scholarly journals Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0256120
Author(s):  
Yue Guo ◽  
Jing Liu ◽  
Xingna Wang ◽  
Ying Li ◽  
Xilin Hou ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Tissue Specificity ◽  
Signal Transduction Pathway ◽  
Evolutionary Forces ◽  
Gene Copies ◽  
Genome Wide ◽  
A Genome ◽  
Function Expression ◽  
Phenotypic Diversification ◽  
Evolution Function

It is believed that positive selection is one of the major evolutionary forces underlying organism phenotypic diversification. Nevertheless, the characteristics of positively selected genes (PSGs), have not been well investigated. In this study, we performed a genome-wide analysis of orthologous genes between Brassica rapa (B. rapa) and Brassica oleracea (B. oleracea), and identified 468 putative PSGs. Our data show that, (1) PSGs are enriched in plant hormone signal transduction pathway and the transcription factor family; (2) PSGs are significantly lower expressed than randomly selected non-PSGs; (3) PSGs with tissue specificity are significantly higher expressed in the callus and reproductive tissues (flower and silique) than in vegetable tissues (root, stem and leaf); (4) the proportion of PSGs is positively correlated with the number of retained triplication gene copies, but the expression level of PSGs decay with the increasing of triplication gene copies; (5) the CG and CHG methylation levels of PSGs are significantly higher in introns and UTRs than in the promoter and exon regions; (6) the percent of transposable element is in proportion to the methylation level, and DNA methylation (especially in the CG content) has the tendency to reduce the expression of PSGs. This study provides insights into the characteristics, evolution, function, expression and methylation of PSGs in B. rapa.

scholarly journals Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shulin Zhang ◽  
Zailong Tian ◽  
Haipeng Li ◽  
Yutao Guo ◽  
Yanqi Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Plant Species ◽  
26S Proteasome ◽  
Genome Wide Analysis ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome ◽  
F Box Protein

Abstract Background F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects. Results In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction. Conclusion The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.

scholarly journals A Genome-wide Survey of the Prevalence and Evolutionary Forces Acting on Human Nonsense SNPs

2009 ◽  
Vol 84 (2) ◽  
pp. 224-234 ◽  
Author(s):  
Bryndis Yngvadottir ◽  
Yali Xue ◽  
Steve Searle ◽  
Sarah Hunt ◽  
Marcos Delgado ◽  
...  
Keyword(s):  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

scholarly journals Genome-wide association study identifies RNF123 locus as associated with chronic widespread musculoskeletal pain

2021 ◽  
pp. annrheumdis-2020-219624
Author(s):  
Md Shafiqur Rahman ◽  
Bendik S Winsvold ◽  
Sergio O Chavez Chavez ◽  
Sigrid Børte ◽  
Yakov A Tsepilov ◽  
...  
Keyword(s):  
Association Study ◽  
Musculoskeletal Pain ◽  
Tissue Specificity ◽  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
The Body ◽  
Genome Wide Association ◽  
Suggestive Association ◽  
Genome Wide ◽  
A Genome

Background and objectivesChronic widespread musculoskeletal pain (CWP) is a symptom of fibromyalgia and a complex trait with poorly understood pathogenesis. CWP is heritable (48%–54%), but its genetic architecture is unknown and candidate gene studies have produced inconsistent results. We conducted a genome-wide association study to get insight into the genetic background of CWP.MethodsNorthern Europeans from UK Biobank comprising 6914 cases reporting pain all over the body lasting >3 months and 242 929 controls were studied. Replication of three independent genome-wide significant single nucleotide polymorphisms was attempted in six independent European cohorts (n=43 080; cases=14 177). Genetic correlations with risk factors, tissue specificity and colocalisation were examined.ResultsThree genome-wide significant loci were identified (rs1491985, rs10490825, rs165599) residing within the genes Ring Finger Protein 123 (RNF123), ATPase secretory pathway Ca2+transporting 1 (ATP2C1) and catechol-O-methyltransferase (COMT). The RNF123 locus was replicated (meta-analysis p=0.0002), the ATP2C1 locus showed suggestive association (p=0.0227) and the COMT locus was not replicated. Partial genetic correlation between CWP and depressive symptoms, body mass index, age of first birth and years of schooling were identified. Tissue specificity and colocalisation analysis highlight the relevance of skeletal muscle in CWP.ConclusionsWe report a novel association of RNF123 locus and a suggestive association of ATP2C1 locus with CWP. Both loci are consistent with a role of calcium regulation in CWP. The association with COMT, one of the most studied genes in chronic pain field, was not confirmed in the replication analysis.

