Evolutionary dynamics and impacts of chromosome regions carrying R-gene clusters in rice.
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ABSTRACT:
SUBMITTER: Mizuno H
PROVIDER: S-EPMC6972905 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundAmong multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity.ResultsThe present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs) and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes.ConclusionsThe organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a more complete picture for understanding the organization of repeated sequences in the genome.
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Project description:BackgroundThe distribution of human disease-associated mutations is not random across the human genome. Despite the fact that natural selection continually removes disease-associated mutations, an enrichment of these variants can be observed in regions of low recombination. There are a number of mechanisms by which such a clustering could occur, including genetic perturbations or demographic effects within different populations. Recent genome-wide association studies (GWAS) suggest that single nucleotide polymorphisms (SNPs) associated with complex disease traits are not randomly distributed throughout the genome, but tend to cluster in regions of low recombination.Principal findingsHere we investigated whether deleterious mutations have accumulated in regions of low recombination due to the impact of recent positive selection and genetic hitchhiking. Using publicly available data on common complex diseases and population demography, we observed an enrichment of hitchhiked disease associations in conserved gene clusters subject to selection pressure. Evolutionary analysis revealed that these conserved gene clusters arose by multiple concerted rearrangements events across the vertebrate lineage. We observed distinct clustering of disease-associated SNPs in evolutionary rearranged regions of low recombination and high gene density, which harbor genes involved in immunity, that is, the interleukin cluster on 5q31 or RhoA on 3p21.ConclusionsOur results suggest that multiple lineage specific rearrangements led to a physical clustering of functionally related and linked genes exhibiting an enrichment of susceptibility loci for complex traits. This implies that besides recent evolutionary adaptations other evolutionary dynamics have played a role in the formation of linked gene clusters associated with complex disease traits.
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Project description:Under the dual impacts of climate change and COVID-19, there are great risks to the world's food security. Rice is one of the three major food crops of the world. Assessing the impact of climate change on future rice production is very important for ensuring global food security. This article divides the world's main rice-producing regions into four regions and uses a multivariate nonlinear model based on historical economic and climatic data to explore the impacts of historical extreme climatic events and economic factors on rice yield. Based on these historical models, future climatic data, and economic data under different shared socioeconomic pathways (SSPs), the yields of four major rice-producing regions of the world under different climate change scenarios (SSP126, SSP245, and SSP585) are predicted. The research results reveal that under different climate change scenarios, extreme high-temperature events (Tx90p) and extreme precipitation events (Rx5day, R99pTOT) in the four major rice-producing regions have an upward trend in the future. Extreme low-temperature events (Tn10p) have a downward trend. In the rice-producing regions of Southeast Asia and South America, extreme precipitation events will increase significantly in the future. The prediction results of this model indicate that the rice output of these four major rice-producing regions will show an upward trend in the future. Although extreme precipitation events will have a negative impact on rice production, future increases in rice planting areas, economic development, and population growth will all contribute to an increase in rice production. The increase in food demand caused by population growth also brings uncertainty to global food security. This research is helpful for further understanding climate change trends and risks to global rice-production areas in the future and provides an important reference for global rice-production planning and risk management.
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Project description:Environmental variability greatly influences the eco-evolutionary dynamics of a population, i.e. it affects how its size and composition evolve. Here, we study a well-mixed population of finite and fluctuating size whose growth is limited by a randomly switching carrying capacity. This models the environmental fluctuations between states of resources abundance and scarcity. The population consists of two strains, one growing slightly faster than the other, competing under two scenarios: one in which competition is solely for resources, and one in which the slow (cooperating) strain produces a public good (PG) that benefits also the fast (free-riding) strain. We investigate how the coupling of demographic and environmental (external) noise affects the population's eco-evolutionary dynamics. By analytical and computational means, we study the correlations between the population size and its composition, and discuss the social-dilemma-like 'eco-evolutionary game' characterizing the PG production. We determine in what conditions it is best to produce a PG; when cooperating is beneficial but outcompeted by free riding, and when the PG production is detrimental for cooperators. Within a linear noise approximation to populations of varying size, we also accurately analyse the coupled effects of demographic and environmental noise on the size distribution.
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Project description:Common wild rice (Oryza rufipogon Griff.) represents an important resource for rice improvement. Genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) are most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, 146 CSSLs were produced; they were derived from the crossing and back-crossing of two rice cultivars: Dongnanihui 810 (Oryza sativa L.), an indica rice cultivar as the recipient, and ZhangPu wild rice, a wild rice cultivar as the donor. First, a physical map of the 146 CSSLs was constructed using 149 molecular markers. Based on this map, the total size of the 147 substituted segments in the population was 1145.65 Mb, or 3.04 times that of the rice genome. To further facilitate gene mapping, heterozygous chromosome segment substitution lines (HCSSLs) were also produced, which were heterozygous in the target regions. Second, a physical map of the 244 HCSSLs was produced using 149 molecular markers. Based on this map, the total length of substituted segments in the HCSSLs was 1683.75 Mb, or 4.47 times the total length of the rice genome. Third, using the 146 CSSLs, two QTLs for plant height, and one major QTL for apiculus coloration were identified. Using the two populations of HCSSLs, the qPa-6-2 gene was precisely mapped to an 88 kb region. These CSSLs and HCSSLs may, therefore, provide powerful tools for future whole genome large-scale gene discovery in wild rice, providing a foundation enabling the development of new rice varieties. This research will also facilitate fine mapping and cloning of quantitative trait genes, providing for the development of superior rice varieties.
