Loliolus sumatrensis
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PROVIDER: PRJDB15292 | ENA |
REPOSITORIES: ENA
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Project description:Whole Genome Sequencing of Dicerorhinus sumatrensis (Sumatran Rhinoceros)
| PRJNA415733 | ENA
Project description:Dicerorhinus sumatrensis harrissoni Genome sequencing and assembly
| PRJNA638009 | ENA
Project description:Conyza sumatrensis (Retz.) E. H. Walker is an obnoxious weed, emerging as an invasive species globally. Seed germination biology of four populations of the species stemming from arid, semi-arid, temperate, and humid regions was determined in this study. Seed germination was recorded under six different environmental cues (i.e., light/dark periods, constant and alternating day and night temperatures, pH, salinity, and osmotic potential levels) in separate experiment for each cue. Populations were main factor, whereas levels of each environmental cue were considered as sub-factor. The impact of seed burial depths on seedling emergence was inferred in a greenhouse pot experiment. Seed germination was recorded daily and four germination indices, i.e., seed germination percentage, mean germination time, time to reach 50% germination, and mean daily germination were computed. Tested populations and levels of different environmental cues had significant impact on various seed germination indices. Overall, seeds stemming from arid and semi-arid regions had higher seed germination potential under stressful and benign environmental conditions compared to temperate and humid populations. Seed of all populations required a definite light period for germination and 12 hours alternating light and dark period resulted in the highest seed germination. Seed germination of all populations occurred under 5-30°C constant and all tested alternate day and night temperatures. However, the highest seed germination was recorded under 20°C. Seeds of arid and semi-arid populations exhibited higher germination under increased temperature, salinity and osmotic potential levels indicating that maternal environment strongly affected germination traits of the tested populations. The highest seed germination of the tested populations was noted under neutral pH, while higher and lower pH than neutral had negative impact on seed germination. Arid and semi-arid populations exhibited higher seed germination under increased pH compared to temperate and humid populations. Seed burial depth had a significant effect on the seedling emergence of all tested populations. An initial increase was noted in seedling emergence percentage with increasing soil depth. However, a steep decline was recorded after 2 cm seed burial depth. These results indicate that maternal environment strongly mediates germination traits of different populations. Lower emergence from >4 cm seed burial depth warrants that deep burial of seeds and subsequent zero or minimum soil disturbance could aid the management of the species in agricultural habitats. However, management strategies should be developed for other habitats to halt the spread of the species.
| S-EPMC8638915 | biostudies-literature
Project description:ObjectiveThe Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling.ResultsDue to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; HO = 0.30). These were sufficient to distinguish among individuals (PID < 0.0001), and to distinguish among siblings (PID(sib) < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos.
| S-EPMC7995689 | biostudies-literature
Project description:The vertebrate extinction rate over the past century is approximately 22-100 times greater than background extinction rates [1], and large mammals are particularly at risk [2, 3]. Quaternary megafaunal extinctions have been attributed to climate change [4], overexploitation [5], or a combination of the two [6]. Rhinoceroses (Family: Rhinocerotidae) have a rich fossil history replete with iconic examples of climate-induced extinctions [7], but current pressures threaten to eliminate this group entirely. The Sumatran rhinoceros (Dicerorhinus sumatrensis) is among the most imperiled mammals on earth. The 2011 population was estimated at ?216 wild individuals [8], and currently the species is extirpated, or nearly so, throughout the majority of its former range [8-12]. Understanding demographic history is important in placing current population status into a broader ecological and evolutionary context. Analysis of the Sumatran rhinoceros genome reveals extreme changes in effective population size throughout the Pleistocene. Population expansion during the early to middle Pleistocene was followed by decline. Ecological niche modeling indicated that changing climate most likely played a role in the decline of the Sumatran rhinoceros, as less suitable habitat on an emergent Sundaland corridor isolated Sumatran rhinoceros populations. By the end of the Pleistocene, the Sundaland corridor was submerged, and populations were fragmented and consequently reduced to low Holocene levels from which they would never recover. Past events denuded the Sumatran rhinoceros of genetic diversity through population decline, fragmentation, or some combination of the two and most likely made the species even more susceptible to later exploitation and habitat loss. VIDEO ABSTRACT.
