title: Untangling the transcriptome from fungus-infected plant tissues.
abstract: The development of sequencing technology allows low-cost generation of sequence data. The huge amount of raw sequence data now available has introduced many challenges associated with analysis of these large-scale data banks. For example, it is very important to distinguish materials of plant and fungal origin in fungus-infected plant tissue. The origin of transcripts that were sequenced from Library 895-M6 (poplar tissue infected by Marssonina brunnea) on Illumina/Solexa GA IIx was determined by combining three methods: (1) based on the taxonomic information of homologous sequences; (2) based on the reference genome sequence; (3) based on the transcriptome sequence of the host and its pathogen obtained from Library 895 (poplar) and Library M6 (M. brunnea) as well as Library 895-M6 (mixture of poplar and M. brunnea). We idenified accurately the origin of 80,978 (99.5%) contigs in the mixed poplar and M. brunnea sample (Library 895-M6) by integrating the results from the three methods. The results of this study demonstrate that a combination of these three approaches described here is an effective strategy for determining the origin of sequences in a mixed pool, and provides a basis for further transcriptome analysis of the mixed sample.
authors: Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing 210037, China.
authors: Sheng
authors: S
authors: Zhu
authors: Yong-Mei
authors: YM
authors: Dai
authors: Xin-Ye
authors: XY
authors: Zhang
authors: Jian-Ren
authors: JR
authors: Ye
authors: Ming-Xiu
authors: MX
authors: Wang
authors: Min-Ren
authors: MR
authors: Huang
mesh_terms: D001203:Ascomycota / Q000235:genetics / Q000472:pathogenicity*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D054884:Host-Pathogen Interactions; D010935:Plant Diseases / Q000382:microbiology*; D018515:Plant Leaves / Q000235:genetics* / Q000382:microbiology; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D010940:Plant Proteins