Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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High throughput sequencing of the small RNAs from banana cv. Grand Naine (AAA group)

ABSTRACT: Small RNAs especially small inhibiting RNAs (siRNAs) and microRNAs (miRNAs) play essential role in the regulation of gene expression in plants. These non coding RNAs are processed by the DICER like proteins into 21-24 nucleotides single stranded molecules that guide the activity of RNA induced silencing complex. This complex along with the processed small RNA identifies the cognate mRNA and brings about sequence specific mRNA degradation thereby silencing the gene expression. The small RNA profile is unique for each plant tissue at a given point of time. High throughput sequencing method allows the study of differential expression of these small RNAs. Deep sequencing of small RNAs derived from the leaves of an elite cultivar of banana cv. Grand Naine (‘Cavendish’ subgroup with AAA genotype) was carried out. Generation of complete small RNA profile of banana cv. Grand Naine for comparison with similar databases

ORGANISM(S): Musa acuminata AA Group

SUBMITTER: T Ganapathi

PROVIDER: E-GEOD-65727 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: Banana (Musa) is one of the most important crops grown in tropical and sub-tropical areas. Cavendish, the most widely grown banana cultivar, is a triploid derived from an intra-species cross. Cavendish is relatively resistant to Race 1 of Fusarium oxysporum f. sp. Cubense (Foc1) which caused wide spread Panama disease during 1960s but is susceptible to Race 4 of Foc (Foc4) which has been causing epidemics in large areas of banana fields in Asia and Australia in the last decade and is threatening world banana production. The genome of the diploid species Musa acuminata (AA) which is the ancestor of a majority of cultivated banana has recently been sequenced. Availability of banana transcriptomes will be highly useful for improving banana genome annotation and assembly and for banana biological research. The knowledge of global gene expression patterns influenced by infection by different Foc races will help to understand the pathogenesis processes and the host responses to the infection. Results: RNA samples extracted from different organs of the Cavendish cultivar were pooled for deep sequencing using the Illumina sequencing technology. The assembled reads were aligned with the genome of M. accuminata and with sequences in the Genbank databases. The analysis led to identification of 842 genes that were not annotated by the Musa genome project. A large number of simple nucleotide polymorphisms (SNPs) and short insertions and deletion (indels) were identified from the transcriptome data. GFP-expressing Foc1 and Foc4 was generated and used to monitor the infection process. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. Both Foc1 and Foc4 were found to be able to invade banana roots and spread to root vascular tissues in the first two days following inoculation. The profiling analysis revealed that inoculation with Foc1 and Foc4 caused similar changes in the gene expression profiles in the infected banana roots. The Foc infection led to induction of many well-known defense-related genes including PATHOGENESIS-RELATED 5 (PR5), PAL, and a lignin-forming peroxidase. The WRKY40 gene, which is a negative regulator of the defense pathway in Arabidopsis, was quickly and strongly suppressed by the infection. Two genes encoding the ethylene biosynthetic enzyme ACC oxidase and several ethylene-responsive transcription factors were among strongly induced genes by both Foc1 and Foc4 Conclusions: Both Foc1 and Foc4 are able to spread into the vascular system of banana roots during the first two days of the infection process and their infection led to similar gene expression profiles in banana roots. The transcriptome profiling analysis indicates that the ethylene synthetic and signalling pathways were activated in response to the Foc infection. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. The plants whose roots were immersed in the culture medium without the pathogen (mock inoculation) were used as a control.

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High throughput sequencing of the small RNAs from banana cv. Grand Naine (AAA group)

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