Chlorella minutissima is considered as one promising feedstock for biofuels in the future.Here,the transcriptome from oil-rich strain UTEX2341 of C.minutissima was generated based on Illumina paired-end sequencing.Through de-novo assembly,14,905 total isogenes was obtained and compacted into 6,216 unigenes.80%of unigenes were assigned with GO terms and further subdivided into 55 sub-categories.KEGG analysis showed that 37.2%of unigenes could be accessed and mapped into 278 pathways.Interestingly,genes encoding key enzymes involved in biosynthesis,elongation,and metabolism of fatty acids were identified,including malonyl-CoA-ACP transacylase,3-ketoacyl-ACP synthase,3-ketoacyl-ACP reductase,and others.Moreover,the genes involved in triacylglycerol (TAG) biosynthesis and metabolism also were found.Therefore,the transcriptome analysis of C.minutissima UTEX2341 not only supplies a comprehensive insight into the molecular pathway involved in biosynthesis of biofuels precursors,but also provides substantial valuable genomic resources to accelerate further development and utilization of biofuels.