scholarly journals Muntjac chromosome evolution and architecture

2019 ◽  
Author(s):  
Austin B. Mudd ◽  
Jessen V. Bredeson ◽  
Rachel Baum ◽  
Dirk Hockemeyer ◽  
Daniel S. Rokhsar
Keyword(s):  
Chromosome Evolution ◽  
Common Ancestor ◽  
Karyotype Evolution ◽  
Karyotype Analysis ◽  
Rapid Evolution ◽  
Unique Case ◽  
Show Evidence ◽  
Genome Assemblies ◽  
Muntiacus Muntjak ◽  
Muntiacus Reevesi

AbstractDespite their recent divergence, muntjac deer show striking karyotype differences. Here we describe new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) and Muntiacus muntjak (2n=6/7), and analyze their evolution and architecture. We identified six fusion events shared by both species relative to the cervid ancestor and therefore present in the muntjac common ancestor, six fusion events unique to the M. reevesi lineage, and twenty-six fusion events unique to the M. muntjak lineage. One of these M. muntjak fusions reverses an earlier fission in the cervid lineage. Although comparative Hi-C analysis revealed differences in long-range genome contacts and A/B compartment structures, we discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. A small number of genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype. Analysis of muntjac genomes reveals new insights into this unique case of rapid karyotype evolution and the resulting biological variation.

scholarly journals Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Austin B. Mudd ◽  
Jessen V. Bredeson ◽  
Rachel Baum ◽  
Dirk Hockemeyer ◽  
Daniel S. Rokhsar
Keyword(s):  
Karyotype Evolution ◽  
Rapid Evolution ◽  
Three Dimensional ◽  
Interphase Nuclei ◽  
Chromatin Compaction ◽  
Show Evidence ◽  
Chromosome Fusions ◽  
Genome Assemblies ◽  
Muntiacus Muntjak ◽  
Muntiacus Reevesi

AbstractClosely related muntjac deer show striking karyotype differences. Here we describe chromosome-scale genome assemblies for Chinese and Indian muntjacs, Muntiacus reevesi (2n = 46) and Muntiacus muntjak vaginalis (2n = 6/7), and analyze their evolution and architecture. The genomes show extensive collinearity with each other and with other deer and cattle. We identified numerous fusion events unique to and shared by muntjacs relative to the cervid ancestor, confirming many cytogenetic observations with genome sequence. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Comparative Hi-C analysis showed that the chromosome fusions on the M. muntjak lineage altered long-range, three-dimensional chromosome organization relative to M. reevesi in interphase nuclei including A/B compartment structure. This reshaping of multi-megabase contacts occurred without notable change in local chromatin compaction, even near fusion sites. A few genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype.

scholarly journals Dynamic Patterns of Sex Chromosome Evolution in Neognath Birds: Many Independent Barriers to Recombination at the ATP5F1A Locus

2021 ◽  
Author(s):  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
Sex Chromosomes ◽  
Substitution Rate ◽  
Chromosome Evolution ◽  
Common Ancestor ◽  
Sex Chromosome ◽  
Purifying Selection ◽  
W Chromosome ◽  
Sex Chromosome Evolution ◽  
Dynamic Nature ◽  
Genome Assemblies

Avian sex chromosomes evolved after the divergence birds and crocodilians from their common ancestor, so they are much younger than the better-studied chromosomes of mammals. It has long been recognized that there may have been several stages to the evolution of avian sex chromosomes. For example, the CHD1 undergoes recombination in paleognaths but not neognaths. Genome assemblies have suggested there may be variation in the timing of barriers to recombination among Neognathae, but there remains little understanding of the extent of this variability. Here, we look at partial sequences of ATP5F1A, which is on the avian Z and W chromosomes. It is known that recombination of this gene has independently ceased in Galliformes, Anseriformes, and at least five neoavian orders, but whether there are other independent cessations of recombination among Neoaves is not understood. We used a combination of data extracted from published chromosomal-level genomes with data collected using PCR and cloning to identify Z and W copies in 22 orders. Our results suggest there may be at least 19 independent cessations of recombination within Neognathae, and 3 clades that may still be undergoing recombination (or have only recently ceased recombination). Analyses of ATP5F1A protein sequences revealed an increased amino acid substitution rate for W chromosome gametologs, suggesting relaxed purifying selection on the W chromosome. Supporting this hypothesis, we found that the increased substitution rate was particularly pronounced for buried residues, which are expected to be more strongly constrained by purifying selection. This highlights the dynamic nature of avian sex chromosomes, and that this level of variation among clades means they should be a good system to understand sex chromosome evolution.

