Microcitrus (citrus microbiome)
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB15329 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1654710_1.fastq.gz | Fastqsanger.gz | |||
| ERR1654710_2.fastq.gz | Fastqsanger.gz | |||
| ERR1654711_1.fastq.gz | Fastqsanger.gz | |||
| ERR1654711_2.fastq.gz | Fastqsanger.gz | |||
| ERR1654712_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis)
2009-12-01 | GSE17255 | GEO
Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis) Total RNA from four replicates for each sample category (Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA or without Fe-EDDHA) were generated and compared.
2010-05-19 | E-GEOD-17255 | biostudies-arrayexpress
Project description:Salt stress, especially saline-alkali stress, has seriously negative effect on citrus production. Ziyang xiangcheng (Citrus junos Sieb.) (Cj) has been reported as a saline-alkali stress and iron deficiency tolerant citrus rootstock. However, the molecular mechanism of its saline-alkali stress tolerance is still not clear. Two citrus rootstocks and one navel orange scion, Cj, Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) (Pt) and ‘Lane Late’ navel orange (Citrus sinensis (L.) Osb.) (LL), were used in this study. The grafted materials Cj+LL and Pt+LL grown in calcareous soil were used to identify genes and pathways responsive to saline-alkali stress using RNA-seq. The seedlings of Cj and Pt grown in the solutions with different gradient pH value were used to perform a supplement experiment. Comprehensively analyzing the data of RNA-seq, physiology and biochemistry, agronomic traits and mineral elements of Cj+LL, Pt+LL, Cj and Pt, several candidate pathways and genes were identified to be highly regulated under saline-alkali stress. Here, we propose citrate is important for the tolerance to iron deficiency and the jasmonate (JA) biosynthesis and signal transduction pathway may play a crucial role in tolerance to saline-alkali stress in citrus by interacting with other plant hormones, calcium signaling, ROS scavenging system and lignin biosynthesis.
2018-07-06 | GSE98996 | GEO
Project description:To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon. Fruits of five different citrus cultivars. Mature, healthy fruits of five different citrus cultivars (M-bM-^@M-^\ValenciaM-bM-^@M-^] and M-bM-^@M-^\NavelM-bM-^@M-^] orange [Citrus sinensis], mandarin [Citrus reticulata], lemon [Citrus M-CM-^W limon], grapefruit [Citrus M-CM-^W paradisi]) were purchased from a food market located in Davis, CA, USA. For all five types of fruit, three tissues (flavedo, albedo, and juice sacs) were compared separately. Each of the three tissues from each of the five types of fruit were sampled in three biological replicates, for a total of 45 samples. Samples were prepared from a 1 cm-thick equatorial disc and four sections (N, S, E, and W) were cut. Each section of flavedo, albedo, and juice sac tissue was dissected. gene expression variation underlying quality trait, different genotypes
2014-01-01 | E-GEOD-50384 | biostudies-arrayexpress
Project description:Alkaline stress has serious negative effects on citrus production. Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) (Cj) has been reported to be a rootstock that is tolerant to alkaline stress and iron deficiency. Poncirus trifoliata (Poncirus trifoliata (L.) Raf.) (Pt), the most widely used rootstock in China, is sensitive to alkaline stress. To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress, next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings which were cultured in nutrient solution with three gradient pH. This two-regulation level data set provides a system-level view of molecular events with precise resolution. The data suggest that the auxin pathway may play a central role in inhibitory effect of alkaline stress on root growth, and the regulation of auxin homeostasis under alkaline stress was important for citrus adapting to alkaline stress. Moreover, the JA pathway shown an opposite response to alkaline stress in Cj and Pt may contributes to the differentials of root system architecture and iron deficiency tolerance between Cj and Pt. The data set provides a wealth of genomic resources and new clues for further studying the mechanisms underlying Cj that resist alkaline stress.
