scholarly journals High-resolution Introgressive Region Map Reveals Spatiotemporal Genome Evolution in Asian Rice Domestication

2019 ◽  
Author(s):  
Hajime Ohyanagi ◽  
Kosuke Goto ◽  
Sónia Negrão ◽  
Rod A. Wing ◽  
Mark A. Tester ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Rice Genome ◽  
Definitive Answer ◽  
Asian Rice ◽  
Multiple Origins ◽  
Genome Wide ◽  
Time Calibration ◽  
History Of ◽  
Genomic Regions ◽  
Rice Domestication

AbstractDomestication is anthropogenic evolution that fulfills mankind’s critical food demand. As such, elucidating the molecular mechanisms behind this process promotes the development of future new food resources including crops. With the aim of understanding the long-term domestication process of Asian rice and by employing the Oryza sativa subspecies (indica and japonica) as an Asian rice domestication model, we scrutinized past genomic introgressions between them as traces of domestication. Here we show the genome-wide introgressive region (IR) map of Asian rice, by utilizing 4,587 accession genotypes with a stable outgroup species, particularly at the finest resolution through a machine learning-aided method. The IR map revealed that 14.2% of the rice genome consists of IRs, including both wide IRs (recent) and narrow IRs (ancient). This introgressive landscape with their time calibration indicates that introgression events happened in multiple genomic regions over multiple periods. From the correspondence between our wide IRs and the so-called selective sweep regions, we provide a definitive answer to a long-standing controversy over the evolutionary origin of Asian rice domestication, single or multiple origins: It heavily depends upon which regions you pay attention to, implying that wider genomic regions represent immediate short history of Asian rice domestication as a likely support to the single origin, while its ancient history is interspersed in narrower traces throughout the genome as a possible support to the multiple origin.

scholarly journals Identification of Selection Signatures in Commercial Asian Rice Subspecies Deciphered Selection Footprints for Four Overrepresented Biological Processes

2020 ◽  
Author(s):  
Siavash Salek Ardestani ◽  
Mahmoud Amiri Roudbar ◽  
Mohammad Hossein Banabazi ◽  
Seyedeh Fatemeh Mousavi ◽  
Madhav Bhatta ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Rice Genome ◽  
Fixation Index ◽  
Biological Processes ◽  
Selection Signatures ◽  
Genomic Changes ◽  
Asian Rice ◽  
Genome Level ◽  
Window Approach ◽  
Genomic Regions

Abstract BackgroundSelective breeding pressures have led to gradual genomic changes in Asian commercial rice, which have shaped selection footprints on its genome level. Tracing genomic selection footprints might be illuminative for better understanding of recent selection breeding objectives, and how breeding strategies have formed the Asian commercial rice genome. ResultsIn this study, the genotypic information (HDRA 700K) of four Asian commercial rice subspecies including Indica (n=498), Aus (n=187), Temperate japonica (n=241), and Tropical japonica (n=361) were downloaded from Rice Diversity Project database (http://www.ricediversity.org) to detect selection signatures by employing the Z-transformed of fixation index and Tajima’s D test, based on a sliding window approach. Although we could not identify overrepresented genomic regions underlying selection pressure among all aforementioned Asian commercial rice subspecies, interestingly, our findings revealed four overrepresented biological processes underlying selection pressure including proteolysis (GO:0006508), phosphorylation (GO:0016310), protein catabolic process (GO:0030163), and transmembrane transport (GO:0055085) that might be associated with immunity, senescing leaves, transporting, and absorption of ions. ConclusionsThese results can provide knowledge on how breeding efforts shaped the Asian commercial rice subspecies genome, and which genomic regions of these subspecies have been targeted in recent decades.

scholarly journals Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators

2019 ◽  
Author(s):  
Ru-pin Alicia Chi ◽  
Tianyuan Wang ◽  
Nyssa Adams ◽  
San-pin Wu ◽  
Steven L. Young ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Rna Seq ◽  
Uterine Receptivity ◽  
Normal Cycle ◽  
Estrogen Response ◽  
Molecular Events ◽  
History Of ◽  
And Function ◽  
Genomic Regions ◽  
Fertile Women

