Project description:Banana bunchy top disease (BBT) is one of the most economically serious viral diseases of banana caused by banana bunchy top virus (BBTV: Nanoviridae: Babuvirus). BBTV is a circular, ssDNA virus which is suitable in the phloem tissue and currently only being transmitted by the banana aphid (Pentalonia nigronervosa) in a persistent, non-propagative, circulative manner. Interaction of BBTV and banana aphid had been studied in several ways, such as transmission and translocation of BBTV inside the banana aphid body at cellular level. However, the molecular mechanism underlying the interaction between BBTV and banana aphid have been poorly understood. Therefore, this transcriptomic study was conducted to obtain the raw data for differential genes expression study in BBTV viruliferous (Vr) and non-viruliferous (NVr) banana aphid. Here, we present two data sets of RNA seq raw reads which is available in GenBank Sequence Read Archive (SRA) database with accession number of SRX6918251 and SRX6918252 for the Vr and NVr banana aphid respectively.
Project description:We report the total number of differentially expressed enzyme genes involved in starch biosynthesis of banana fruit using transcriptome profiling analysis. A sequencing depth of over 4.4 billion raw reads for each of six libraries was obtained using RNA-seq analysis.
Project description:Klutuk Wulung banana (<i>Musa balbisiana</i> Colla, BB Group) is a climacteric fruit whose ripening is influenced by ethylene production. This banana fruit has a relatively slow ripening process time and long shelf-life compared with A genome banana (<i>Musa acuminata</i>, AA). Bananas are usually harvested at a pre-climacteric stage and ripened artificially by exogenous ethylene. Hence, the application of exogenous ethylene at the pre-climacteric stage can accelerate the Klutuk Wulung banana ripening. However, there is no report regarding the effect of exogenous ethylene treatment on Klutuk Wulung banana global gene expression. The knowledge of global gene expression of ethylene treated Klutuk Wulung banana will help to understand this fruit ripening process. In this study, global gene expression data of untreated and ethylene treated Klutuk Wulung banana fruit during ripening were available. Total RNA was extracted from fruit pulp for differential expressed gene analysis using RNA-Seq. The RNA-Seq results obtained were ranged from 34,565,252 to 44,752,129 total reads, with 80.5% to 86.7% of reads were mapped against Klutuk Wulung banana genome reference derived from The Banana Genome Hub. In total, 29,968,128 to 37,776,907 transcripts were detected. The transcriptome data discussed in this article were deposited into NCBI's Gene Expression Omnibus (GEO) Series with an accession number GSE162077. These data can be used as information to identify gene candidates involved in fruit ripening for the application in banana postharvest program.
Project description:Banana is one of the world's favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/
Project description:Banana is a climacteric fruit and its ripening process is greatly influenced by presence of ethylene. This physiological climacteric characteristic of banana fruit leads to a fast ripening and a short shelf-life. Application of edible coating such as chitosan aims to prolong fruit shelf life. The knowledge on gene expression will help to understand the fruit ripening process itself and chitosan effect on global gene expression. Global gene expression data of chitosan treated and control of Cavendish banana during fruit ripening were provided. Total RNA was isolated from banana pulp for differential gene expression analysis. The RNA-sequencing generated ranged from 16,155,947 to 23,587,110 total reads, with 75.8%-83.8% of reads were mapped against the genome reference. In total, 33,797-35,944 transcripts were detected. The transcriptomics data discussed in this publication are accessible through NCBI's Gene Expression Omnibus with GEO Series accession number GSE139457. These data provide information to identify candidate genes involved in fruit ripening in response to chitosan coating to design a better banana postharvest management.
