scholarly journals Reconstruction of evolutionary trajectories of coffee chromosomes

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.

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

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhikang Zhang ◽  
Fanbo Meng ◽  
Pengchuan Sun ◽  
Jiaqing Yuan ◽  
Ke Gong ◽  
...  
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 Epigenetic dynamics of centromeres and neocentromeres in Cryptococcus deuterogattii

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009743
Author(s):  
Klaas Schotanus ◽  
Vikas Yadav ◽  
Joseph Heitman
Keyword(s):  
Dna Methylation ◽  
Transposable Element ◽  
Fungal Pathogen ◽  
Fusion Partner ◽  
Epigenetic Memory ◽  
Chromosome Fusion ◽  
Human Fungal Pathogen ◽  
Chromosome Fusions ◽  
The Impact ◽  
Active Centromere

Deletion of native centromeres in the human fungal pathogen Cryptococcus deuterogattii leads to neocentromere formation. Native centromeres span truncated transposable elements, while neocentromeres do not and instead span actively expressed genes. To explore the epigenetic organization of neocentromeres, we analyzed the distribution of the heterochromatic histone modification H3K9me2, 5mC DNA methylation and the euchromatin mark H3K4me2. Native centromeres are enriched for both H3K9me2 and 5mC DNA methylation marks and are devoid of H3K4me2, while neocentromeres do not exhibit any of these features. Neocentromeres in cen10Δ mutants are unstable and chromosome-chromosome fusions occur. After chromosome fusion, the neocentromere is inactivated and the native centromere of the chromosome fusion partner remains as the sole, active centromere. In the present study, the active centromere of a fused chromosome was deleted to investigate if epigenetic memory promoted the re-activation of the inactive neocentromere. Our results show that the inactive neocentromere is not re-activated and instead a novel neocentromere forms directly adjacent to the deleted centromere of the fused chromosome. To study the impact of transcription on centromere stability, the actively expressed URA5 gene was introduced into the CENP-A bound regions of a native centromere. The introduction of the URA5 gene led to a loss of CENP-A from the native centromere, and a neocentromere formed adjacent to the native centromere location. Remarkably, the inactive, native centromere remained enriched for heterochromatin, yet the integrated gene was expressed and devoid of H3K9me2. A cumulative analysis of multiple CENP-A distribution profiles revealed centromere drift in C. deuterogattii, a previously unreported phenomenon in fungi. The CENP-A-binding shifted within the ORF-free regions and showed a possible association with a truncated transposable element. Taken together, our findings reveal that neocentromeres in C. deuterogattii are highly unstable and are not marked with an epigenetic memory, distinguishing them from native centromeres.

scholarly journals Heterozygosity and Chain Multivalents during Meiosis Illustrate Ongoing Evolution as a Result of Multiple Holokinetic Chromosome Fusions in the Genus Melinaea (Lepidoptera, Nymphalidae)

2017 ◽  
Vol 153 (4) ◽  
pp. 213-222 ◽  
Author(s):  
Melanie McClure ◽  
Bernard Dutrillaux ◽  
Anne-Marie Dutrillaux ◽  
Vladimir Lukhtanov ◽  
Marianne Elias
Keyword(s):  
Chromosome Evolution ◽  
Taxonomic Revision ◽  
Variable Number ◽  
Chromosome Fusion ◽  
Meiotic Chromosomes ◽  
In Captivity ◽  
Chromosome Fusions ◽  
The Common ◽  
Multiple Spindle ◽  
Complex Chromosome

Mitotic and meiotic chromosomes from 2 taxa of the genus Melinaea, M. satevis cydon and M. “satevis” tarapotensis (Lepidoptera: Nymphalidae), and from hybrids produced in captivity were obtained using an improved spreading technique and were subsequently analyzed. In one of the taxa, the presence of trivalents and tetravalents at diakinesis/metaphase I is indicative of heterozygosity for multiple chromosome fusions or fissions, which might explain the highly variable number of chromosomes previously reported in this genus. Two large and complex multivalents were observed in the meiotic cells of the hybrid males (32 chromosomes) obtained from a cross between M. “s.” tarapotensis (28 chromosomes) and M. s. cydon (40-43 chromosomes). The contribution of the 2 different haploid karyotypes to these complex figures during meiosis is discussed, and a taxonomic revision is proposed. We conclude that chromosome evolution is active and ongoing, that the karyotype of the common ancestor consisted of at least 48 chromosomes, and that evolution by chromosome fusion rather than fission is responsible for this pattern. Complex chromosome evolution in this genus may drive reproductive isolation and speciation, and highlights the difficulties inherent to the systematics of this group. We also show that Melinaea chromosomes, classically considered as holocentric, are attached to unique, rather than multiple, spindle fibers.