ABSTRACTContextPoor uterine receptivity is one major factor leading to pregnancy loss and infertility. Understanding the molecular events governing successful implantation is hence critical in combating infertility.ObjectiveTo define PGR-regulated molecular mechanisms and epithelial roles in receptivity.DesignRNA-seq and PGR-ChIP-seq were conducted in parallel to identify PGR-regulated pathways during the WOI in endometrium of fertile women.SettingEndometrial biopsies from the proliferative and mid-secretory phases were analyzed.Patients or Other ParticipantsParticipants were fertile, reproductive aged (18-37) women with normal cycle length; and without any history of dysmenorrhea, infertility, or irregular cycles. In total, 42 endometrial biopsies obtained from 42 women were analyzed in this study.InterventionsThere were no interventions during this study.Main Outcome MeasuresHere we measured the alterations in gene expression and PGR occupancy in the genome during the WOI, based on the hypothesis that PGR binds uterine chromatin cycle-dependently to regulate genes involved in uterine cell differentiation and function.Results653 genes were identified with regulated PGR binding and differential expression during the WOI. These were involved in regulating inflammatory response, xenobiotic metabolism, EMT, cell death, interleukin/STAT signaling, estrogen response, and MTORC1 response. Transcriptome of the epithelium identified 3,052 DEGs, of which 658 were uniquely regulated. Transcription factors IRF8 and MEF2C were found to be regulated in the epithelium during the WOI at the protein level, suggesting potentially important functions that are previously unrecognized.ConclusionPGR binds the genomic regions of genes regulating critical processes in uterine receptivity and function.PrécisUsing a combination of RNA-seq and PGR ChIP-seq, novel signaling pathways and epithelial regulators were identified in the endometrium of fertile women during the window of implantation.

scholarly journals A Genome-Wide Identification of Genes Undergoing Recombination and Positive Selection inNeisseria

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Dong Yu ◽  
Yuan Jin ◽  
Zhiqiu Yin ◽  
Hongguang Ren ◽  
Wei Zhou ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Molecular Mechanisms ◽  
Acid Sites ◽  
Gram Negative Bacteria ◽  
Orthologous Genes ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Functional Analyses

Currently, there is particular interest in the molecular mechanisms of adaptive evolution in bacteria.Neisseriais a genus of gram negative bacteria, and there has recently been considerable focus on its two human pathogenic speciesN. meningitidisandN. gonorrhoeae. Until now, no genome-wide studies have attempted to scan for the genes related to adaptive evolution. For this reason, we selected 18Neisseriagenomes (14N. meningitidis, 3N. gonorrhoeaeand 1 commensalN. lactamics) to conduct a comparative genome analysis to obtain a comprehensive understanding of the roles of natural selection and homologous recombination throughout the history of adaptive evolution. Among the 1012 core orthologous genes, we identified 635 genes with recombination signals and 10 genes that showed significant evidence of positive selection. Further functional analyses revealed that no functional bias was found in the recombined genes. Positively selected genes are prone to DNA processing and iron uptake, which are essential for the fundamental life cycle. Overall, the results indicate that both recombination and positive selection play crucial roles in the adaptive evolution ofNeisseriagenomes. The positively selected genes and the corresponding amino acid sites provide us with valuable targets for further research into the detailed mechanisms of adaptive evolution inNeisseria.

