Whole genome sequencing of weedy rice variants from Peninsular Malaysia
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PROVIDER: PRJEB96009 | ENA |
REPOSITORIES: ENA
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Project description:<p>Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However the CNV data from diverse populations is rather limited. Here we report the first investigation of copy number variation (CNV) in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 62 putative novel CNVs, consisting of 25 gains and 37 losses. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), as well as the metabolic pathways (GO:0001852). Copy number gains in CNVRs enriched with genes were significantly higher than the losses (P value <0.001). Therefore, in view of the small population size, relative isolation and semi-normadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.</p>
| phs000664.v1.p1 | EGA
Project description:Background: Weedy rice (Oryza sativa L.) is a worldwide problem in rice production, being highly tolerant to sub-optimal nutrient levels hence competitive in nutrient acquisition. To understand the function of genes that are potentially involved in the high nutrient acquisition ability of weedy rice, we compared the transcriptomes of strawhull weedy red rice (tolerant to N deficit) with the rice cultivar ‘Wells’ (intolerant to N deficit), by examining profiles in flag leaves at panicle initiation under low and optimum N levels. Strawhull weedy red rice and cultivar ‘Wells’ were grown in nutrient solution with NH4NO3 concentration manipulated to simulate optimum and deficient N conditions. Changes in gene expression in leaf tissues were analyzed at three conditions: N deficiency, and at 24- and 48-h NH4NO3 supplementation after N starvation. Differential gene expression on weedy red rice was evaluated using oligonucleotide arrays representing 44,974 rice gene models. Overall, comparative real-time PCR analysis of 21 candidate genes identified from the microarray data between weedy red rice and cultivar ‘Wells’ supported our hypothesis that key genes involved in N assimilation are expressed differentially at N- deficient conditions between the tolerant and intolerant strains. Results: Eight candidate genes showed significant differences in expression at one of the time points: N and starch metabolism-related [alanine aminotransferase (OsAlaAT) locus ID Os10g25140.1; soluble starch synthase 2-1(OsSSSII1), Os10g30156.1; and soluble starch synthase 2-3(OsSSSII3), Os06g12450.1]; cell structure-related [alpha-L-fucosidase 2 precursor (OsFUCA2), Os06g06250.1]; signal transduction [two-component response regulator-like(OsPRR1), Os02g40510.1 and EF hand family protein (OsPOLC2_JUNOX), Os02g50060.1]; and transcription factors [zinc finger, C2H2 type family protein(OsC2H2Znf), Os11g06840.1 and Myb-like DNA-binding domain (OsMYB), Os01g62660.1]. Genome-wide gene expression analysis of weedy rice showed that nitrite reductase (Os01g25484.1; Os01g25484.2; Os01g25484.3) was most highly induced at N starvation and was most deeply repressed at 24 h of N-stress recovery. A few other genes, namely SANT/MYB (Os01g47370.1), chaperonin (Os02g54060.1; Os02g54060.2), protein phosphatase (Os09g15670.1), polyamine transporter (Os01g61044.1), trehalose-6-phosphate synthase (Os02g54820.2), uracil phosphoribosyltransferase (Os05g38170.1), an MIKCc type-box transcription factor (Os02g52340.1), a cell homeostasis-related uncharacterized protein (Os02g16880.1), a protease inhibitor (Os07g18990.1), dehydrin (Os11g26760.1), and cytochrome P450 (Os11g05380.1) were also strong indicators of starvation and recovery. Conclusions: Weedy rice has N-stress adaptive mechanisms that are probably distinct to the mechanisms in most cultivars. This mechanism potentially contributes to its high vigor and competitive advantage over most rice cultivars under sub-optimal nutrient levels. Expression of key genes involved in nitrate assimilation, trehalose synthesis, and protein modification appeared to be critical for adaptation to N stress in weedy rice. N-stress tolerance of weedy red rice appeared to be due at least in part to the ability to sustain C fixation and starch synthesis during N starvation.
