A Mechanism for Genome Size Reduction Following Genomic Rearrangements.

Abstract:

:The factors behind genome size evolution have been of great interest, considering that eukaryotic genomes vary in size by more than three orders of magnitude. Using a model of two wild peanut relatives, Arachis duranensis and Arachis ipaensis, in which one genome experienced large rearrangements, we find that the main determinant in genome size reduction is a set of inversions that occurred in A. duranensis, and subsequent net sequence removal in the inverted regions. We observe a general pattern in which sequence is lost more rapidly at newly distal (telomeric) regions than it is gained at newly proximal (pericentromeric) regions - resulting in net sequence loss in the inverted regions. The major driver of this process is recombination, determined by the chromosomal location. Any type of genomic rearrangement that exposes proximal regions to higher recombination rates can cause genome size reduction by this mechanism. In comparisons between A. duranensis and A. ipaensis, we find that the inversions all occurred in A. duranensis. Sequence loss in those regions was primarily due to removal of transposable elements. Illegitimate recombination is likely the major mechanism responsible for the sequence removal, rather than unequal intrastrand recombination. We also measure the relative rate of genome size reduction in these two Arachis diploids. We also test our model in other plant species and find that it applies in all cases examined, suggesting our model is widely applicable.

journal_name

Front Genet

journal_title

Frontiers in genetics

authors

Ren L,Huang W,Cannon EKS,Bertioli DJ,Cannon SB

doi

10.3389/fgene.2018.00454

subject

Has Abstract

pub_date

2018-10-09 00:00:00

pages

454

issn

1664-8021

journal_volume

9

pub_type

杂志文章
  • Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent.

    abstract::Among people of European descent, the ability to digest lactose into adulthood arose via strong positive selection of a highly advantageous allele encompassing the lactase gene. Lactose-tolerant and intolerant individuals may have different disease risks due to the shared genetics of their haplotype block. Therefore, ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.558762

    authors: Joslin SEK,Durbin-Johnson BP,Britton M,Settles ML,Korf I,Lemay DG

    更新日期:2020-10-29 00:00:00

  • Comparison of the Transcriptome of the Ovine Mammary Gland in Lactating and Non-lactating Small-Tailed Han Sheep.

    abstract::Small-Tailed Han (STH) sheep are known for their high fecundity, but the survival of lambs is compromised and influences the commercial return from farming these sheep, with this being attributed in part to starvation from insufficient milk production by the ewes. In this study, the transcriptome profiles of the mamma...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00472

    authors: Wang J,Zhou H,Hickford JGH,Hao Z,Shen J,Luo Y,Hu J,Liu X,Li S

    更新日期:2020-05-21 00:00:00

  • The Toolbox for Fiber Flax Breeding: A Pipeline From Gene Expression to Fiber Quality.

    abstract::The goal of any plant breeding program is to improve quality of a target crop. Crop quality is a comprehensive feature largely determined by biological background. To improve the quality parameters of crops grown for the production of fiber, a functional approach was used to search for genes suitable for the effective...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.589881

    authors: Galinousky D,Mokshina N,Padvitski T,Ageeva M,Bogdan V,Kilchevsky A,Gorshkova T

    更新日期:2020-11-12 00:00:00

  • The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics.

    abstract::The study of microorganisms that pervade each and every part of this planet has encountered many challenges through time such as the discovery of unknown organisms and the understanding of how they interact with their environment. The aim of this review is to take the reader along the timeline and major milestones tha...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2015.00348

    authors: Escobar-Zepeda A,Vera-Ponce de León A,Sanchez-Flores A

    更新日期:2015-12-17 00:00:00

  • Exploring the RNA Gap for Improving Diagnostic Yield in Primary Immunodeficiencies.

    abstract::Challenges in diagnosing primary immunodeficiency are numerous and diverse, with current whole-exome and whole-genome sequencing approaches only able to reach a molecular diagnosis in 25-60% of cases. We assess these problems and discuss how RNA-focused analysis has expanded and improved in recent years and may now be...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.01204

    authors: Lye JJ,Williams A,Baralle D

    更新日期:2019-12-11 00:00:00

  • Multi-genome alignment for quality control and contamination screening of next-generation sequencing data.

    abstract::The availability of massive amounts of DNA sequence data, from 1000s of genomes even in a single project has had a huge impact on our understanding of biology, but also creates several problems for biologists carrying out those experiments. Bioinformatic analysis of sequence data is perhaps the most obvious challenge ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2014.00031

    authors: Hadfield J,Eldridge MD

    更新日期:2014-02-20 00:00:00

  • Aberrant epigenetic regulators control expansion of human CD34+ hematopoietic stem/progenitor cells.

