On the species of origin diagnosing the source of symbiotic transcripts 英文参考文献.docVIP

/2001/2/9/research/0037.1 Research On the species of origin: diagnosing the source of symbiotic transcripts Peter T Hraber* and Jennifer W Weller? Addresses: *Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. ?Virginia Bioinformatics Institute, 1750 Kraft Drive, Suite 400, Blacksburg, VA 24061, USA. Correspondence: Peter T Hraber. E-mail: pth@ Published: 23 August 2001 Received: 11 June 2001 Revised: 11 July 2001 Accepted: 25 July 2001 GenomeBiology 2001, 2(9):research0037.1–0037.14 The electronic version of this article is the complete one and can be found online at /2001/2/9/research/0037 ? 2001 Hraber and Weller, licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Most organisms have developed ways to recognize and interact with other species. Symbiotic interactions range from pathogenic to mutualistic. Some molecular mechanisms of interspecific interaction are well understood, but many remain to be discovered. Expressed sequence tags (ESTs) from cultures of interacting symbionts can help identify transcripts that regulate symbiosis, but present a unique challenge for functional analysis. Given a sequence expressed in an interaction between two symbionts, the challenge is to determine from which organism the transcript originated. For high-throughput sequencing from interaction cultures, a reliable computational approach is needed. Previous investigations into GC nucleotide content and comparative similarity searching provide provisional solutions, but a comparative lexical analysis, which uses a likelihood-ratio test of hexamer counts, is more powerful. Results: Validation with genes whose origin and function are known yielded 94% accuracy. Microbial (non-plant) transcripts comprised 75% of a Phytophthora sojae-infected soybean (Glycine max cv Harasoy) library, contrasted with 15% or less in root tissue librar