2014-07-16 | GSE59438 | GEO
Project description:Background: Weedy rice (Oryza sativa L.) is a worldwide problem in rice production, being highly tolerant to sub-optimal nutrient levels hence competitive in nutrient acquisition. To understand the function of genes that are potentially involved in the high nutrient acquisition ability of weedy rice, we compared the transcriptomes of strawhull weedy red rice (tolerant to N deficit) with the rice cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y (intolerant to N deficit), by examining profiles in flag leaves at panicle initiation under low and optimum N levels. Strawhull weedy red rice and cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y were grown in nutrient solution with NH4NO3 concentration manipulated to simulate optimum and deficient N conditions. Changes in gene expression in leaf tissues were analyzed at three conditions: N deficiency, and at 24- and 48-h NH4NO3 supplementation after N starvation. Differential gene expression on weedy red rice was evaluated using oligonucleotide arrays representing 44,974 rice gene models. Overall, comparative real-time PCR analysis of 21 candidate genes identified from the microarray data between weedy red rice and cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y supported our hypothesis that key genes involved in N assimilation are expressed differentially at N- deficient conditions between the tolerant and intolerant strains. Results: Eight candidate genes showed significant differences in expression at one of the time points: N and starch metabolism-related [alanine aminotransferase (OsAlaAT) locus ID Os10g25140.1; soluble starch synthase 2-1(OsSSSII1), Os10g30156.1; and soluble starch synthase 2-3(OsSSSII3), Os06g12450.1]; cell structure-related [alpha-L-fucosidase 2 precursor (OsFUCA2), Os06g06250.1]; signal transduction [two-component response regulator-like(OsPRR1), Os02g40510.1 and EF hand family protein (OsPOLC2_JUNOX), Os02g50060.1]; and transcription factors [zinc finger, C2H2 type family protein(OsC2H2Znf), Os11g06840.1 and Myb-like DNA-binding domain (OsMYB), Os01g62660.1]. Genome-wide gene expression analysis of weedy rice showed that nitrite reductase (Os01g25484.1; Os01g25484.2; Os01g25484.3) was most highly induced at N starvation and was most deeply repressed at 24 h of N-stress recovery. A few other genes, namely SANT/MYB (Os01g47370.1), chaperonin (Os02g54060.1; Os02g54060.2), protein phosphatase (Os09g15670.1), polyamine transporter (Os01g61044.1), trehalose-6-phosphate synthase (Os02g54820.2), uracil phosphoribosyltransferase (Os05g38170.1), an MIKCc type-box transcription factor (Os02g52340.1), a cell homeostasis-related uncharacterized protein (Os02g16880.1), a protease inhibitor (Os07g18990.1), dehydrin (Os11g26760.1), and cytochrome P450 (Os11g05380.1) were also strong indicators of starvation and recovery. Conclusions: Weedy rice has N-stress adaptive mechanisms that are probably distinct to the mechanisms in most cultivars. This mechanism potentially contributes to its high vigor and competitive advantage over most rice cultivars under sub-optimal nutrient levels. Expression of key genes involved in nitrate assimilation, trehalose synthesis, and protein modification appeared to be critical for adaptation to N stress in weedy rice. N-stress tolerance of weedy red rice appeared to be due at least in part to the ability to sustain C fixation and starch synthesis during N starvation. Plants were subjected to four treatments: T1 M-bM-^@M-^S Full N; T2 M-bM-^@M-^S NH4NO3starvation until NSI <95%; T3 - 24-h NH4NO3 readdition post-starvation; and T4 M-bM-^@M-^S 48-h NH4NO3 readdition post-starvation. The 24- and 48-h time points for NH4NO3 supplementation were selected to assess both the early and late molecular responses. There were four replications, with three plants per replication per N treatment.