Project description:Banana shrimp (<i>Fenneropenaeus merguiensis</i>) is an economically important shrimp in marine aquaculture. Although there is plenty of transcriptome research for this species, the molecular mechanisms in thoracic ganglia of banana shrimp during ovarian maturation have not yet been investigated. Here we report the transcriptomic data of female banana shrimp obtained from thoracic ganglia during ovarian developmental stages. The samples were collected from four stages of ovarian development with two individual shrimps per stage. Total RNA was extracted and used to prepare the sequencing library. Approximately 188 million pair-end raw reads, ranging from 21 to 31 million reads for each library, were generated using an Illumina HiSeq 2500 platform. Quality control was applied to the raw reads before the assembly process. After <i>de novo</i> assembly, the final transcript assembly was generated by vector decontamination, coding regions prediction, redundancy reduction, and foreign sequence depletion. A total of 77,681 transcripts, ranging between 255 and 23,016 bp with an N50 value of 1,167 were obtained to the final assembly. Finally, the final transcripts assembly was evaluated by calculated assembly completeness with Arthropoda orthologous genes dataset. A total of 92.1% of Arthropoda orthologous genes were found in our final assembly. These data might provide benefits for gene discovery, gene annotation, transcript profiling, and other research topics in the context of banana shrimp.
Project description:In banana, drought responsive gene expression profiles of drought-tolerant and sensitive genotypes remain largely unexplored. In this research, the transcriptome of drought-tolerant banana cultivar (Saba, ABB genome) and sensitive cultivar (Grand Naine, AAA genome) was monitored using mRNA-Seq under control and drought stress condition. A total of 162.36 million reads from tolerant and 126.58 million reads from sensitive libraries were produced and mapped onto the Musa acuminata genome sequence and assembled into 23,096 and 23,079 unigenes. Differential gene expression between two conditions (control and drought) showed that at least 2268 and 2963 statistically significant, functionally known, non-redundant differentially expressed genes (DEGs) from tolerant and sensitive libraries. Drought has up-regulated 991 and 1378 DEGs and down-regulated 1104 and 1585 DEGs respectively in tolerant and sensitive libraries. Among DEGs, 15.9% are coding for transcription factors (TFs) comprising 46 families and 9.5% of DEGs are constituted by protein kinases from 82 families. Most enriched DEGs are mainly involved in protein modifications, lipid metabolism, alkaloid biosynthesis, carbohydrate degradation, glycan metabolism, and biosynthesis of amino acid, cofactor, nucleotide-sugar, hormone, terpenoids and other secondary metabolites. Several, specific genotype-dependent gene expression pattern was observed for drought stress in both cultivars. A subset of 9 DEGs was confirmed using quantitative reverse transcription-PCR. These results will provide necessary information for developing drought-resilient banana plants.
Project description:The increasing production of banana is hampered by the spread of banana plant diseases, one of which is caused by a group of bacteria, including those of causing wilt diseases. In Indonesia, blood disease is one of the important banana wilt diseases since loss due to the infection can reach up to 50%. There are numerous publications on the pathogen identification causing banana blood disease based on the molecular approach, however to date, no detailed molecular data are available for the interaction of banana host plant against the pathogen. Here, we present three raw data sets of the total RNA-seq from the inoculated Musa balbisiana cutivar kepok (ABB genome) inoculated with Ralstonia syzigii subsp. celebesensis, Ralstonia solanacearum and mock. The data provide essential knowledge for differentiating the banana response against pathogen, reveal pathogenesis-related genes and gene functions in the plant system, and research development to design blood disease-resistance of banana as one of the management strategies. Raw reads of RNA-seq data can be found in NCBI's Sequence Read Archive (SRA) database with the accession number of SRR10547839 (RSC), SRR10547840 (RS), and SRR10547841 (Mock).
Project description:On a worldwide scale, food demand is increasing as a consequence of global population growth. This makes companies push their food supply chains' limits with a consequent increase in generation of large amounts of untreated waste that are considered of no value to them. Biorefinery technologies offer a suitable alternative for obtaining high-value products by using unconventional raw materials, such as agro-industrial waste. Currently, most biorefineries aim to take advantage of specific residues (by either chemical, biotechnological, or physical treatments) provided by agro-industry in order to develop high-value products for either in-house use or for sale purposes. This article reviews the currently explored possibilities to apply biorefinery-known processes to banana agro-industrial waste in order to generate high-value products out of this residual biomass source. Firstly, the Central and Latin American context regarding biomass and banana residues is presented, followed by advantages of using banana residues as raw materials for the production of distinct biofuels, nanocellulose fibers, different bioplastics, and other high-value products Lastly, additional uses of banana biomass residues are presented, including energy generation and water treatment.