SMART-RDA: A Galaxy Workflow for RNA-Seq Data Analysis

RNA-seq using the Next Generation Sequencing (NGS) approach is a common technology to analyze large-scale RNA transcript data for gene expression studies. However, an appropriate bioinformatics tool is needed to analyze a large amount of transcriptomes data from RNA-seq experiment. The aim of this study was to construct a system that can be easily applied to analyze RNA-seq data. RNA-seq analysis tool as SMART-RDA was constructed in this study. It is a computational workflow based on Galaxy framework to be used for analyzing RNA-seq raw data into gene expression information. This workflow was adapted from a well-known Tuxedo Protocol for RNA-seq analysis with some modifications. Expression value from each transcriptome was quantitatively stated as Fragments Per Kilobase of exon per Million fragments (FPKM). RNA-seq data of sterile and fertile oil palm (Pisifera) pollens derived from Sequence Read Archive (SRA) NCBI were used to test this workflow in local facility Galaxy server. The results showed that differentially gene expression in pollens might be responsible for sterile and fertile characteristics in palm oil Pisifera.Keywords: FPKM; Galaxy workflow; Gene expression; RNA sequencing

Biological Network Analysis of Genes Involve in Embryogenesis of Oil Palm using ClueGO

The application of DNA sequencing technologies has a major impact on molecular biology, especially in understanding genes interaction in a certain condition. Due to a large number of genes produced by this high-throughput technology, a proper analysis tool is needed for data interpretation. ClueGO is a bioinformatics tool, an easy to use Cytoscape plug-in that strongly improves biological function interpretation of genes. It analyzes a cluster or comparing two clusters and comprehensively visualizes their group functions. This tool is applied to identify biological networks of genes involved in embryogenesis of oil palm, the most critical phase in oil palm tissue culture process. Two ESTs sequencing data from the GenBank database under accession number EY396120-EY413718 and DW247764-DW248770 were used in this study. Fifty-two and one hundred eight groups of genes were identified using biological process in Gene Ontology setting from the database of EY396120-EY413718 and DW247764-DW248770, respectively. Thirty-one groups of genes were consistently occurred in both ESTs. According to the literature, these genes play an important role in cell formations and developments, stresses and stimulus responses, photosynthesis and metabolic processes that indicate the involvement of these groups of genes in oil palm embryogenesis processes. ClueGO is the appropriate tool to analyze a large data set of genes in a specific condition, such as embryogenesis of oil palm. Keywords: callus embryogenesis; Cytoscape plug-in; DNA sequencing; expressed sequence tag; KEGG pathway

Book ReviewHandbook of the Birds of the World, Volume 14: Bush-Shrikes to Old World SparrowsBy Josep del Hoyo, Andrew Elliott and David A Christie (2009)

Lynx Edicions, Montseny 8, E-08193 Bellaterra, Barcelona, Spain896 pages, 51 colour plates, hardcoverISBN-13: 978-84-96553-50-7. Price €212OSTRICH 2010, 81(3): 277–27

Transcriptome Profiling of Elaeis guineensis Jacq. Under Heat Stress Condition

Global warming is predicted to have a generally negative effect on agriculture activity. High temperatures stress could affect plant growth negatively. Developing plants with improved thermal tolerance using molecular genetic approaches could mitigate these heat stress effects. Elite palms with better adaptation to heat can be selected from germplasm using molecular markers. Transcriptome profiling by RNA sequencing is a way to find molecular markers of a particular trait. The objective of the study was to obtain differential expressed genes (DEGs) related to the heat stress effect. RNA sequencing results were displayed using heat maps which were useful for visualizing the expression of genes across the high-temperature treatment and control samples. In total, where 1,087 genes were identified involved in oil palm heat stress. Sixty-four (64) of them were differentially expressed, consisted of seventeen (17) up-regulated and forty-seven (47) down-regulated. The uni-gene was summarized in Gene Ontology (GO) categories, namely: biological process, molecular function, and cellular component, subsequently divided into 53 sub-categories. The single organism process, biosynthetic process, response to stimulus, oxidation-reduction process, and response stress were the five primary sub-categories. Sixty-four genes related to heat stress were found, and eight (12.5%) of them were determined as heat shock protein (HSP) family. The highest transcription level was the uncharacterized gene, a member of the heat response sub-category, and the others up-regulated gene consisted of HSP family gene, Bcl-2-associated athanogene (BAG) family and HIPP gene, slr0575 gene, CML14 gene, and PARP gene

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

Abstract The hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina and long-read Pacific Biosciences (PacBio) sequencing platforms combined with chromatin conformation capture data from the Chicago and Hi-C platforms. The genome was 55.87 Mb in length and assembled to a high contiguity (N50: 304.34 kb) of 12 chromosomes built from 112 scaffolds, with a total of only 4.34 Mb (~ 7.77%) remaining unplaced. The final assemblies were evaluated for completeness of the genome by using Benchmarking Universal Single Copy Orthologs (BUSCO) v4.1.4, and based on 4464 total BUSCO polyporales group searches, the assemblies yielded 4264 (95.52%) of the conserved orthologs as complete and only a few fragmented BUSCO of 42 (0.94%) as well as a missing BUSCO of 158 (3.53%). Genome annotation predicted a total of 21,074 coding genes, with a GC content ratio of 59.2%. The genome features were analyzed with different databases, which revealed 2471 Gene Ontology/GO (11.72%), 5418 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthologous/KO (25.71%), 13,913 Cluster of Orthologous Groups of proteins/COG (66.02%), 60 ABC transporter (0.28%), 1049 Carbohydrate-Active Enzymes/CAZy (4.98%), 4005 pathogen–host interactions/PHI (19%), and 515 fungal transcription factor/FTFD (2.44%) genes. The results obtained in this study provide deep insight for further studies in the future