scholarly journals Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq)

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 124
Author(s):  
Alessio Iannucci ◽  
Alexey I. Makunin ◽  
Artem P. Lisachov ◽  
Claudio Ciofi ◽  
Roscoe Stanyon ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Karyotype Evolution ◽  
Genomic Data ◽  
Anolis Carolinensis ◽  
Vertebrate Genome ◽  
Single Chromosome ◽  
Sequencing Technologies ◽  
Novel Approaches ◽  
Genome Assemblies ◽  
Generation Sequencing

The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.

scholarly journals Donkey genome and insight into the imprinting of fast karyotype evolution

2015 ◽  
Vol 5 (1) ◽  
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.

Karyotype, C-banding, and Ag-NOR analysis in Diplodus bellottii (Sparidae, Perciforms). Intra-individual polymorphism involving heterochromatic regions

Genome ◽  
1993 ◽  
Vol 36 (4) ◽  
pp. 672-675 ◽  
Author(s):  
A. Amores ◽  
G. Martinez ◽  
J. Reina ◽  
M. C. Alvarez
Keyword(s):  
Karyotype Evolution ◽  
Karyotype Analysis ◽  
Centric Fusion ◽  
Active Regions ◽  
Chromosome Polymorphism ◽  
Terminal Position ◽  
C Banding ◽  
Metacentric Pair ◽  
Pericentric Inversions ◽  
Nucleolus Organizers

A karyotype analysis was carried out in nine specimens of the Sparid species Diplodus bellottii using conventional staining, as well as C-banding and Ag-NOR banding techniques, showing, respectively, 2n = 46 and fundamental number (FN) = 54, and scarce heterochromatic areas irregularly distributed and up to four NOR active regions that were C positive. When compared with the karyotypes of other related species, one centric fusion giving rise to a large metacentric pair and several pericentric inversions seem to have been involved in the karyotype evolution. An intra-individual polymorphism was detected in one specimen, resulting in two karyotypic forms in roughly identical proportion, owing to a larger C-band by the NOR regions, appearing either in a terminal position of the short arms of pair 2 or in telomeric position of pair 3. These findings suggest that the extra heterochromatic segment responsible for the heteromorphism apparently only involves associated heterochromatin and not the NORs themselves. This C-positive block seems to have eventually been transferred between heterologous NOR chromosomes by a somatic event, facilitated by the physical proximity of NOR pairs in the nucleolus.Key words: Sparidae, karyotype, heterochromatin, nucleolus organizers, chromosome polymorphism.

Chromosome evolution in kangaroos (Marsupialia: Macropodidae): Cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n = 22 ancestral macropodid karyotype

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 525-530 ◽  
Author(s):  
RJ Waugh O'Neill ◽  
MDB Eldridge ◽  
R Toder ◽  
MA Ferguson-Smith ◽  
P C O'Brien ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Chromosome Evolution ◽  
Karyotype Evolution ◽  
Tammar Wallaby ◽  
Fusion Process ◽  
Ancestral Karyotype ◽  
Karyotypic Diversity ◽  
Species Groups ◽  
Cross Species Chromosome Painting ◽  
Karyotype Stability

Marsupial mammals show extraordinary karyotype stability, with 2n = 14 considered ancestral. However, macropodid marsupials (kangaroos and wallabies) exhibit a considerable variety of karyotypes, with a hypothesised ancestral karyotype of 2n = 22. Speciation and karyotypic diversity in rock wallabies (Petrogale) is exceptional. We used cross species chromosome painting to examine the chromosome evolution between the tammar wallaby (2n = 16) and three 2n = 22 rock wallaby species groups with the putative ancestral karyotype. Hybridization of chromosome paints prepared from flow sorted chromosomes of the tammar wallaby to Petrogale spp., showed that this ancestral karyotype is largely conserved among 2n = 22 rock wallaby species, and confirmed the identity of ancestral chromosomes which fused to produce the bi-armed chromosomes of the 2n = 16 tammar wallaby. These results illustrate the fission-fusion process of karyotype evolution characteristic of the kangaroo group.

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.

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