Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution

Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins.

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Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.703163 ◽

2021 ◽

Vol 9 ◽

Author(s):

Madeleine E. Aase-Remedios ◽

David E. K. Ferrier

Keyword(s):

Chromosomal Rearrangements ◽

Expression Patterns ◽

Gene Families ◽

Evolutionary Transitions ◽

Whole Genome Duplications ◽

Chordate Evolution ◽

Genome Duplications ◽

The Many ◽

Genome Assemblies ◽

The Impact

Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.

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Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

GigaScience ◽

10.1093/gigascience/giaa004 ◽

2020 ◽

Vol 9 (2) ◽

Cited By ~ 8

Author(s):

Zheng Li ◽

Michael S Barker

Keyword(s):

Gene Family ◽

False Positive Rate ◽

Nuclear Gene ◽

Plant Evolution ◽

Plant Genome ◽

Total Evidence ◽

Whole Genome ◽

Green Plants ◽

Whole Genome Duplications ◽

Genome Duplications

Abstract Background Polyploidy, or whole-genome duplications (WGDs), repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced >1,000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project. Results In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walk-through examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole-genome synteny analyses and our total evidence approach may minimize the false-positive rate throughout the dataset. Conclusions We release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.

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Molecular definition of a narrow interval at 7q22.1 associated with myelodysplasia

Blood ◽

10.1182/blood.v87.9.3579.bloodjournal8793579 ◽

1996 ◽

Vol 87 (9) ◽

pp. 3579-3586 ◽

Cited By ~ 66

Author(s):

EJ Johnson ◽

SW Scherer ◽

L Osborne ◽

LC Tsui ◽

D Oscier ◽

...

Keyword(s):

Myeloid Leukemia ◽

Poor Prognosis ◽

Yeast Artificial Chromosome ◽

Chromosomal Rearrangements ◽

Artificial Chromosome ◽

Specific Gene ◽

Chromosomal Anomalies ◽

Inversion Breakpoint ◽

Definition Of

Chromosome 7 translocations, deletions, or monosomy are associated with myelodysplasia (MDS) and acute myeloid leukemia both in children and adults. These chromosomal anomalies represent one of the most common cytogenetic abnormalities associated with these diseases and usually herald a poor prognosis. In this study two cosmid DNA probes that mapped to 7q22.1 and were known to be separated by approximately 500 kb were identified to flank the proximal inversion breakpoint in a patient carrying a constitutional inversion (7q22.1–34) associated with MDS. A yeast artificial chromosome (YAC) clone that encompassed the two cosmids was identified and shown to span the breakpoint. Fluorescence in situ hybridization was then used to analyze six additional patients with myelodysplasia and chromosomal rearrangements of the 7q22 region (three patients had translocations and three carried deletions). The breakpoint in one of the patients was found to be contained within the same YAC clone that spanned the inversion breakpoint. Moreover, this same interval was determined to be absent in all three patients with chromosomal deletions. These results suggest that this segment of DNA on chromosome 7q22.1 may contain specific gene(s) that have a significant role in myeloid malignancies.

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Yeast artificial chromosome mapping of the cystinosis locus on chromosome 17p by fluorescence in situ hybridization

Human Genetics ◽

10.1007/s004390050215 ◽

1996 ◽

Vol 98 (3) ◽

pp. 321-322 ◽

Cited By ~ 3

Author(s):

Ingrid Stec ◽

Ulrike Peters ◽

Erik Harms ◽

Michael R. Koehler ◽

M. Schmid ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Yeast Artificial Chromosome ◽

Chromosome Mapping ◽

Artificial Chromosome

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Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy

Frontiers in Plant Science ◽

10.3389/fpls.2021.629898 ◽

2021 ◽

Vol 12 ◽

Cited By ~ 1

Author(s):

Nomar Espinosa Waminal ◽

Remnyl Joyce Pellerin ◽

Sang-Ho Kang ◽

Hyun Hee Kim

Keyword(s):

Clustering Algorithm ◽

Tandem Repeats ◽

Karyotype Evolution ◽

Chromosomal Rearrangements ◽

Intergenic Spacer ◽

Telomeric Repeat ◽

Chromosomal Mapping ◽

Chromosomal Distribution ◽

Copy Numbers

Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant Senna tora dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the S. tora genome and compared the chromosomal distribution of these repeats between S. tora and a closely related euploid, Senna occidentalis. Using a read clustering algorithm, we identified the major S. tora tandem repeats and visualized their chromosomal distribution by fluorescence in situ hybridization. We identified eight independent repeats covering ~85 Mb or ~12% of the S. tora genome. The unit lengths and copy numbers had ranges of 7–5,833 bp and 325–2.89 × 106, respectively. Three short duplicated sequences were found in the 45S rDNA intergenic spacer, one of which was also detected at an extra-NOR locus. The canonical plant telomeric repeat (TTTAGGG)n was also detected as very intense signals in numerous pericentromeric and interstitial loci. StoTR05_180, which showed subtelomeric distribution in Senna occidentalis, was predominantly pericentromeric in S. tora. The unusual chromosomal distribution of tandem repeats in S. tora not only enabled easy identification of individual chromosomes but also revealed the massive chromosomal rearrangements that have likely played important roles in shaping its dysploid karyotype.

