Project description:Purpose: The goal of this study is to provided a comprehensive genomic information for functional genomic studies in Q. mongolica. Methods:The Quercus mongolica leaves were generated by deep sequencing, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The transcriptome were de novo assembly. Results:A total of 52934562 raw reads were obtained from Illumina sequencing platform. After filtering out the low quality reads, we obtained 52076914 clean reads, which assembled into 39130 transcripts with a mean length of 742 bp and GC content of 42.12%, and 24196 unigenes with a mean length of 732 bp and GC content of 42.34%, based on Trinity assembly platform. Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. mongolica to obtain the transcriptome. De novo assembly was then applied followed by gene annotation and functional classification. The SSRs and SNPs were also obtained using assembled transcripts as reference sequences. The results of this study lay the foundation for further research on genetic diversity of Quercus.
Project description:We have sequenced a wild Prunus mume and constructed a reference sequence for this genome. In order to improve quality of gene models, RNA samples of five tissues (bud, leaf, root, stem, fruit) were extracted from the Prunus mume. To investigate tissue specific expression using the reference genome assembly and annotated genes, we extracted RNA samples of different tissues and conducted transcriptome sequencing and DEG analysis. Five RNA pools were created corresponding to different tissues of the Prunus mume.