Multidimensional epistasis and fitness landscapes in enzyme evolution

2012 ◽  
Vol 445 (1) ◽  
pp. 39-46 ◽  
Author(s):  
Wei Zhang ◽  
Daniel F. A. R. Dourado ◽  
Pedro Alexandrino Fernandes ◽  
Maria João Ramos ◽  
Bengt Mannervik
Keyword(s):  
Glutathione Transferase ◽  
Fitness Landscape ◽  
Evolutionary Process ◽  
Salient Feature ◽  
Selective Advantage ◽  
Enzyme Evolution ◽  
Conventional Analysis ◽  
Evolutionary Response ◽  
Single Protein ◽  
Evolutionary Trajectories

The conventional analysis of enzyme evolution is to regard one single salient feature as a measure of fitness, expressed in a milieu exposing the possible selective advantage at a given time and location. Given that a single protein may serve more than one function, fitness should be assessed in several dimensions. In the present study we have explored individual mutational steps leading to a triple-point-mutated human GST (glutathione transferase) A2-2 displaying enhanced activity with azathioprine. A total of eight alternative substrates were used to monitor the diverse evolutionary trajectories. The epistatic effects of the mutations on catalytic activity were variable in sign and magnitude and depended on the substrate used, showing that epistasis is a multidimensional quality. Evidently, the multidimensional fitness landscape can lead to alternative trajectories resulting in enzymes optimized for features other than the selectable markers relevant at the origin of the evolutionary process. In this manner the evolutionary response is robust and can adapt to changing environmental conditions.

scholarly journals Mortality and coexistence time both cause changes in predator-prey co-evolutionary dynamics

2020 ◽  
Author(s):  
Thomas Scheuerl ◽  
Veijo Kaitala
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Process ◽  
Mortality Rates ◽  
Predator Prey ◽  
Ecological Changes ◽  
Evolutionary Changes ◽  
Predation Efficiency ◽  
Evolutionary Trajectories ◽  
Predator Defence ◽  
Transfer Interval

AbstractAll organisms are sensitive to the abiotic environment, and in multispecies communities a deteriorating environment increasing mortality and limiting coexistence time can cause ecological changes. When interaction within the community is changed this can impact co-evolutionary processes. Here we use a mathematical model to predict ecological and evolutionary changes in a simple predator-prey community under different mortality rates and times of coexistence, both controlled by various transfer volume and transfer interval. In the simulated bacteria-ciliate system, we find species densities to be surprisingly robust under changed mortality rates and times both species coexist, resulting in stable densities. Confirming a theoretical prediction however, the evolution of anti-predator defence in the bacteria and evolution of predation efficiency in ciliates relax under high mortalities and limited times both partners interact. In contrast, evolutionary trajectories intensify when global mortalities are low, and the predator-prey community has more time for close interaction. These results provide testable hypotheses for future studies of predator-prey systems and we hope this work will help to bridge the gap in our knowledge how ecological and evolutionary process together shape composition of microbial communities.

scholarly journals Neocentromeres lack epigenetic memory and hallmarks of native centromeres in Cryptococcus deuterogattii

2020 ◽  
Author(s):  
Klaas Schotanus ◽  
Vikas Yadav ◽  
Joseph Heitman
Keyword(s):  
Dna Methylation ◽  
Transposable Element ◽  
Fungal Pathogen ◽  
Fusion Partner ◽  
Epigenetic Memory ◽  
Chromosome Fusion ◽  
Human Fungal Pathogen ◽  
Dna Modifications ◽  
Chromosome Fusions ◽  
Active Centromere

AbstractDeletion of native centromeres in the human fungal pathogen Cryptococcus deuterogattii leads to neocentromere formation. Native centromeres span truncated transposable elements, while neocentromeres span actively expressed genes. Neocentromeres in cen10Δ mutants are unstable and chromosome-chromosome fusions occur. After chromosome fusion, the neocentromere is silenced and the native centromere of the chromosome fusion partner remains as the sole active centromere. In the present study, the active centromere of a fused chromosome was deleted to investigate if epigenetic memory promoted re-activation of a silenced neocentromere. Our results show that the silenced neocentromere is not re-activated and instead a novel neocentromere forms directly adjacent to the deleted centromere of the fused chromosome. To explore the epigenetic organization of neocentromeres, we characterized the distribution of the heterochromatic histone modification H3K9me2 and 5mC DNA methylation. Native centromeres were enriched for both H3K9me2 and 5mC DNA methylation marks, while neocentromeres lacked these specific histone and DNA modifications. To study centromere dynamics, the actively expressed URA5 gene was introduced into a native centromere. Introduction of the URA5 gene led to loss of CENP-A from the native centromere, and a neocentromere formed directly adjacent to the native centromere location. Remarkably, the silenced native centromere remained enriched for heterochromatin, yet the integrated gene was expressed and devoid of H3K9me2. Analysis of multiple CENP-A distribution profiles revealed centromere drift in C. deuterogattii, a previously unknown phenomenon in fungi. The CENP-A-enriched region shifted within the pericentric regions, and a truncated transposable element in centromere 5 acted as a barrier between the CENP-A-associated regions of chromatin. Interestingly, this truncated transposable element was devoid of CENP-A binding or H3K9me2 modification and was instead marked by 5mC DNA methylation. Taken together, our findings reveal novel aspects about the epigenetic mechanisms that distinguish native centromeres and neocentromeres.

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