scholarly journals Chromosome evolution at the origin of the ancestral vertebrate genome

2018 ◽  
Author(s):  
Christine Sacerdot ◽  
Alexandra Louis ◽  
Céline Bon ◽  
Hugues Roest Crollius
Keyword(s):  
Common Ancestor ◽  
Duplicate Gene ◽  
Vertebrate Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Chromosome Fusions ◽  
The Common ◽  
Insight Into ◽  
Ancestral Vertebrate ◽  
Animal Genomes

ABSTRACTAbout 450 million years ago, a marine chordate was subject to two successive whole genome duplications (WGDs) before becoming the common ancestor of vertebrates and diversifying into the more than 60,000 species found today. Here, we reconstruct in details the evolution of chromosomes of this early vertebrate along successive steps of the two WGD. We first compared 61 extant animal genomes to build a highly contiguous order of genes in a 326 million years old ancestral Amniota genome. In this genome, we established a well-supported list of duplicated genes originating from the WGDs to link chromosomes in tetrads, a telltale signature of these events. This enabled us to reconstruct a scenario where a pre-vertebrate genome composed of 17 chromosomes duplicated into 34 chromosomes, and was subject to 7 chromosome fusions before duplicating again into 54 chromosomes. After the separation of Agnatha (jawless fish) and Gnathostomata, four more fusions took place to form the ancestral Euteleostomi genome of 50 chromosomes. These results firmly establish the occurrence of the two WGD, resolving in particular the ambiguity raised by the analysis of the lamprey genetic map. In addition, we provide insight into the origin of homologous micro-chromosomes found in the chicken and the gar genomes. This work provides a foundation for studying the evolution of vertebrate chromosomes from the standpoint of a common ancestor, and particularly the pattern of duplicate gene retention and loss that resulted in the gene composition of extant genomes.

scholarly journals Reconstruction of ancestral diploid karyotype and evolutionary trajectories leading to the formation of Camelina sativa chromosomes

2020 ◽  
Author(s):  
Zhikang Zhang ◽  
Fanbo Meng ◽  
Pengchuan Sun ◽  
Jiaqing Yuan ◽  
Ke Ge ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Karyotype Evolution ◽  
Camelina Sativa ◽  
End Joining ◽  
Chromosome Fusion ◽  
Evolutionary Trajectories ◽  
Chromosome Fusions ◽  
Circular Chromosomes ◽  
Insight Into ◽  
Lines Of Evidence

Abstract Background: Belonging to lineage Ⅰ of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineage Ⅰ (Ancestral Crucifer karyotype, ACK). The karyotype evolutionary trajectories of the C. sativa chromosomes are currently unknown. Here, we managed to adopt a telomere-centric theory proposed previously to explain the karyotype evolution in C. sativa. Results: By characterizing the homology between A. lyrate and C. sativa chromosomes, we inferred ancestral diploid karyotype of C. sativa (ADK), including 7 ancestral chromosomes, and reconstructed the karyotype evolutionary trajectories leading to the formation of C. sativa genome. The process involved 2 chromosome fusions. We found that sub-genomes Cs-G1 and Cs-G2 may share a closer common ancestor than Cs-G3. Together with other lines of evidence from Arabidopsis, we propose that the Brassicaceae plants, even the eudicots, follow a chromosome fusion mechanism favoring end-end joining of different chromosomes, rather than a mechanism favoring the formation circular chromosomes and nested chromosome fusion preferred by the monocots. Conclusions: The present work will contribute to understanding the structural and functional innovation of C. sativa chromosomes, providing insight into Brassicaceae karyotype evolution.

scholarly journals An updated explanation of ancestral karyotype changes and reconstruction of evolutionary trajectories to form Camelina sativa chromosomes

2020 ◽  
Author(s):  
Zhikang Zhang ◽  
Fanbo Meng ◽  
Pengchuan Sun ◽  
Jiaqing Yuan ◽  
Ke Ge ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Karyotype Evolution ◽  
Camelina Sativa ◽  
End Joining ◽  
Chromosome Fusion ◽  
Evolutionary Trajectories ◽  
Chromosome Fusions ◽  
Circular Chromosomes ◽  
Insight Into ◽  
Lines Of Evidence