Phylogeny of Mycobacterium avium strains inferred from glycopeptidolipid biosynthesis pathway genes

Microbiology ◽  
2004 ◽  
Vol 150 (6) ◽  
pp. 1699-1706 ◽  
Author(s):  
Elzbieta Krzywinska ◽  
Jaroslaw Krzywinski ◽  
Jeffrey S. Schorey
Keyword(s):  
Mycobacterium Avium ◽  
Epidemiological Studies ◽  
Genomic Region ◽  
Opportunistic Pathogens ◽  
Apparent Lack ◽  
Alternative Placement ◽  
Multiple Origins ◽  
Serotype 1 ◽  
History Of ◽  
Genomic Regions

The Mycobacterium avium complex (MAC) encompasses two species, M. avium and Mycobacterium intracellulare, which are opportunistic pathogens of humans and animals. The standard method of MAC strain differentiation is serotyping based on a variation in the antigenic glycopeptidolipid (GPL) composition. To elucidate the relationships among M. avium serotypes a phylogenetic analysis of 13 reference and clinical M. avium strains from 8 serotypes was performed using as markers two genomic regions (890 bp of the gtfB gene and 2150 bp spanning the rtfA–mtfC genes) which are associated with the strains' serological properties. Strains belonging to three other known M. avium serotypes were not included in the phylogeny inference due to apparent lack of the marker sequences in their genomes, as revealed by PCR and Southern blot analysis. These studies suggest that serotypes prevalent in AIDS patients have multiple origins. In trees inferred from both markers, serotype 1 strains, known to have the simplest and shortest GPLs among all other serotypes, were polyphyletic. Likewise, comparisons of the inferred phylogenies with the molecular typing results imply that the existing tools used in epidemiological studies may be poor estimators of M. avium strain relatedness. Additionally, trees inferred from each marker had significantly incongruent topologies due to a well supported alternative placement of strain 2151, suggesting a complex evolutionary history of this genomic region.

scholarly journals FINEMAP: Efficient variable selection using summary data from genome-wide association studies

2015 ◽  
Author(s):  
Christian Benner ◽  
Chris C.A. Spencer ◽  
Samuli Ripatti ◽  
Matti Pirinen
Keyword(s):  
Fine Mapping ◽  
Molecular Mechanisms ◽  
Search Algorithm ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Promising Tool ◽  
Genome Wide ◽  
Genomic Regions ◽  
Summary Data

Motivation: The goal of fine-mapping in genomic regions associated with complex diseases and traits is to identify causal variants that point to molecular mechanisms behind the associations. Recent fine-mapping methods using summary data from genome-wide association studies rely on exhaustive search through all possible causal configurations, which is computationally expensive. Results: We introduce FINEMAP, a software package to efficiently explore a set of the most important causal configurations of the region via a shotgun stochastic search algorithm. We show that FINEMAP produces accurate results in a fraction of processing time of existing approaches and is therefore a promising tool for analyzing growing amounts of data produced in genome-wide association studies. Availability: FINEMAP v1.0 is freely available for Mac OS X and Linux at http://www.christianbenner.com.

scholarly journals MCRiceRepGP: a framework for identification of sexual reproduction associated coding and lincRNA genes in rice

2018 ◽  
Author(s):  
Agnieszka A. Golicz ◽  
Prem L. Bhalla ◽  
Mohan B. Singh
Keyword(s):  
Machine Learning ◽  
Decision Analysis ◽  
Sexual Reproduction ◽  
Web Application ◽  
Molecular Mechanisms ◽  
Rice Genome ◽  
Protein Coding ◽  
Genome Wide ◽  
Plant Sexual Reproduction ◽  
Global Food