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Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions

10.1101/735076 ◽

2019 ◽

Cited By ~ 2

Author(s):

Zheng Li ◽

Michael S Barker

Keyword(s):

Gene Family ◽

Nuclear Gene ◽

Plant Evolution ◽

Plant Genome ◽

Total Evidence ◽

Whole Genome ◽

Data Set ◽

Green Plants ◽

Whole Genome Duplications ◽

Genome Duplications

AbstractPolyploidy or whole genome duplications (WGDs) repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced over 1000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place ancient WGDs. Overall, 244 putative ancient WGDs were inferred across the Viridiplantae. Here, we describe these analyses and evaluate the consistency of the WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole genome synteny analyses and our total evidence approach may minimize the false positive rate throughout the data set. Given these resources will be useful for many future analyses on gene and genome evolution in green plants, we release 383,679 nuclear gene family phylogenies and 2,306 gene age distribution (Ks) plots from the 1KP capstone paper.

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Recent advances in understanding the roles of whole genome duplications in evolution

F1000Research ◽

10.12688/f1000research.11792.2 ◽

2018 ◽

Vol 6 ◽

pp. 1623 ◽

Cited By ~ 4

Author(s):

Carol MacKintosh ◽

David E.K. Ferrier

Keyword(s):

Regulatory Networks ◽

Chromosomal Rearrangements ◽

Cost Benefit ◽

Cell Types ◽

Whole Genome ◽

Short Term ◽

Unicellular Eukaryotes ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Neurological Conditions

Ancient whole-genome duplications (WGDs)—paleopolyploidy events—are key to solving Darwin’s ‘abominable mystery’ of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.

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One thousand plant transcriptomes and the phylogenomics of green plants

Nature ◽

10.1038/s41586-019-1693-2 ◽

2019 ◽

Vol 574 (7780) ◽

pp. 679-685 ◽

Cited By ~ 241

Author(s):

Keyword(s):

Genome Evolution ◽

Nuclear Gene ◽

Gene Families ◽

Plant Genome ◽

Gene Trees ◽

Green Plants ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Multiple Species ◽

The One

Abstract Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

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Interstitial Telomeric Repeats Are Rare in Turtles

Genes ◽

10.3390/genes11060657 ◽

2020 ◽

Vol 11 (6) ◽

pp. 657 ◽

Cited By ~ 2

Author(s):

Lorenzo Clemente ◽

Sofia Mazzoleni ◽

Eleonora Pensabene Bellavia ◽

Barbora Augstenová ◽

Markus Auer ◽

...

Keyword(s):

In Situ Hybridization ◽

Karyotype Evolution ◽

Chromosomal Rearrangements ◽

Telomeric Repeats ◽

Squamate Reptiles ◽

Nucleoprotein Complexes ◽

Interstitial Telomeric Repeats ◽

Eukaryotic Organisms ◽

Genomic Regions

Telomeres are nucleoprotein complexes protecting chromosome ends in most eukaryotic organisms. In addition to chromosome ends, telomeric-like motifs can be accumulated in centromeric, pericentromeric and intermediate (i.e., between centromeres and telomeres) positions as so-called interstitial telomeric repeats (ITRs). We mapped the distribution of (TTAGGG)n repeats in the karyotypes of 30 species from nine families of turtles using fluorescence in situ hybridization. All examined species showed the expected terminal topology of telomeric motifs at the edges of chromosomes. We detected ITRs in only five species from three families. Combining our and literature data, we inferred seven independent origins of ITRs among turtles. ITRs occurred in turtles in centromeric positions, often in several chromosomal pairs, in a given species. Their distribution does not correspond directly to interchromosomal rearrangements. Our findings support that centromeres and non-recombining parts of sex chromosomes are very dynamic genomic regions, even in turtles, a group generally thought to be slowly evolving. However, in contrast to squamate reptiles (lizards and snakes), where ITRs were found in more than half of the examined species, and birds, the presence of ITRs is generally rare in turtles, which agrees with the expected low rates of chromosomal rearrangements and rather slow karyotype evolution in this group.

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