2014-07-16 | E-GEOD-59438 | biostudies-arrayexpress
Project description:The differences in pungency of 'sirih' imply the probable occurrence of several variants of <i>Piper betle</i> L. in Malaysia. However, the metabolite profiles underlying the pungency of the different variants remain a subject of further research. The differences in metabolite profiles of selected Malaysian <i>P. betle</i> variants were thus investigated; specifically, the leaf aqueous methanolic extracts and essential oils were analyzed via <sup>1</sup>H-NMR and GC-MS metabolomics, respectively. Principal component analysis (PCA) of the <sup>1</sup>H-NMR spectral data showed quantitative differences in the metabolite profiles of 'sirih melayu' and 'sirih india' and revealed an ambiguous group of samples with low acetic acid content, which was identified as <i>Piper rubro-venosum</i> hort. ex Rodigas based on DNA sequences of the internal transcribed spacer 2 (ITS2) region. The finding was supported by PCA of two GC-MS datasets of <i>P. betle</i> samples obtained from several states in Peninsular Malaysia, which displayed clustering of the samples into 'sirih melayu' and 'sirih india' groups. Higher abundance of chavicol acetate was consistently found to be characteristic of 'sirih melayu'. The present research has provided preliminary evidence supporting the notion of occurrence of two <i>P. betle</i> variants in Malaysia based on chemical profiles, which may be related to the different genders of <i>P. betle</i>.
2022-03-21 | MTBLS2585 | MetaboLights
Project description:<p>Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However the CNV data from diverse populations is rather limited. Here we report the first investigation of copy number variation (CNV) in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 62 putative novel CNVs, consisting of 25 gains and 37 losses. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), as well as the metabolic pathways (GO:0001852). Copy number gains in CNVRs enriched with genes were significantly higher than the losses (P value <0.001). Therefore, in view of the small population size, relative isolation and semi-normadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.</p>
| phs000664 | dbGaP
Project description:Resource partitioning among tropical bats in agricultural areas of Peninsular Malaysia remains unclear. This study was conducted to evaluate resource partitioning among bats by examining their fecal samples. The main bat species sampled included: Rhinolophus coelophyllus, Rhinolophus malayanus, Rhinolophus pusillus, Rhinolophus refulgens, Taphozous melanopogon and Hipposideros larvatus. Two harp traps were set at different elevations on a hilltop (Gunung Keriang) and two high nets were used in neighboring rice fields at three sites, for three consecutive nights per sampling from April 2021 to February 2022. A total of 301 bats and 1,505 pellets were analyzed using a conventional approach which examined the fecal sample under the microscope. All of the bat species within the study had insects from the order Coleoptera, Lepidoptera, Diptera and Hemiptera in their diet. Larger bats exhibited a greater variety of prey consumption. Male individuals were observed to be generalists while female individuals were specialists, particularly during pregnancy and lactating reproductive stages. Bat species and insect order had a significant impact on the percentage fragment frequency of the insects consumed. Rhinolophus coelophyllus specialized in feeding on Coleoptera and Diptera, H. larvatus fed on Coleoptera, R. malayanus fed on Hemiptera, R. pusillus and T. melanopogon fed on Lepidoptera. Future molecular analysis can be carried out to further identify the insect pests consumed by these bats up to species level. These findings enhance our understanding of bats' ecological roles in agricultural landscapes and contribute to conservation and pest management strategies.
| S-EPMC10800099 | biostudies-literature
Project description:Red rice fully dormant seeds do not germinate even under favourable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and nondormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and nondormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 hours and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and nondormant imbibed seeds.
2018-05-10 | E-MTAB-6740 | biostudies-arrayexpress
Project description:Oryza sativa strain:weedy rice Raw sequence reads
| PRJNA344937 | ENA
Project description:Molecular characterization of B. pseudomallei isolates from Malaysia
| PRJEB48970 | ENA
Project description:Low temperature is one of the major factors affecting rice germination, and low tempera-ture germination (LTG) is an important agronomic trait. Although genetic variation is abundant in rice germplasm resources, the molecular mechanism of LTG remains poorly understood. In this study, we first proved that weedy rice WR04-6 had significantly better low-temperature germination (LTG) ability at 10°C than the cultivated rice Qishanzhan (QSZ). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10, 12 and 14 days of seed germination at 10°C. The results of GO enrichment and KEGG en-richment revealed that the differentially expressed genes between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to ab-scisic acid. This is consistent with the results of α-amylase activity, ABA and GA treat-ment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high density SNP genetic map were used to detect quantitative trait loci (QTL) for low temperature germination rates at 10°C for 14 days. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq differential genes (DEGs), sixteen candidate genes potentially associated with LTG were identified. Validation of expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to under-stand the genetic basis of LTG in weedy rice and provide new genetic resources for gener-ation of rice germplasm with LTG.
2023-03-01 | GSE222929 | GEO