AbstractSexual reproduction in plants underpins global food production and evolution. It is a complex process, requiring intricate signalling pathways integrating a multitude of internal and external cues. However, key players and especially non-coding genes controlling plant sexual reproduction remain elusive. We report the development of MCRiceRepGP a novel machine learning framework, which integrates genomic, transcriptomic, homology and available phenotypic evidence and employs multi-criteria decision analysis and machine learning to predict coding and non-coding genes involved in rice sexual reproduction.The rice genome was re-annotated using deep sequencing transcriptomic data from reproduction-associated tissues/cell types identifying novel putative protein coding genes, transcript isoforms and long intergenic non-coding RNAs (lincRNAs). MCRiceRepGP was used for genome-wide discovery of sexual reproduction associated genes in rice; 2,275 protein-coding and 748 lincRNA genes were predicted to be involved in sexual reproduction. The annotation performed and the genes identified, especially the ones for which mutant lines with phenotypes are available provide a valuable resource. The analysis of genes identified gives insights into the genetic architecture of plant sexual reproduction. MCRiceRepGP can be used in combination with other genome-wide studies, like GWAS, giving more confidence that the genes identified are associated with the biological process of interest. As more data, especially about mutant plant phenotypes will become available, the power of MCRiceRepGP with grow providing researchers with a tool to identify candidate genes for future experiments. MCRiceRepGP is available as a web application (http://mcgplannotator.com/MCRiceRepGP/)Significance statementRice is a staple food crop plant for over half of the world’s population and sexual reproduction resulting in grain formation is a key process underpinning global food security. Despite considerable research efforts, much remains to be learned about the molecular mechanisms involved in rice sexual reproduction. We have developed MCRiceRepGP, a novel framework which allows prediction of sexual reproduction associated genes using multi-omics data, multicriteria decision analysis and machine learning. The genes identified and the methodology developed will become a significant resource for the plant research community.

scholarly journals Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1480
Author(s):  
Adam Abied ◽  
Lei Xu ◽  
Bahlibi W. Sahlu ◽  
Feng Xing ◽  
Abulgasim Ahbara ◽  
...  
Keyword(s):  
Demographic History ◽  
Adaptive Immune Response ◽  
Conservation Strategies ◽  
Distribution Analysis ◽  
Runs Of Homozygosity ◽  
Sheep Breeds ◽  
Indigenous Sheep ◽  
Genome Wide ◽  
History Of ◽  
Genomic Regions

Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five local Chinese sheep breeds belonging to different geographical locations. We identified 3046 ROHs within the study breed individuals, among which the longer segments (>1–5 Mb) were dominant. On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the history of modern and ancient inbreeding, which may affect the genomes of Chinese indigenous sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi, Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection signatures frequently in line with long ROH. These regions included candidate genes associated with disease resistance traits (5S_rRNA), the innate and adaptive immune response (HERC2 and CYFIP1), digestion and metabolism (CENPJ), growth (SPP1), body size and developments (GJB2 and GJA3). This study highlighted new insights into the ROH patterns and provides a basis for future breeding and conservation strategies of Chinese sheep breeds.

Genome-wide association mapping and candidate gene analysis for seed shape in soybean (Glycine max)

2019 ◽  
Vol 70 (8) ◽  
pp. 684 ◽  
Author(s):  
Xue Zhao ◽  
Wenjing Li ◽  
Xiaoyue Zhao ◽  
Jinyang Wang ◽  
Zhiyang Liu ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Analysis ◽  
Quantitative Trait ◽  
Molecular Mechanisms ◽  
Environmental Stability ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Seed Shape ◽  
Genome Wide ◽  
Genomic Regions

Seed shape (SS) of soybean (Glycine max (L.) Merr.) is an important morphological trait that significantly affects the quality of marketable seed. Study of the genetic architecture of SS is important and basic to soybean molecular breeding. In the present study, a natural soybean population of 202 diverse accessions mainly from China was used to analyse the genetic basis of SS via genome-wide association analysis (GWAS), which was based on single-nucleotide polymorphisms (SNP) generated by specific-locus amplified fragment sequencing method. In total, 27335 SNPs were finally identified with minor allele frequencies >5%. By using GWAS, 14 quantitative trait nucleotides (QTNs) were identified to be associated with seed length, 13 with seed width and 21 with seed thickness in four tested environments. Among these QTNs, 21 QTNs overlapped or were located in the linked genomic regions of the reported quantitative trait loci related to SS or seed weight; and the other 27 QTNs were novel loci for SS. Ten QTNs showed environmental stability and were detected under at least two environments. In total, 83 genes were predicted in the 200-kbp flanking region of six stable QTNs that could be detected under >three environments. Gene-based association analysis was performed by using 38 accessions of diverse SS; 778 SNPs were found in the 83 genes based on 38 accessions, and 270 SNPs from 41 genes were found significantly associated with SS. Twenty-eight genes were environmentally stable and/or pleiotropic in controlling two or more SS-related traits at the same time. The identified loci along with the candidate genes could be of great value for studying the molecular mechanisms underlying SS and improving the potential seed yield of soybean.

