A DISCRETE MODEL OF EVOLUTION OF SMALL PARALOG FAMILIES

2007 ◽  
Vol 17 (06) ◽  
pp. 933-955 ◽  
Author(s):  
JERZY TIURYN ◽  
DAMIAN WÓJTOWICZ ◽  
RYSZARD RUDNICKI
Keyword(s):  
Discrete Model ◽  
Gene Loss ◽  
Gene Families ◽  
Paralogous Gene ◽  
Discrete Time Markov Chain ◽  
Microbial Genomes ◽  
Asymptotic Size ◽  
A Genome ◽  
Logarithmic Distribution ◽  
Paralog Family

We introduce and analyze a simple probabilistic model of genome evolution. It is based on three fundamental evolutionary events: gene loss, duplication and accumulated change. We are mainly interested in asymptotic size distribution of small paralogous gene families in a genome. This is motivated by previous works which consisted in fitting the available genomic data into, what is called, paralog distributions. This formalism is described as a discrete-time Markov chain. The formulas for equilibrium paralog family sizes are derived. Moreover, we show that when probabilities of gene removal and duplication are small and close to each other, then the resulting distribution is close to logarithmic distribution. Some empirical results for microbial genomes are presented.

SIZE DISTRIBUTION OF GENE FAMILIES IN A GENOME

2014 ◽  
Vol 24 (04) ◽  
pp. 697-717 ◽  
Author(s):  
RYSZARD RUDNICKI ◽  
JERZY TIURYN
Keyword(s):  
Size Distribution ◽  
Genome Evolution ◽  
Gene Mutation ◽  
Probabilistic Model ◽  
Gene Loss ◽  
Genomic Data ◽  
Gene Families ◽  
Paralogous Gene ◽  
A Genome ◽  
Theoretical Results

We consider a probabilistic model of genome evolution. We are interested in size distribution of gene families. The model is based on three fundamental evolutionary events: gene loss, duplication and accumulated change. We assume that the probability of gene loss and duplication is constant and the probability of gene mutation mi depends on the size i of a family. We prove that size distribution of paralogous gene families in a genome converges to the equilibrium as time goes to infinity. Moreover, we show how this equilibrium depends on the sequence (mi). Theoretical results are compared with the available genomic data.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

scholarly journals Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes

2021 ◽  
Author(s):  
Lina Kloub ◽  
Sean Gosselin ◽  
Matthew Fullmer ◽  
Joerg Graf ◽  
J Peter Gogarten ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Large Scale ◽  
Single Gene ◽  
Gene Families ◽  
Microbial Evolution ◽  
Phylogenetic Distance ◽  
Secretion Systems ◽  
Type Iii Secretion Systems ◽  
A Genome ◽  
Conserved Gene

Abstract Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multi-gene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale dataset of over 22000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multi-gene transfer. Among other insights, we find that (i) the observed relative frequency of HMGT increases as divergence between genomes increases, (ii) HMGTs often have conserved gene functions, and (iii) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.

scholarly journals De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps

2020 ◽  
Vol 12 (6) ◽  
pp. 905-910 ◽  
Author(s):  
Ruoyu Liu ◽  
Kun Wang ◽  
Jun Liu ◽  
Wenjie Xu ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Metal Ion ◽  
De Novo ◽  
Demographic History ◽  
Gene Families ◽  
Phylogenetic Position ◽  
Cold Seeps ◽  
Nitrogen And Phosphorus ◽  
De Novo Genome Assembly ◽  
A Genome

Abstract Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.

Novel paralogous gene families with potential function in legume nodules and seeds

2006 ◽  
Vol 9 (2) ◽  
pp. 142-146 ◽  
Author(s):  
Kevin AT Silverstein ◽  
Michelle A Graham ◽  
Kathryn A VandenBosch
Keyword(s):  
Potential Function ◽  
Gene Families ◽  
Paralogous Gene

scholarly journals A Genome-Wide Analysis of the Pentatricopeptide Repeat (PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (Citrullus lanatus)

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1125
Author(s):  
Saminathan Subburaj ◽  
Luhua Tu ◽  
Kayoun Lee ◽  
Gwang-Soo Park ◽  
Hyunbae Lee ◽  
...  
Keyword(s):  
Gene Family ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Citrullus Lanatus ◽  
Gene Families ◽  
Nucleotide Polymorphisms ◽  
Pentatricopeptide Repeat ◽  
Flesh Color ◽  
Large Gene ◽  
A Genome

Watermelon (Citrullus lanatus) is an economically important fruit crop grown for consumption of its large edible fruit flesh. Pentatricopeptide-repeat (PPR) encoding genes, one of the large gene families in plants, are important RNA-binding proteins involved in the regulation of plant growth and development by influencing the expression of organellar mRNA transcripts. However, systematic information regarding the PPR gene family in watermelon remains largely unknown. In this comprehensive study, we identified and characterized a total of 422 C. lanatus PPR (ClaPPR) genes in the watermelon genome. Most ClaPPRs were intronless and were mapped across 12 chromosomes. Phylogenetic analysis showed that ClaPPR proteins could be divided into P and PLS subfamilies. Gene duplication analysis suggested that 11 pairs of segmentally duplicated genes existed. In-silico expression pattern analysis demonstrated that ClaPPRs may participate in the regulation of fruit development and ripening processes. Genotyping of 70 lines using 4 single nucleotide polymorphisms (SNPs) from 4 ClaPPRs resulted in match rates of over 0.87 for each validated SNPs in correlation with the unique phenotypes of flesh color, and could be used in differentiating red, yellow, or orange watermelons in breeding programs. Our results provide significant insights for a comprehensive understanding of PPR genes and recommend further studies on their roles in watermelon fruit growth and ripening, which could be utilized for cultivar development of watermelon.

scholarly journals Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata

2020 ◽  
Vol 12 (6) ◽  
pp. 948-964
Author(s):  
Melissa B DeBiasse ◽  
William N Colgan ◽  
Lincoln Harris ◽  
Bradley Davidson ◽  
Joseph F Ryan
Keyword(s):  
Gene Loss ◽  
Morphological Diversity ◽  
Gene Families ◽  
Model Species ◽  
Hox Gene ◽  
Hox Cluster ◽  
Species Phylogeny ◽  
Potential Impact ◽  
Important Nodes ◽  
Hox Clusters

Abstract Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, “inflated” atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.

scholarly journals Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 730 ◽  
Author(s):  
Sun ◽  
Wang ◽  
Ma ◽  
Li ◽  
Liu
Keyword(s):  
Somatic Embryogenesis ◽  
Upland Cotton ◽  
Expression Profiles ◽  
Gene Families ◽  
Early Response ◽  
Auxin Signaling ◽  
Evolutionary Divergence ◽  
Genome Wide ◽  
A Genome ◽  
Early Response Genes

Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.

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