    abstract::Transcription is a tightly regulated process ensuring the proper expression of numerous genes regulating all aspects of cellular behavior. Transcription factors regulate multiple genes including other transcription factors that together control a highly complex gene network. The transcriptional machinery can be "hijac...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2013.00254

    authors: Faridi F,Ponnusamy K,Quagliano-Lo Coco I,Chen-Wichmann L,Grez M,Henschler R,Wichmann C

    更新日期:2013-11-28 00:00:00

  • Transcript Isoforms of SLC7A11-AS1 Are Associated With Varicocele-Related Male Infertility.

    abstract::Oxidative stress is one of the crucial mediators of varicocele-related male infertility. Recently, roles of long noncoding RNAs (lncRNAs) in oxidative stress have begun to emerge, however, little is known about their role in male infertility. The aim of this study was to determine the role of lncRNA SLC7A11-AS1 in var...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.01015

    authors: Sanei-Ataabadi N,Mowla SJ,Nasr-Esfahani MH

    更新日期:2020-09-11 00:00:00

  • Sulfite Alters the Mitochondrial Network in Molybdenum Cofactor Deficiency.

    abstract::Molybdenum cofactor deficiency (MoCD) is an autosomal recessive disorder belonging to the large family of inborn errors in metabolism. Patients typically present with encephalopathy and seizures early after birth and develop severe neurodegeneration within the first few weeks of life. The main pathomechanism underlyin...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.594828

    authors: Mellis AT,Roeper J,Misko AL,Kohl J,Schwarz G

    更新日期:2021-01-07 00:00:00

  • Beta 1, Beta 2 and Beta 3 Adrenergic Receptor Gene Polymorphisms in a Southeastern European Population.

    abstract::Genetic polymorphisms in β1-, β2- and β3-adrenergic receptors (β-ARs) have been associated with chronic non-communicable disorders, such as cardiovascular diseases, asthma, chronic obstructive pulmonary disease (COPD) and obesity, as well as β-agonists and antagonists response and toxicity. The purpose of this study w...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00560

    authors: Katsarou MS,Karathanasopoulou A,Andrianopoulou A,Desiniotis V,Tzinis E,Dimitrakis E,Lagiou M,Charmandari E,Aschner M,Tsatsakis AM,Chrousos GP,Drakoulis N

    更新日期:2018-11-28 00:00:00

  • Differentially Expressed MiRNAs and tRNA Genes Affect Host Homeostasis During Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Infections in Young Pigs.

    abstract::Background: Porcine respiratory and reproductive syndrome virus (PRRSV) is a single-stranded RNA virus member that infects pigs and causes losses to the commercial industry reaching upward of a billion dollars annually in combined direct and indirect costs. The virus can be separated into etiologies that contain multi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00691

    authors: Fleming DS,Miller LC

    更新日期:2019-08-02 00:00:00

  • Insights Into Non-coding RNAs as Novel Antimicrobial Drugs.

    abstract::Multidrug resistant bacteria are a serious worldwide problem, especially carbapenem-resistant Enterobacteriaceae (such as Klebsiella pneumoniae and Escherichia coli), Acinetobacter baumannii and Pseudomonas aeruginosa. Since the emergence of extensive and pan-drug resistant bacteria there are few antibiotics left to t...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.00057

    authors: Parmeciano Di Noto G,Molina MC,Quiroga C

    更新日期:2019-02-22 00:00:00

  • Phthalate Exposure and Long-Term Epigenomic Consequences: A Review.

    abstract::Phthalates are esters of phthalic acid which are used in cosmetics and other daily personal care products. They are also used in polyvinyl chloride (PVC) plastics to increase durability and plasticity. Phthalates are not present in plastics by covalent bonds and thus can easily leach into the environment and enter the...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2020.00405

    authors: Dutta S,Haggerty DK,Rappolee DA,Ruden DM

    更新日期:2020-05-06 00:00:00

  • Revisiting Non-BRCA1/2 Familial Whole Exome Sequencing Datasets Implicates NCK1 as a Cancer Gene.