scholarly journals Genomic properties of variably methylated retrotransposons in mouse

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jessica L. Elmer ◽  
Amir D. Hay ◽  
Noah J. Kessler ◽  
Tessa M. Bertozzi ◽  
Eve A. C. Ainscough ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Tissue Specificity ◽  
Cytosine Methylation ◽  
Individual Variability ◽  
Endogenous Retroviruses ◽  
Ctcf Binding ◽  
Genome Wide ◽  
A Genome ◽  
Physical Interactions ◽  
Intracisternal A Particle

Abstract Background Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. Results Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. Conclusion Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.

Genome-wide expression-monitoring of jasmonate-responsive genes of Arabidopsis using cDNA arrays

2000 ◽  
Vol 28 (6) ◽  
pp. 863-864 ◽  
Author(s):  
Y. Sasaki ◽  
E. Asamizu ◽  
D. Shibata ◽  
Y. Nakamura ◽  
T. Kaneko ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Signal Transduction Pathway ◽  
Cdna Macroarray ◽  
Genome Wide ◽  
A Genome ◽  
Defence Responses ◽  
Wide Scale ◽  
Expressed Sequence ◽  
Genome Wide Expression ◽  
Good Agreement

Jasmonates are generally considered to mediate signalling, such as defence responses, flowering and senescence. However, factors involved in the jasmonate signal-transduction pathway remain unclear. To clarify the functions and signalling mechanisms of jasmonates on a genome-wide level, we adopted a cDNA macroarray technique. We prepared nylon filters of a cDNA macroarray on which 2880 independent expressed sequence tag clones of Arabidopsis were blotted, and hybridized 33P-labelled single-strand DNAs synthesized from mRNAs of methyl jasmonate (MeJA)- treated and untreated Arabidopsis plants to the nylon filters. By analysing the data from the cDNA macroarray, we identified many function-known and unknown genes as MeJA-responsive genes, and confirmed that the profiles of the expression showed good agreement with Northernblot analysis. These results demonstrate the efficiency of the cDNA macroarray for systematically analysing jasmonate-responsive genes on a genome-wide scale.

scholarly journals The Potential Role of FREM1 and Its Isoform TILRR in HIV-1 Acquisition through Mediating Inflammation

2021 ◽  
Vol 22 (15) ◽  
pp. 7825
Author(s):  
Mohammad Abul Kashem ◽  
Hongzhao Li ◽  
Lewis Ruxi Liu ◽  
Binhua Liang ◽  
Robert Were Omange ◽  
...  
Keyword(s):  
Sex Workers ◽  
Inflammatory Responses ◽  
Interleukin 1 ◽  
Signal Transduction Pathway ◽  
Polymorphism Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Immunodeficiency Virus ◽  
Hiv 1

FREM1 (Fras-related extracellular matrix 1) and its splice variant TILRR (Toll-like interleukin-1 receptor regulator) have been identified as integral components of innate immune systems. The potential involvement of FREM1 in HIV-1 (human immunodeficiency virus 1) acquisition was suggested by a genome-wide SNP (single nucleotide polymorphism) analysis of HIV-1 resistant and susceptible sex workers enrolled in the Pumwani sex worker cohort (PSWC) in Nairobi, Kenya. The studies showed that the minor allele of a FREM1 SNP rs1552896 is highly enriched in the HIV-1 resistant female sex workers. Subsequent studies showed that FREM1 mRNA is highly expressed in tissues relevant to mucosal HIV-1 infection, including cervical epithelial tissues, and TILRR is a major modulator of many genes in the NF-κB signal transduction pathway. In this article, we review the role of FREM1 and TILRR in modulating inflammatory responses and inflammation, and how their influence on inflammatory responses of cervicovaginal tissue could enhance the risk of vaginal HIV-1 acquisition.