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Project description:Two genomic regions duplicated in distal ends of the short arms of chromosomes 11 and 12 in rice (Oryza sativa L.) were characterized by YAC ordering with 46 genetic markers. Physical maps covering most of the duplicated regions were generated. Thirty-five markers, including 21 rice cDNA clones, showed the duplicated loci arrayed strictly in the same order along the two specific genomic regions. Regardless of their different genetic distances, the two duplicated segments may have a similar and minimum physical size with an expected length of about 2.5 Mb. However, differences of RFLP frequency for the duplicated DNA copies and recombination frequency for a given homoeologous area between the two regions were observed, indicating that these changes in genome organization occurred after the duplication. Our results establish a good model system for resolving the relationships between gene duplication, expression of duplicated genes, and the frequency of meiotic recombination in small chromosomal regions.
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Project description:The caenophidian (assigned also as "advanced") snakes are traditionally viewed as a group of reptiles with a limited karyotypic variation and stable ZZ/ZW sex chromosomes. The W chromosomes of the caenophidian snakes are heterochromatic, and pioneering studies demonstrated that they are rich in repetitive elements. However, a comparative study of the evolutionary dynamics of the repetitive content of the W chromosome across the whole lineage is missing. Using molecular-cytogenetic techniques, we explored the distribution of four repetitive motifs (microsatellites GATA, GACA, AG and telomeric-like sequences), which are frequently accumulated in differentiated sex chromosomes in vertebrates, in the genomes of 13 species of the caenophidian snakes covering a wide phylogenetic spectrum of the lineage. The results demonstrate a striking variability in the morphology and the repetitive content of the W chromosomes even between closely-related species, which is in contrast to the homology and long-term stability of the gene content of the caenophidian Z chromosome. We uncovered that the tested microsatellite motifs are accumulated on the degenerated, heterochromatic W chromosomes in all tested species of the caenophidian snakes with the exception of the Javan file snake representing a basal clade. On the other hand, the presence of the accumulation of the telomeric-like sequences on the caenophidian W chromosome is evolutionary much less stable. Moreover, we demonstrated that large accumulations of telomeric-like motifs on the W chromosome contribute to sexual differences in the number of copies of the telomeric and telomeric-like repeats estimated by quantitative PCR, which might be confusing and incorrectly interpreted as sexual differences in telomere length.
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Project description:Two Telomeric Associated Sequences, TAS-R and TAS-L, form the principal subtelomeric repeat families identified in Drosophila melanogaster. They are PIWI-interacting RNA (piRNA) clusters involved in repression of Transposable Elements. In this study, we revisited TAS structural and functional dynamics in D. melanogaster and in related species. In silico analysis revealed that TAS-R family members are composed of previously uncharacterized domains. This analysis also showed that TAS-L repeats are composed of arrays of a region we have named "TAS-L like" (TLL) identified specifically in one TAS-R family member, X-TAS. TLL were also present in other species of the melanogaster subgroup. Therefore, it is possible that TLL represents an ancestral subtelomeric piRNA core-cluster. Furthermore, all D. melanogaster genomes tested possessed at least one TAS-R locus, whereas TAS-L can be absent. A screen of 110 D. melanogaster lines showed that X-TAS is always present in flies living in the wild, but often absent in long-term laboratory stocks and that natural populations frequently lost their X-TAS within 2 years upon lab conditioning. Therefore, the unexpected structural and temporal dynamics of subtelomeric piRNA clusters demonstrated here suggests that genome organization is subjected to distinct selective pressures in the wild and upon domestication in the laboratory.
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Project description:In bacteria, genes with related functions often are grouped together in operons and are cotranscribed as a single polycistronic mRNA. In eukaryotes, functionally related genes generally are scattered across the genome. Notable exceptions include gene clusters for catabolic pathways in yeast, synthesis of secondary metabolites in filamentous fungi, and the major histocompatibility complex in animals. Until quite recently it was thought that gene clusters in plants were restricted to tandem duplicates (for example, arrays of leucine-rich repeat disease-resistance genes). However, operon-like clusters of coregulated nonhomologous genes are an emerging theme in plant biology, where they may be involved in the synthesis of certain defense compounds. These clusters are unlikely to have arisen by horizontal gene transfer, and the mechanisms behind their formation are poorly understood. Previously in thale cress (Arabidopsis thaliana) we identified an operon-like gene cluster that is required for the synthesis and modification of the triterpene thalianol. Here we characterize a second operon-like triterpene cluster (the marneral cluster) from A. thaliana, compare the features of these two clusters, and investigate the evolutionary events that have led to cluster formation. We conclude that common mechanisms are likely to underlie the assembly and control of operon-like gene clusters in plants.
| S-EPMC3179108 | biostudies-literature
Project description:MotivationThe evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism.ResultsWe present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons.Availability and implementationhttps://github.com/Gabaldonlab/EvolClust/.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC7703780 | biostudies-literature