    abstract::Through linkage and candidate gene screening, many breast cancer (BC) predisposition genes have been identified in the past 20 years. However, the majority of genetic risks that contribute to familial BC remains undetermined. In this study, we revisited whole exome sequencing datasets from non-BRCA1/2 familial BC pati...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00527

    authors: Yin J,Wu K,Ma Q,Dong H,Zhu Y,Hu L,Kong X

    更新日期:2019-06-04 00:00:00

  • Mathematical Models of Organoid Cultures.

    abstract::Organoids are engineered three-dimensional tissue cultures derived from stem cells and capable of self-renewal and self-organization into a variety of progenitors and differentiated cell types. An organoid resembles the cellular structure of an organ and retains some of its functionality, while still being amenable to...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.00873

    authors: Montes-Olivas S,Marucci L,Homer M

    更新日期:2019-09-19 00:00:00

  • Gene and Blood Analysis Reveal That Transfer from Brackish Water to Freshwater Is More Stressful to the Silverside Odontesthes humensis.

    abstract::Silversides are fish that inhabit marine coastal waters, coastal lagoons, and estuarine regions in southern South America. The freshwater (FW) silversides have the ability to tolerate salinity variations. Odontesthes humensis have similar habitats and biological characteristics of congeneric O. bonariensis, the most s...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00028

    authors: Silveira TLR,Martins GB,Domingues WB,Remião MH,Barreto BF,Lessa IM,Santos L,Pinhal D,Dellagostin OA,Seixas FK,Collares T,Robaldo RB,Campos VF

    更新日期:2018-02-06 00:00:00

  • Construction and Analysis of a ceRNA Network Reveals Potential Prognostic Markers in Colorectal Cancer.

    abstract::Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide and is derived from an accumulation of genetic and epigenetic changes. This study explored potential prognostic markers in CRC via the construction and in-depth analysis of a competing endogenous RNA (ceRNA) network, which was gene...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00418

    authors: Guo L,Yang G,Kang Y,Li S,Duan R,Shen L,Jiang W,Qian B,Yin Z,Liang T

    更新日期:2020-05-08 00:00:00

  • Using mice to model Alzheimer's dementia: an overview of the clinical disease and the preclinical behavioral changes in 10 mouse models.

    abstract::The goal of this review is to discuss how behavioral tests in mice relate to the pathological and neuropsychological features seen in human Alzheimer's disease (AD), and present a comprehensive analysis of the temporal progression of behavioral impairments in commonly used AD mouse models that contain mutations in amy...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2014.00088

    authors: Webster SJ,Bachstetter AD,Nelson PT,Schmitt FA,Van Eldik LJ

    更新日期:2014-04-23 00:00:00

  • A Causality Perspective of Genomic Breed Composition for Composite Animals.

    abstract::Genomic breed composition (GBC) of an individual animal refers to the partition of its genome according to the inheritance from its ancestors or ancestral breeds. For crossbred or composite animals, knowing their GBC is useful to estimate heterosis, to characterize their actual inheritance from foundation breeds, and ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.546052

    authors: Wu XL,Li Z,Wang Y,He J,Rosa GJM,Ferretti R,Genho J,Tait RG Jr,Parham J,Schultz T,Bauck S

    更新日期:2020-10-30 00:00:00

  • Quantifying Gene Essentiality Based on the Context of Cellular Components.

    abstract::Different genes have their protein products localized in various subcellular compartments. The diversity in protein localization may serve as a gene characteristic, revealing gene essentiality from a subcellular perspective. To measure this diversity, we introduced a Subcellular Diversity Index (SDI) based on the Gene...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.01342

    authors: Jia K,Zhou Y,Cui Q

    更新日期:2020-01-21 00:00:00

  • DNA methyltransferases and TETs in the regulation of differentiation and invasiveness of extra-villous trophoblasts.

    abstract::Specialized cell types of trophoblast cells form the placenta in which each cell type has particular properties of proliferation and invasion. The placenta sustains the growth of the fetus throughout pregnancy and any aberrant trophoblast differentiation or invasion potentially affects the future health of the child a...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2013.00265

    authors: Logan PC,Mitchell MD,Lobie PE

    更新日期:2013-12-04 00:00:00

  • Genomic basis of evolutionary change: evolving immunity.

    abstract::Complex traits are manifestations of intricate gene interaction networks. Evolution of complex traits revolves around the genetic variation in such networks. Genomics has increased our ability to investigate the complex gene interaction networks, and characterize the extent of genetic variation in these networks. Immu...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00222

    authors: Wertheim B

    更新日期:2015-06-19 00:00:00

  • Spectrum of RB1 Germline Mutations and Clinical Features in Unrelated Chinese Patients With Retinoblastoma.