scholarly journals A general model to explain repeated turnovers of sex determination in the Salicaceae

2020 ◽  
Author(s):  
Wenlu Yang ◽  
Zhiyang Zhang ◽  
Deyan Wang ◽  
Yiling Li ◽  
Shaofei Tong ◽  
...  
Keyword(s):  
Sex Determination ◽  
General Model ◽  
Genome Wide Association Study ◽  
Sex Chromosome ◽  
Response Regulator ◽  
Single Gene ◽  
Entire Family ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome

AbstractDioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms through which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosome in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.

scholarly journals Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species Haloferax volcanii

Genetics ◽  
2020 ◽  
Vol 215 (4) ◽  
pp. 1107-1116 ◽  
Author(s):  
Sibel Kucukyildirim ◽  
Megan Behringer ◽  
Emily M. Williams ◽  
Thomas G. Doak ◽  
Michael Lynch
Keyword(s):  
Molecular Mechanisms ◽  
Model Organism ◽  
Optimal Growth ◽  
Haloferax Volcanii ◽  
Base Substitution ◽  
Spontaneous Mutations ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Archaeal Species ◽  
A Genome

Organisms adapted to life in extreme habitats (extremophiles) can further our understanding of the mechanisms of genetic stability, particularly replication and repair. Despite the harsh environmental conditions they endure, these extremophiles represent a great deal of the Earth’s biodiversity. Here, for the first time in a member of the archaeal domain, we report a genome-wide assay of spontaneous mutations in the halophilic species Haloferax volcanii using a direct and unbiased method: mutation accumulation experiments combined with deep whole-genome sequencing. H. volcanii is a key model organism not only for the study of halophilicity, but also for archaeal biology in general. Our methods measure the genome-wide rate, spectrum, and spatial distribution of spontaneous mutations. The estimated base substitution rate of 3.15 × 10−10 per site per generation, or 0.0012 per genome per generation, is similar to the value found in mesophilic prokaryotes (optimal growth at ∼20–45°). This study contributes to a comprehensive phylogenetic view of how evolutionary forces and molecular mechanisms shape the rate and molecular spectrum of mutations across the tree of life.

scholarly journals Genome-wide identification and comprehensive analysis of the NAC transcription factor family in sunflower during salt and drought stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenhui Li ◽  
Youling Zeng ◽  
Fangliu Yin ◽  
Ran Wei ◽  
Xiaofei Mao
Keyword(s):  
Phylogenetic Analysis ◽  
Abiotic Stress ◽  
Drought Stress ◽  
Tissue Specificity ◽  
Large Family ◽  
Strong Response ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stress ◽  
Nac Family

AbstractThe NAC (NAM, ATAF1/2, and CUC2), is a large family of plant-specific transcription factors (TFs) that exert crucial regulatory roles in various physiological processes and abiotic stresses. There is scanty information on the role of the NAC family in sunflower (Helianthus annuus L.). In this study, we conducted a genome-wide survey and expression analysis of the NAC family in sunflower. A total of 150 HaNACs were identified in sunflower. Phylogenetic analysis to compare HaNACs with Arabidopsis NACs generated 15 clusters. Among them, eight membrane-bound NAC TFs with transmembrane helixes were found (designated as NTLs), which were suggested to be localized in the membrane and transferred to the nucleus through proteolysis. Notably, 12 HaNACs were potentially regulated via miR164 cleavage or translational inhibition. By analyzing RNA-seq data from Sequence Read Archive (SRA), the expression of HaNACs showed tissue specificity and strong response to drought stress. Additionally, phylogenetic analysis of 150 HaNACs with the previously reported NACs related to abiotic stress revealed that 75% of the abiotic stress-related NACs were clustered into the SNAC (abiotic stress-related NAC) group, and only 25% were in the Non-SNAC group. qRT-PCR further demonstrated that about 75% of the HaNACs in the SNAC subgroup were induced by salt and drought stress, and the expression of some HaNACs showed tissue specificity. These findings provide valuable information that can deepen the understanding of how NAC TFs in sunflower respond to abiotic stress.

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