| S-EPMC5894340 | biostudies-literature
Project description:Cases of weed resistant to herbicides have changed the dynamics of agricultural areas in Brazil, and in recent years, Erigeron species have caused major problems to farmers in the country, mainly in relation to the ineffectiveness of herbicide treatments used. The objective of this study was to confirm the cross-resistance to ALS inhibitors in populations of Erigeron sumatrensis as well as to investigate the existence of mutations in the site of action of ALS-inhibiting herbicides. To do this, 30 populations collected in the 2016/2017 crop season were grown in a greenhouse. Dose-response (chlorimuron-ethyl and cloransulam-methyl), inhibition of cytochrome P-450 with malathion, and ALS gene sequencing experiments were carried out in the F1 generations of two fleabane populations. The results proved the cross-resistance to chlorimuron-ethyl and cloransulam-methyl herbicides applied in the post-emergence of the resistant population of E. sumatrensis. The higher activity of P450 enzymes is unlikely responsible for the resistance of the population studied. The resistance mechanism found in R was the target site mutation Pro197Ser at the ALS gene. This is the first study in Brazil to identify a target-site change as a survival mechanism in E. sumatrensis for the resistance to ALS-inhibiting herbicides.
| S-EPMC8879965 | biostudies-literature
Project description:ObjectivesEfforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socio-economic factors and ecological dynamics attributed to lack of knowledge on the adaptive mechanisms of potential tree species such as Kapur (Dryobalanops aromatica C.F.Gaertn Syn. Dryobalanops sumatrensis J.F. Gmelin A.J.G.H Kostermans). This species is a multi-purpose tree that, commonly grows in mineral soils, but also in peat swamp as previously reported, which raised a fundamental question regarding the molecular mechanism of this adaptation. Therefore, a dataset was created aiming to detect candidates of adaptive genes in D. aromatica seedlings, cultivated in two contrasting potting media, namely mineral soil and peat media, based on RNA Sequencing Transcriptome Analysis.Data descriptionThe RNA transcriptome data of D. aromatica's seedlings derived from young leaves of three one-year-old seedlings, raised in each dry mineral soil media and peat media, were generated by using Illumina HiSeq 4000 platform in NovogenAIT, Singapore. The acquired data, as the first transcriptome dataset for D. aromatica, is of a great importance in understanding molecular mechanism and responses of the involved genes of D. aromatica to the contrasting, growing potting media conditions that could also be useful to generate molecular markers.
| S-EPMC7456001 | biostudies-literature
Project description:A variety of wildlife species maintained in captivity are susceptible to iron storage disease (ISD), or hemochromatosis, a disease resulting from the deposition of excess iron into insoluble iron clusters in soft tissue. Sumatran rhinoceros (Dicerorhinus sumatrensis) is one of the rhinoceros species that has evolutionarily adapted to a low-iron diet and is susceptible to iron overload. Hemosiderosis is reported at necropsy in many African black and Sumatran rhinoceroses but only a small number of animals reportedly die from hemochromatosis. The underlying cause and reasons for differences in susceptibility to hemochromatosis within the taxon remains unclear. Although serum ferritin concentrations have been useful in monitoring the progression of ISD in many species, there is some question regarding their value in diagnosing hemochromatosis in the Sumatran rhino. To investigate the metabolic changes during the development of hemochromatosis and possibly increase our understanding of its progression and individual susceptibility differences, the serum metabolome from a Sumatran rhinoceros was investigated by nuclear magnetic resonance (NMR)-based metabolomics. The study involved samples from female rhinoceros at the Cincinnati Zoo (n = 3), including two animals that died from liver failure caused by ISD, and the Sungai Dusun Rhinoceros Conservation Centre in Peninsular Malaysia (n = 4). Principal component analysis was performed to visually and statistically compare the metabolic profiles of the healthy animals. The results indicated that significant differences were present between the animals at the zoo and the animals in the conservation center. A comparison of the 43 serum metabolomes of three zoo rhinoceros showed two distinct groupings, healthy (n = 30) and unhealthy (n = 13). A total of eighteen altered metabolites were identified in healthy versus unhealthy samples. Results strongly suggest that NMR-based metabolomics is a valuable tool for animal health monitoring and may provide insight into the progression of this and other insidious diseases.
| S-EPMC4883739 | biostudies-literature
Project description:We used RNAseq to quantify trascript expression from three populations of Conyza sumatrensis before and 5 hours after treatment with 2,4-D. This study investigates different responses between a 2,4-D resistant biotype compared to a 2,4-D sensitive biotype.
2023-06-30 | GSE226337 | GEO