Hoolock leuconedys
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA82969 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR26028276_1.fastq.gz | Fastqsanger.gz | |||
| SRR26028276_2.fastq.gz | Fastqsanger.gz | |||
| SRR30454108_1.fastq.gz | Fastqsanger.gz | |||
| SRR30454109_1.fastq.gz | Fastqsanger.gz |
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Project description:Hoolock leuconedys isolate:Arthur Raw sequence reads
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Project description:Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH and selective sequencing in two of the four karyomorphs, has shown that high resolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. Here we use these tools to precisely define the rearrangements that have occurred in the remaining two karyomorphs, genera Symphalangus (2n=50), and Hoolock (2n=38). This research provides the most comprehensive insight into the evolutionary origins of chromosome rearrangements involved in transforming small apes genome. Bioinformatics analyses of the human-gibbon synteny breakpoints revealed association with transposable elements and segmental duplications providing some insight into the mechanisms that might have promoted rearrangements in small apes. In the near future, the comparison of gibbon genome sequences will provide novel insights to test hypotheses concerning the mechanisms of chromosome evolution. The precise definition of synteny block boundaries and orientation, chromosomal fusions, and centromere repositioning event presented here will facilitate genome sequence assembly for these close relatives of humans.
2012-08-10 | GSE40024 | GEO
Project description:Array-Painting with Hoolock sorted chromosomes
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Project description:Fecal microbiota of wild and captive skywalker hoolock gibbon Raw sequence reads
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Project description:Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. A near universal feature of centromeres is the presence of repetitive sequences, such as satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. Previously, we identified a novel composite retrotransposon, LAVA, that is exclusive to gibbons and expanded within the centromere regions of one gibbon genus, Hoolock. In this study, we use ChIP-seq, RNA-seq and fluorescence in situ hybridization to comprehensively investigate the repeat content of centromeres of the four extant gibbon genera (Hoolock, Hylobates, Nomascus and Siamang). We find that CENP-A nucleosomes and the DNA-protein interface with the inner kinetochore are enriched in retroelements in all gibbon genera, rather than satellite DNA. We find that LAVA in Hoolock is enriched in the centromeres of most chromosomes and shows centromere- and species-specific sequence and structural differences compared to other genera, potentially as a result of its co-option to a centromeric function. In contrast, we found that a centromeric retroelement-derived macrosatellite, SST1, corresponds with chromosome breakpoint reuse across gibbons and shows high sequence conservation across genera. Finally, using de novo assembly of centromere-specific sequences, we determine that transcripts originating from gibbon centromeres recapitulate species-specific TE diversity. Combined, our data reveals dynamic, species-specific shifts in repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity observed within this lineage.
2021-05-24 | GSE161308 | GEO
Project description:Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. A near universal feature of centromeres is the presence of repetitive sequences, such as satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. Previously, we identified a novel composite retrotransposon, LAVA, that is exclusive to gibbons and expanded within the centromere regions of one gibbon genus, Hoolock. In this study, we use ChIP-seq, RNA-seq and fluorescence in situ hybridization to comprehensively investigate the repeat content of centromeres of the four extant gibbon genera (Hoolock, Hylobates, Nomascus and Siamang). We find that CENP-A nucleosomes and the DNA-protein interface with the inner kinetochore are enriched in retroelements in all gibbon genera, rather than satellite DNA. We find that LAVA in Hoolock is enriched in the centromeres of most chromosomes and shows centromere- and species-specific sequence and structural differences compared to other genera, potentially as a result of its co-option to a centromeric function. In contrast, we found that a centromeric retroelement-derived macrosatellite, SST1, corresponds with chromosome breakpoint reuse across gibbons and shows high sequence conservation across genera. Finally, using de novo assembly of centromere-specific sequences, we determine that transcripts originating from gibbon centromeres recapitulate species-specific TE diversity. Combined, our data reveals dynamic, species-specific shifts in repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity observed within this lineage.
2021-05-24 | GSE161191 | GEO
Project description:The present study aimed at predicting the potential habitat of Western Hoolock Gibbon (Hoolock hoolock) in the upper Brahmaputra River Valley, Assam, India, and identifying priority conservation areas for the species, taking canopy cover into account. We used the maximum entropy algorithm for the prediction of the potential habitat of the gibbon using its current distribution with 19 environmental parameters as primary predictors. Spatio-temporal analyses of the habitat were carried out using satellite-based remote sensing and GIS techniques for two decades (1998-2018) along with Terra Modis Vegetation Continuous Field product to examine land use land cover (LULC), habitat fragmentation, Normalized Difference Vegetation Index (NDVI) and tree cover percentage of the study area. To identify the conservation priority area, we applied a cost-effective decision-making analysis using systematic conservation prioritization in R programming. The model predicted an area of 6025 km2 under high potential habitat, a major part of which was found to overlap with dense forest (80%), followed by moderately open forest (74%) and open forest (66%). The LULC change matrix showed a reduction of forest area in the predicted high potential habitat during the study period, while agricultural class showed an increasing trend. The fragmentation analysis indicated that the number of patches and patch density increased from 2008 to 2018 in the 'very dense' and 'dense' canopy regions of the gibbon habitat. Based on the conservation priority analysis, a 640 km2 area has been proposed to conserve a minimum of 10% of gibbon habitat. The current analysis revealed that in the upper Brahmaputra Valley most areas under dense forest and dense canopy have remained intact over the last two decades, at least within the high potential habitat zone of gibbons independent of the degree of area change in forest, agriculture and plantation.
| S-EPMC8322352 | biostudies-literature