scholarly journals Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis

2015 ◽  
Vol 112 (34) ◽  
pp. E4802-E4810 ◽  
Author(s):  
Dawn H. Nagel ◽  
Colleen J. Doherty ◽  
Jose L. Pruneda-Paz ◽  
Robert J. Schmitz ◽  
Joseph R. Ecker ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Critical Role ◽  
Gene Promoters ◽  
Biological Processes ◽  
Functional Studies ◽  
Genome Wide ◽  
Genomic Regions

The circadian clock in Arabidopsis exerts a critical role in timing multiple biological processes and stress responses through the regulation of up to 80% of the transcriptome. As a key component of the clock, the Myb-like transcription factor CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is able to initiate and set the phase of clock-controlled rhythms and has been shown to regulate gene expression by binding directly to the evening element (EE) motif found in target gene promoters. However, the precise molecular mechanisms underlying clock regulation of the rhythmic transcriptome, specifically how clock components connect to clock output pathways, is poorly understood. In this study, using ChIP followed by deep sequencing of CCA1 in constant light (LL) and diel (LD) conditions, more than 1,000 genomic regions occupied by CCA1 were identified. CCA1 targets are enriched for a myriad of biological processes and stress responses, providing direct links to clock-controlled pathways and suggesting that CCA1 plays an important role in regulating a large subset of the rhythmic transcriptome. Although many of these target genes are evening expressed and contain the EE motif, a significant subset is morning phased and enriched for previously unrecognized motifs associated with CCA1 function. Furthermore, this work revealed several CCA1 targets that do not cycle in either LL or LD conditions. Together, our results emphasize an expanded role for the clock in regulating a diverse category of genes and key pathways in Arabidopsis and provide a comprehensive resource for future functional studies.

scholarly journals Reappraisal of Atrial fibrillation: interaction between hyperCoagulability, Electrical remodelling and Vascular destabilisation in the progression of AF (RACE V) Tissue Bank Project: study design

2021 ◽  
Author(s):  
M. D. Gilbers ◽  
E. Bidar ◽  
B. Maesen ◽  
S. Zeemering ◽  
A. Isaacs ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Cardiac Surgery ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Tissue Bank ◽  
Project Study ◽  
Genome Wide ◽  
History Of ◽  
The Individual

Abstract Background The development of atrial fibrillation (AF) is a complex multifactorial process. Over the past few decades, much has been learned about the pathophysiological processes that can lead to AF from a variety of specific disease models in animals. However, our ability to recognise these disease processes in AF patients is still limited, which has contributed to the limited progress in improving rhythm control in AF. Aims/objectives We believe that a better understanding and detection of the individual pathophysiological mechanisms underlying AF is a prerequisite for developing patient-tailored therapies. The RACE V Tissue Bank Project will contribute to the unravelling of the main molecular mechanisms of AF by studying histology and genome-wide RNA expression profiles and combining this information with detailed phenotyping of patients undergoing cardiac surgery. Methods As more and more evidence suggests that AF may occur not only during the first days but also during the months and years after surgery, we will systematically study the incidence of AF during the first years after cardiac surgery in patients with or without a history of AF. Both the overall AF burden as well as the pattern of AF episodes will be studied. Lastly, we will study the association between the major molecular mechanisms and the clinical presentation of the patients, including the incidence and pattern of AF during the follow-up period. Conclusion The RACE V Tissue Bank Project combines deep phenotyping of patients undergoing cardiac surgery, including rhythm follow-up, analysis of molecular mechanisms, histological analysis and genome-wide RNA sequencing. This approach will provide detailed insights into the main pathological alterations associated with AF in atrial tissue and thereby contribute to the development of individualised, mechanistically informed patient-tailored treatment for AF.

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