Abstract Background: Belonging to lineage Ⅰ of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineage Ⅰ (Ancestral Crucifer karyotype, ACK). The karyotype evolutionary trajectories of the C. sativa chromosomes are currently unknown. Here, we managed to adopt a telomere-centric theory proposed previously to explain the karyotype evolution in C. sativa . Results: By characterizing the homology between A. lyrata and C. sativa chromosomes, we inferred ancestral diploid karyotype of C. sativa (ADK), including 7 ancestral chromosomes, and reconstructed the evolutionary trajectories leading to the formation of extant C. sativa genome. The process involved 2 chromosome fusions. We found that sub-genomes Cs-G1 and Cs-G2 may share a closer common ancestor than Cs-G3. Together with other lines of evidence from Arabidopsis, we propose that the Brassicaceae plants, even the eudicots, follow a chromosome fusion mechanism favoring end-end joining of different chromosomes, rather than a mechanism favoring the formation circular chromosomes and nested chromosome fusion preferred by the monocots. Conclusions: The present work will contribute to understanding the formation of C. sativa chromosomes, providing insight into Brassicaceae karyotype evolution.

scholarly journals Evolution of Lysine-Specific Demethylase 1 and REST Corepressor Gene Families and Their Molecular Interaction

2021 ◽  
Author(s):  
Montserrat Olivares ◽  
Gianluca Merello ◽  
Daniel Verbel ◽  
Marcela Gonzalez ◽  
María Andrés ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Molecular Biology ◽  
Gene Families ◽  
Whole Genome ◽  
Model Species ◽  
Whole Genome Duplications ◽  
Lysine Specific Demethylase ◽  
Genome Duplications ◽  
History Of ◽  
The Common

Abstract Lysine-specific demethylase 1A (LSD1) binds to RCOR gene family of corepressors to erase transcriptionally active marks on histones. Functional diversity in these complexes depends on the type of RCOR included, which modulates the complex´s catalytic activity. We studied the duplicative history of RCOR and LSD gene families, and analyzed the evolution of their interaction. We found that RCOR genes are the product of the two rounds of whole-genome duplications that occurred early in vertebrate evolution. In contrast, the origin of the LSD genes traces back before to the divergence of animals and plants. Coimmunoprecipitation experiments using resurrected RCOR and LSD1 proteins of the jawed vertebrate ancestor, and the common hop, date the origin of LSD1-RCOR interaction to the ancestor of animals, fungi, and plants. Overall, we trace LSD1-RCOR complex evolution and propose that animal, fungi, and plant non-model species offer advantages in addressing questions about the molecular biology of this epigenetic complex.

scholarly journals Dogon pronominal systems their nature and evolution

1994 ◽  
Vol 23 (3) ◽  
pp. 315-344
Author(s):  
Cristopher Culy ◽  
Kungarma Kodio
Keyword(s):  
Common Ancestor ◽  
Language Family ◽  
Binding Properties ◽  
The Common ◽  
Pronominal System ◽  
Insight Into

The Dogon language family has received little attention in the linguistics literature to date. In this paper we examine the binding properties of the pronominal systems of three Dogon languages, Donno S:>, T:>r:> S:>, and Togo Ka. We also posit the pronominal system of their common ancestor, and the changes from the common ancestor to the contemporary languages. In doing so, we find two ways in which languages can lose logophoricity: (1) the logophoric pronoun becomes a subject oriented reflexive, and (2) the logophoric pronoun is lost without any reflex. The Dogon languages thus give us insight into the nature of pronominal systems and how they evolve.

scholarly journals The power of synteny : deep evolutionary insights from comparative genomics

2021 ◽  
Author(s):  
◽  
Richard Shawn Abrahams
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Evolutionary Mechanisms ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Orthologous Locus ◽  
Orthology Detection ◽  
Insight Into