    abstract::Retinoblastoma (Rb) is a primary intraocular malignant tumor that occurs primarily in children, and results from loss-of-function mutations in the RB transcriptional corepressor 1 (RB1) gene. Genetic testing forms the basis of genetic counseling for affected families, as well as for clinical management of this disease...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00142

    authors: Lan X,Xu W,Tang X,Ye H,Song X,Lin L,Ren X,Yu G,Zhang H,Wu S

    更新日期:2020-03-11 00:00:00

  • Identifying Discriminative Biological Function Features and Rules for Cancer-Related Long Non-coding RNAs.

    abstract::Cancer has been a major public health problem worldwide for many centuries. Cancer is a complex disease associated with accumulative genetic mutations, epigenetic aberrations, chromosomal instability, and expression alteration. Increasing lines of evidence suggest that many non-coding transcripts, which are termed as ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.598773

    authors: Zhu L,Yang X,Zhu R,Yu L

    更新日期:2020-12-16 00:00:00

  • Profiling Transcriptional Regulation and Functional Roles of Schistosoma mansoni c-Jun N-Terminal Kinase.

    abstract::Mitogen-activated protein kinases (MAPKs) play a regulatory role and influence various biological activities, such as cell proliferation, differentiation, and survival. Our group has demonstrated through functional studies that Schistosoma mansoni c-Jun N-terminal kinase (SmJNK) MAPK is involved in the parasite's deve...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.01036

    authors: Gava SG,Tavares NC,Falcone FH,Oliveira G,Mourão MM

    更新日期:2019-10-18 00:00:00

  • Association of Apelin and Apelin Receptor Polymorphisms With the Risk of Comorbid Depression and Anxiety in Coronary Heart Disease Patients.

    abstract::The Apelin (APLN)/apelin receptor (APLNR) signaling pathway is a newly identified regulator in various cardiovascular diseases, which is considered as a candidate pathway for the occurrence of coronary heart disease (CHD), depression, and anxiety. The goal of this study was to investigate the association between APLN/...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00893

    authors: Wang Y,Liu W,Xiao Y,Yuan H,Wang F,Jiang P,Luo Z

    更新日期:2020-08-11 00:00:00

  • A Transcriptomics-Based Meta-Analysis Combined With Machine Learning Identifies a Secretory Biomarker Panel for Diagnosis of Pancreatic Adenocarcinoma.

    abstract::Pancreatic ductal adenocarcinoma (PDAC) is generally incurable due to the late diagnosis and absence of markers that are concordant with expression in several sample sources (i.e., tissue, blood, plasma) and platforms (i.e., Microarray, sequencing). We optimized meta-analysis of 19 PDAC (tissue and blood) transcriptom...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.572284

    authors: Khatri I,Bhasin MK

    更新日期:2020-09-10 00:00:00

  • Functional evaluation of DNA repair in human biopsies and their relation to other cellular biomarkers.

    abstract::Thousands of DNA lesions are estimated to occur in each cell every day and almost all are recognized and repaired. DNA repair is an essential system that prevents accumulation of mutations which can lead to serious cellular malfunctions. Phenotypic evaluation of DNA repair activity of individuals is a relatively new a...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2014.00116

    authors: Slyskova J,Langie SA,Collins AR,Vodicka P

    更新日期:2014-05-23 00:00:00

  • Perspectives on the Role of Histone Modification in Breast Cancer Progression and the Advanced Technological Tools to Study Epigenetic Determinants of Metastasis.

    abstract::Metastasis is a complex process that involved in various genetic and epigenetic alterations during the progression of breast cancer. Recent evidences have indicated that the mutation in the genome sequence may not be the key factor for increasing metastatic potential. Epigenetic changes were revealed to be important f...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2020.603552

    authors: Zhuang J,Huo Q,Yang F,Xie N

    更新日期:2020-10-29 00:00:00

  • Identification of 13 Key Genes Correlated With Progression and Prognosis in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis.

    abstract::Hepatocellular carcinoma (HCC) remains hard to diagnose early and cure due to a lack of accurate biomarkers and effective treatments. Hence, it is necessary to explore the tumorigenesis and tumor progression of HCC to discover new biomarkers for clinical treatment. We performed weighted gene co-expression network anal...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00153

    authors: Gu Y,Li J,Guo D,Chen B,Liu P,Xiao Y,Yang K,Liu Z,Liu Q

    更新日期:2020-02-28 00:00:00