherichia coli motility identifies 95% of the known flagellar and chemotaxis genes, and r...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.0030154
更新日期:2007-09-01 00:00:00
abstract::Cytokinesis terminates mitosis, resulting in separation of the two sister cells. Septins, a conserved family of GTP-binding cytoskeletal proteins, are an absolute requirement for cytokinesis in budding yeast. We demonstrate that septin-dependence of mammalian cytokinesis differs greatly between cell types: genetic los...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004558
更新日期:2014-08-14 00:00:00
abstract::Wnt signaling provides a paradigm for cell-cell signals that regulate embryonic development and stem cell homeostasis and are inappropriately activated in cancers. The tumor suppressors APC and Axin form the core of the multiprotein destruction complex, which targets the Wnt-effector beta-catenin for phosphorylation, ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1007339
更新日期:2018-04-11 00:00:00
abstract::In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we d...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004208
更新日期:2014-03-20 00:00:00
abstract::Studies in model organisms suggest that epistasis may play an important role in the etiology of complex diseases and traits in humans. With the era of large-scale genome-wide association studies fast approaching, it is important to quantify whether it will be possible to detect interacting loci using realistic sample ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.0020157
更新日期:2006-09-22 00:00:00
abstract::Hypercholesterolemia is a causal and modifiable risk factor for atherosclerotic cardiovascular disease. A critical pathway regulating cholesterol homeostasis involves the receptor-mediated endocytosis of low-density lipoproteins into hepatocytes, mediated by the LDL receptor. We applied genome-scale CRISPR screening t...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1009285
更新日期:2021-01-29 00:00:00
abstract::Malaria parasites follow a complex life cycle that consists of multiple stages that span from the human host to the mosquito vector. Among the species causing malaria, Plasmodium falciparum is the most lethal, with clinical symptoms manifesting during the intraerythrocytic developmental cycle (IDC). During the IDC, P....
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1008506
更新日期:2019-12-19 00:00:00
abstract::Molybdenum (Mo) is an essential micronutrient for plants, serving as a cofactor for enzymes involved in nitrate assimilation, sulfite detoxification, abscisic acid biosynthesis, and purine degradation. Here we show that natural variation in shoot Mo content across 92 Arabidopsis thaliana accessions is controlled by va...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000004
更新日期:2008-02-29 00:00:00
abstract::Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes t...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1008013
更新日期:2019-08-22 00:00:00
abstract::In haploid cells of Ogataea (Hansenula) polymorpha an environmental signal, nitrogen starvation, induces a reversible change in the structure of a chromosome. This process, mating-type switching, inverts a 19-kb DNA region to place either MATa or MATα genes under centromeric repression of transcription, depending on t...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1007092
更新日期:2017-11-27 00:00:00
abstract::DNA interstrand crosslinks (ICLs) are among the most toxic types of damage to a cell. For this reason, many ICL-inducing agents are effective therapeutic agents. For example, cisplatin and nitrogen mustards are used for treating cancer and psoralen plus UVA (PUVA) is useful for treating psoriasis. However, repair mech...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000189
更新日期:2008-09-12 00:00:00
abstract::At least 25 inherited disorders in humans result from microsatellite repeat expansion. Dramatic variation in repeat instability occurs at different disease loci and between different tissues; however, cis-elements and trans-factors regulating the instability process remain undefined. Genomic fragments from the human s...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000257
更新日期:2008-11-01 00:00:00
abstract::Quantitative genetic analysis has long been used to study how natural variation of genotype can influence an organism's phenotype. While most studies have focused on genetic determinants of phenotypic average, it is rapidly becoming understood that stochastic noise is genetically determined. However, it is not known h...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002295
更新日期:2011-09-01 00:00:00
abstract::We recently discovered a secreted and diffusible midline cue called MADD-4 (an ADAMTSL) that guides migrations along the dorsoventral axis of the nematode Caenorhabditis elegans. We showed that the transmembrane receptor, UNC-40 (DCC), whose canonical ligand is the UNC-6 (netrin) guidance cue, is required for extensio...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004521
更新日期:2014-08-14 00:00:00
abstract::Chemosensory pheromonal information regulates aggression and reproduction in many species, but how pheromonal signals are transduced to reliably produce behavior is not well understood. Here we demonstrate that the pheromonal signals detected by Gr32a-expressing chemosensory neurons to enhance male aggression are filt...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004356
更新日期:2014-05-22 00:00:00
abstract::The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The spec...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.0030023
更新日期:2007-02-16 00:00:00
abstract::Plant pathogens with a broad host range are able to infect plant lineages that diverged over 100 million years ago. They exert similar and recurring constraints on the evolution of unrelated plant populations. Plants generally respond with quantitative disease resistance (QDR), a form of immunity relying on complex ge...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1007143
更新日期:2017-12-22 00:00:00
abstract::Considerable evidence now supports the idea that the moderate telomere lengthening produced by recombinational telomere elongation (RTE) in a Kluyveromyces lactis telomerase deletion mutant occurs through a roll-and-spread mechanism. However, it is unclear whether this mechanism can account for other forms of RTE that...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1003017
更新日期:2012-01-01 00:00:00
abstract::Methylcytosine-binding proteins decipher the epigenetic information encoded by DNA methylation and provide a link between DNA methylation, modification of chromatin structure, and gene silencing. VARIANT IN METHYLATION 1 (VIM1) encodes an SRA (SET- and RING-associated) domain methylcytosine-binding protein in Arabidop...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000156
更新日期:2008-08-15 00:00:00
abstract::Successful reproduction is critical to pass genes to the next generation. Seminal proteins contribute to important reproductive processes that lead to fertilization in species ranging from insects to mammals. In Drosophila, the male's accessory gland is a source of seminal fluid proteins that affect the reproductive o...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.0030238
更新日期:2007-12-01 00:00:00
abstract::Although tumor size and lymph node involvement are the current cornerstones of breast cancer prognosis, they have not been extensively explored in relation to tumor methylation attributes in conjunction with other tumor and patient dietary and hormonal characteristics. Using primary breast tumors from 162 (AJCC stage ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1001043
更新日期:2010-07-29 00:00:00