Synteny, or the order of genes in a given genome, is an emergent property of individuals and species that has only, with the implementation of next gen-sequencing, become available for evolutionary consideration. In this dissertation, I leverage syntenic information in concert with sequence data to draw connections between evolutionary mechanisms, species divergence, and trait innovation. In Chapter I, I review the major themes that ties my dissertation research together, highlighting important mechanisms at work in evolutionary complexity and introducing the system of which it will be a part. In Chapter II, I use a phylogenomic approach to better understand species relationships within the tribe. I utilize transcriptome sequences and genome derived synteny information to improve orthology detection over standard sequence similarity approaches and gain greater insight into the relationships of the tribe. I also implement differential fractionation rate orthology inference information to address gene tree-species tree incongruence. In Chapter III, as published in Abrahams et al., 2020, I utilize a microsynteny network and phylogenetic inference to investigate the origin and diversification of the MAM/IPMS gene family. I uncover unique MAM-like genes found at the orthologous locus in the Cleomaceae that shed light on the transition from IPMS to MAM. In the Brassicaceae, I identify six distinct MAM clades across Lineages I, II, and III. I characterize the evolutionary impact and consequences of local duplications, transpositions, whole genome duplications, and gene fusion events, generating several new hypotheses on the function and diversity of the MAM locus.

scholarly journals Phylogenetic characterization and evolution of the VP4 gene of P[9] rotaviruses

2020 ◽  
Author(s):  
Sharnali Ahmed ◽  
Takaaki Yahiro ◽  
Nor Amalina Emran ◽  
Lia Natasha Amit ◽  
Hidekatsu Iha ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Genetic Characterization ◽  
Specific Region ◽  
Phylogenetic Characterization ◽  
The World ◽  
The Common ◽  
Different Origins ◽  
Insight Into ◽  
Different Parts ◽  
Children Under 5

Abstract Objectives: Rotavirus is one of the major causes of gastroenteritis in children under 5 years of age and is responsible for over 200,000 deaths annually. Rotavirus can evolve by reassortment, in which gene segments are exchanged between strains of different origins. Rotavirus strains with the P[9] genotype is an example of reassortment, in which the P[9] genotype is from feline species. A number of outbreaks by P[9] strains have been documented in several countries. However, details regarding the epidemiological relationships between the strains remains largly unknown. Therefore, in the present study, genetic characterization and evolutionary analyses were perforemd to gain insight into P[9] strains circulating in different parts of the world. Results: The P[9] strains could be divided into five lineages, and that the common ancestor of currently circulating P[9] strains is around 168 years old. In each lineage, the strains were not only from different countries, but also from different continents. These findings suggest that none of the lineages has a specific region of distribution, and although humans have had interactions with cats for thousands of years, the ancestor of the current P[9] strain is relatively recent.

scholarly journals Phylogenetic and evolutionary analyses of the VP4 gene of P[9] rotaviruses

2020 ◽  
Author(s):  
Sharnali Ahmed ◽  
Takaaki Yahiro ◽  
Nor Amalina Emran ◽  
Lia Natasha Amit ◽  
Hidekatsu Iha ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Genetic Characterization ◽  
Specific Region ◽  
The World ◽  
The Common ◽  
Different Origins ◽  
Insight Into ◽  
Different Parts ◽  
Children Under 5

Abstract Objectives: Rotavirus is one of the major causes of gastroenteritis in children under 5 years of age and is responsible for over 200,000 deaths annually. Rotavirus can evolve by reassortment, in which gene segments are exchanged between strains of different origins. Rotavirus strains with the P[9] genotype is an example of reassortment, in which the P[9] genotype is from feline species. A number of outbreaks associated with P[9] strains have been documented in several countries. However, details regarding the epidemiological relationships between the strains remains largely unknown. Therefore, in the present study, genetic characterization and evolutionary analyses were performed to gain insight into P[9] strains circulating in different parts of the world. Results: The VP4 gene of the P[9] strains could be divided into six lineages, and P[9] strains characterized in this study share a common ancestor that circulated in circa 1864. In each lineage, the strains were not only from different countries, but also from different continents. These findings suggest that none of the lineages has a specific region of distribution, and although humans have had interactions with cats for thousands of years, the common ancestor of the VP4 gene of the current P[9] strains is relatively recent.

