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

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.

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

10.21203/rs.2.20143/v1 ◽

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.

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

10.21203/rs.2.20143/v2 ◽

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.

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

10.21203/rs.2.20143/v4 ◽

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.

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

10.21203/rs.2.20143/v3 ◽

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.

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Reconstruction of evolutionary trajectories of coffee chromosomes

10.21203/rs.2.11248/v1 ◽

2019 ◽

Author(s):

Jing Li ◽

Jiaqing Yuan ◽

Yuhao Zhao ◽

Fanbo Meng ◽

Chao Liu ◽

...

Keyword(s):

Evolutionary Process ◽

End Joining ◽

Chromosome Fusion ◽

Plant Chromosomes ◽

Evolutionary Trajectories ◽

Widespread Phenomenon ◽

Satellite Chromosomes ◽

Chromosome Fission ◽

Chromosome Fusions ◽

Fusion Mode

Abstract Background Polyploidization is a widespread phenomenon in plants, especially in angiosperms. Because of the rearrangement of chromosomes and the loss of genes, the number of plant chromosomes will reduce. Studies have shown that core dicotyledons are derived from ancestors with seven proto-chromosomes, which triplicated in a core-eudicot-common hexaploidization. Therefore, dicotyledon with different chromosome numbers have evolved on the basis of 21 chromosomes. On this basis, we selected grape as the intermediate reference species to infer the karyotype evolutionary process of coffee. Results We found that all the chromosome fusion forms in grape were end-end joining, and 7 (70.0%) chromosome fusion forms in coffee were end-end joining. In the process of grape forming 19 chromosomes, there were three chromosome fusions and one chromosome fission. In the process of coffee 11 chromosomes formation, 10 chromosome fusions occurred. During the process, we inferred that satellite chromosomes formed by telomeres from the same or different chromosomes were produced; and the lost of them resulted in chromosome number reduction Conclusions Notably, we found that the major fusion mode of chromosomes in coffee is end-end joining, which is well explained by telomere-centric model, shared by grape and possibly by many other eudicots. This is contrastively different from the observation of monocot plants like grasses, in which nested chromosome fusions often occurred. The present work will help to understand the structural and functional innovations of plant chromosomes.

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Chromosome evolution at the origin of the ancestral vertebrate genome

10.1101/253104 ◽

2018 ◽

Cited By ~ 1

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.

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Volatile Anesthetics Affect Nutrient Availability in Yeast

Genetics ◽

10.1093/genetics/161.2.563 ◽

2002 ◽

Vol 161 (2) ◽

pp. 563-574

Author(s):

Laura K Palmer ◽

Darren Wolfe ◽

Jessica L Keeley ◽

Ralph L Keil

Keyword(s):

Amino Acids ◽

Nutrient Availability ◽

Wild Type Strain ◽

Volatile Anesthetic ◽

Volatile Anesthetics ◽

Wild Type ◽

Anesthetic Exposure ◽

Sites Of Action ◽

Insight Into ◽

Lines Of Evidence

Abstract Volatile anesthetics affect all cells and tissues tested, but their mechanisms and sites of action remain unknown. To gain insight into the cellular activities of anesthetics, we have isolated genes that, when overexpressed, render Saccharomyces cerevisiae resistant to the volatile anesthetic isoflurane. One of these genes, WAK3/TAT1, encodes a permease that transports amino acids including leucine and tryptophan, for which our wild-type strain is auxotrophic. This suggests that availability of amino acids may play a key role in anesthetic response. Multiple lines of evidence support this proposal: (i) Deletion or overexpression of permeases that transport leucine and/or tryptophan alters anesthetic response; (ii) prototrophic strains are anesthetic resistant; (iii) altered concentrations of leucine and tryptophan in the medium affect anesthetic response; and (iv) uptake of leucine and tryptophan is inhibited during anesthetic exposure. Not all amino acids are critical for this response since we find that overexpression of the lysine permease does not affect anesthetic sensitivity. These findings are consistent with models in which anesthetics have a physiologically important effect on availability of specific amino acids by altering function of their permeases. In addition, we show that there is a relationship between nutrient availability and ubiquitin metabolism in this response.