2019-03-18 | GSE115049 | GEO
Project description:Citrus and most other fruit crops are commercially propagated via grafting, which ensures trees have consistent fruit traits combined with favorable traits from the rootstock such as soil adaptability, vigor, and resistance to soil pathogens. Breeding new rootstocks requires careful agronomic evaluations, and widespread use of new rootstocks and scions requires graft compatibility with commercially important scions and rootstocks. Graft incompatibility can occur when the scion and rootstock are not able to form a permanent, healthy union. Understanding and preventing graft incompatibility is therefore of paramount importance in the breeding of new fruit cultivars and in the choice of scion and rootstock by growers. The rootstock US-1283 is a citrandarin generated from a cross of ‘Ninkat’ mandarin (Citrus reticulata) and ‘Gotha Road’ #6 trifoliate orange (Poncirus trifoliata). It was released in 2014 after years of field evaluation because of its superior productivity and good fruit quality on ‘Hamlin’ sweet orange (C. sinensis) under Florida’s growing conditions. Subsequently, it was observed that trees of ‘Bearss’ lemon (C. limon) and ‘Valencia’ sweet orange (C. sinensis) grafted onto US-1283 exhibited apparent incompatible and unhealthy growth near the graft union. The incompatibility manifested as stem grooving and necrosis underneath the bark on the rootstock side of the graft. A genetically similar citrandarin rootstock, US-812 (C. reticulata ‘Sunki’ × P. trifoliata ‘Benecke’), is fully graft compatible with the same scions. Transcriptome analysis was performed on the vascular tissues above and below the graft union of compatible US-812 and incompatible US-1283 graft combinations with ‘Bearss’ and ‘Valencia’ to identify expression networks associated with incompatibility and help understand the processes and potential causes of incompatibility in citrus. Transcriptional reprogramming was stronger in the incompatible rootstock than in the grafted scions. Functional analysis of the transcriptional events below the graft unions of US-1283 incompatible combinations revealed differentially expression genes (DEGs) associated with oxidative stress and plant defense, among other pathways, similar to a pathogen-induced immune response localized to the rootstock, although no known pathogens were detected in the assayed plants. These changes were not observed above the graft unions.Differentially expressed genes (DEGs) in US-1283, but not the scions, were associated with oxidative stress and plant defense, among others, similar to a pathogen-induced immune response localized to the rootstock. No pathogen infection was detected. It is hypothesized this response could have been triggered by signaling miscommunications between rootstock and scion either through 1) unknown molecules from the scion that were perceived as danger signals by the rootstock, 2) missing signals from the scion or missing receptors in the rootstock necessary for the formation of a healthy graft union, 3) the overall perception of the scion by the rootstock as non-self, or 4) a combination of the above.
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Project description:Huanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. A powerful oligonucleotide microarray of high-density 16S rRNA genes, the PhyloChip microarray, has been developed and effectively used to study bacterial diversity, especially from environmental samples. In this article, we aim to decipher the bacterial microbiome in HLB-affected citrus versus non-infected citrus as well as in citrus plants treated with ampicillin and gentamicin using PhyloChip-based metagenomics.
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Project description:Alkaline stress has serious negative effects on citrus production. Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) (Cj) has been reported to be a rootstock that is tolerant to alkaline stress and iron deficiency. Poncirus trifoliata (Poncirus trifoliata (L.) Raf.) (Pt), the most widely used rootstock in China, is sensitive to alkaline stress. To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress, next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings which were cultured in nutrient solution with three gradient pH. This two-regulation level data set provides a system-level view of molecular events with precise resolution. The data suggest that the auxin pathway may play a central role in inhibitory effect of alkaline stress on root growth, and the regulation of auxin homeostasis under alkaline stress was important for citrus adapting to alkaline stress. Moreover, the JA pathway shown an opposite response to alkaline stress in Cj and Pt may contributes to the differentials of root system architecture and iron deficiency tolerance between Cj and Pt. The data set provides a wealth of genomic resources and new clues for further studying the mechanisms underlying Cj that resist alkaline stress.
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Project description:MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation. miRNAs have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues, Based on sequence similarity and hairpin structure prediction, we found that 178,102 reads representing 89 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates, whose precursors were all potentially generated from citrus ESTs. And of them five miRNA* sequences were also sequenced. These sequences had not been described in other plant species and accumulation of these 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes included one encoding IRX12 copper ion binding/ oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata.
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