scholarly journals An updated explanation of ancestral karyotype changes and reconstruction of evolutionary trajectories to form Camelina sativa chromosomes

2020 ◽  
Author(s):  
Zhikang Zhang ◽  
Fanbo Meng ◽  
Pengchuan Sun ◽  
Jiaqing Yuan ◽  
Ke Ge ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Karyotype Evolution ◽  
Camelina Sativa ◽  
End Joining ◽  
Chromosome Fusion ◽  
Evolutionary Trajectories ◽  
Chromosome Fusions ◽  
Circular Chromosomes ◽  
Insight Into ◽  
Lines Of Evidence

Abstract Background: Belonging to lineage Ⅰ of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineage Ⅰ (Ancestral Crucifer karyotype, ACK). The karyotype evolutionary trajectories of the C. sativa chromosomes are currently unknown. Here, we managed to adopt a telomere-centric theory proposed previously to explain the karyotype evolution in C. sativa. Results: By characterizing the homology between A. lyrata and C. sativa chromosomes, we inferred ancestral diploid karyotype of C. sativa (ADK), including 7 ancestral chromosomes, and reconstructed the evolutionary trajectories leading to the formation of extant C. sativa genome. The process involved 2 chromosome fusions. We found that sub-genomes Cs-G1 and Cs-G2 may share a closer common ancestor than Cs-G3. Together with other lines of evidence from Arabidopsis, we propose that the Brassicaceae plants, even the eudicots, follow a chromosome fusion mechanism favoring end-end joining of different chromosomes, rather than a mechanism favoring the formation circular chromosomes and nested chromosome fusion preferred by the monocots. Conclusions: The present work will contribute to understanding the formation of C. sativa chromosomes, providing insight into Brassicaceae karyotype evolution.

scholarly journals Tumor Necrosis Factor Superfamily: Ancestral Functions and Remodeling in Early Vertebrate Evolution

2020 ◽  
Vol 12 (11) ◽  
pp. 2074-2092
Author(s):  
Ignacio Marín
Keyword(s):  
Tumor Necrosis Factor ◽  
Tumor Necrosis ◽  
Death Domain ◽  
Apoptotic Pathway ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Tumor Necrosis Factor Superfamily ◽  
Additional Losses ◽  
Ancestral Vertebrate ◽  
Necrosis Factor

Abstract The evolution of the tumor necrosis factor superfamily (TNFSF) in early vertebrates is inferred by comparing the TNFSF genes found in humans and nine fishes: three agnathans, two chondrichthyans, three actinopterygians, and the sarcopterygian Latimeria chalumnae. By combining phylogenetic and synteny analyses, the TNFSF sequences detected are classified into five clusters of genes and 24 orthology groups. A model for their evolution since the origin of vertebrates is proposed. Fifteen TNFSF genes emerged from just three progenitors due to the whole-genome duplications (WGDs) that occurred before the agnathan/gnathostome split. Later, gnathostomes not only kept most of the genes emerged in the WGDs but soon added several tandem duplicates. More recently, complex, lineage-specific patterns of duplications and losses occurred in different gnathostome lineages. In agnathan species only seven to eight TNFSF genes are detected, because this lineage soon lost six of the genes emerged in the ancestral WGDs and additional losses in both hagfishes and lampreys later occurred. The orthologs of many of these lost genes are, in mammals, ligands of death-domain-containing TNFSF receptors, indicating that the extrinsic apoptotic pathway became simplified in the agnathan lineage. From the patterns of emergence of these genes, it is deduced that both the regulation of apoptosis and the control of the NF-κB pathway that depends in modern mammals on TNFSF members emerged before the ancestral vertebrate WGDs.

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