title: Transcriptome sequencing and annotation of the predatory mite Metaseiulus occidentalis (Acari: Phytoseiidae): a cautionary tale about possible contamination by prey sequences.
abstract: Next-generation sequencing was applied to the transcriptome of the phytoseiid Metaseiulus occidentalis to characterize gene expression in all life stages reared under different conditions to optimize the recovery of as many genes as possible. One production and one titration run produced a total of 862,069 reads (average size: 314.87 bp), which generated 255.6 Mbp of sequences on the GS-FLX Titanium sequencing platform. After removal of putative prey sequences 850,543 reads were used in NewBler and PTA assemblies to produce 74,172 non-redundant sequences, including 30,691 contigs and 43,481 singlets with 11,994 contigs consisting of more than 500 bp and 37,278 sequences >300 bp, constituting 48.7 % of all sequences. There were 25,888 hits with the NCBI non-redundant database and 15,376 unique transcripts. There were 26,225 hits with the Ixodes scapularis genome and 6,634 unique transcripts. There were 22,225 hits with the RefSeq of Homo sapiens with 6,465 unique transcripts, and 23,656 hits with the RefSeq of Drosophila melanogaster with 9,216 unique transcripts. Selected ESTs corresponding to genes of interest were analyzed including those related to transposable elements, GPCRs, Sox transcription factors, diapause and foraging behavior, and pesticide resistances. Novel and important genes appear to have been discovered that provide insight into the evolution, biology, and physiology of this important predator of pest mites in agriculture and will be useful in analyzing complete genome sequences of this natural enemy.
authors.affiliation: Department of Entomology and Nematology, The University of Florida, PO Box 110620, Gainesville, FL 32611-0620, USA. mahoy@ifas.ufl.edu
authors.forename: Marjorie A
authors.initials: MA
authors.lastname: Hoy
authors.forename: Fahong
authors.initials: F
authors.lastname: Yu
authors.forename: Jason M
authors.initials: JM
authors.lastname: Meyer
authors.forename: Oscar A
authors.initials: OA
authors.lastname: Tarazona
authors.forename: A
authors.initials: A
authors.lastname: Jeyaprakash
authors.forename: Ke
authors.initials: K
authors.lastname: Wu
mesh_terms: D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D018884:Ixodes / Q000235:genetics; D007814:Larva / Q000378:metabolism; D008297:Male; D008925:Mites / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009758:Nymph / Q000378:metabolism; D010063:Ovum / Q000378:metabolism; D017422:Sequence Analysis, DNA; D059467:Transcriptome