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Interspecies Chromosome Mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): Cytogenomic Insight into Microchromosome Organization and Karyotype Evolution in Birds

Cells ◽

10.3390/cells10040826 ◽

2021 ◽

Vol 10 (4) ◽

pp. 826

Author(s):

Rafael Kretschmer ◽

Marcelo Santos de Souza ◽

Ivanete de Oliveira Furo ◽

Michael N. Romanov ◽

Ricardo José Gunski ◽

...

Keyword(s):

Convergent Evolution ◽

Karyotype Evolution ◽

Rare Events ◽

Rare Event ◽

Chromosome Mapping ◽

The Other ◽

Other Hand ◽

Interchromosomal Rearrangement ◽

Insight Into ◽

Phalacrocorax Brasilianus

Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred.

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A New Saccharomyces cerevisiae Strain with a Mutant Smt3-Deconjugating Ulp1 Protein Is Affected in DNA Replication and Requires Srs2 and Homologous Recombination for Its Viability

Molecular and Cellular Biology ◽

10.1128/mcb.24.12.5130-5143.2004 ◽

2004 ◽

Vol 24 (12) ◽

pp. 5130-5143 ◽

Cited By ~ 32

Author(s):

Christine Soustelle ◽

Laurence Vernis ◽

Karine Fréon ◽

Anne Reynaud-Angelin ◽

Roland Chanet ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Homologous Recombination ◽

Nonhomologous End Joining ◽

End Joining ◽

Recombination Mechanism ◽

Growth Defects ◽

Protein Conjugates ◽

Synthetically Lethal ◽

Mutant Cells ◽

Insight Into

ABSTRACT The Saccharomyces cerevisiae Srs2 protein is involved in DNA repair and recombination. In order to gain better insight into the roles of Srs2, we performed a screen to identify mutations that are synthetically lethal with an srs2 deletion. One of them is a mutated allele of the ULP1 gene that encodes a protease specifically cleaving Smt3-protein conjugates. This allele, ulp1-I615N, is responsible for an accumulation of Smt3-conjugated proteins. The mutant is unable to grow at 37°C. At permissive temperatures, it still shows severe growth defects together with a strong hyperrecombination phenotype and is impaired in meiosis. Genetic interactions between ulp1 and mutations that affect different repair pathways indicated that the RAD51-dependent homologous recombination mechanism, but not excision resynthesis, translesion synthesis, or nonhomologous end-joining processes, is required for the viability of the mutant. Thus, both Srs2, believed to negatively control homologous recombination, and the process of recombination per se are essential for the viability of the ulp1 mutant. Upon replication, mutant cells accumulate single-stranded DNA interruptions. These structures are believed to generate different recombination intermediates. Some of them are fixed by recombination, and others require Srs2 to be reversed and fixed by an alternate pathway.

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Donkey genome and insight into the imprinting of fast karyotype evolution

Scientific Reports ◽

10.1038/srep14106 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 12

Author(s):

Jinlong Huang ◽

Yiping Zhao ◽

Dongyi Bai ◽

Wunierfu Shiraigol ◽

Bei Li ◽

...

Keyword(s):

Target Genes ◽

Karyotype Evolution ◽

De Novo ◽

Cycle Phase ◽

Satellite Sequences ◽

Chromatid Segregation ◽

Karyotypic Instability ◽

Wild Ass ◽

Genome Assemblies ◽

Insight Into

Abstract The donkey, like the horse, is a promising model for exploring karyotypic instability. We report the de novo whole-genome assemblies of the donkey and the Asiatic wild ass. Our results reflect the distinct characteristics of donkeys, including more effective energy metabolism and better immunity than horses. The donkey shows a steady demographic trajectory. We detected abundant satellite sequences in some inactive centromere regions but not in neocentromere regions, while ribosomal RNAs frequently emerged in neocentromere regions but not in the obsolete centromere regions. Expanded miRNA families and five newly discovered miRNA target genes involved in meiosis may be associated with fast karyotype evolution. APC/C, controlling sister chromatid segregation, cytokinesis and the establishment of the G1 cell cycle phase were identified by analysis of miRNA targets and rapidly evolving genes.

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