INTRODUCTION
============

The diamondback moth, *Plutella xylostella* (Lepidoptera: Plutellidae), is one of the most devastating insect pests in more than 100 countries around the world; affecting cruciferous plants, especially *Brassica oleracea* crops including cabbage, brussels sprout, broccoli, cauliflower, and turnip [@B1]. Estimated global damage and control costs for this insect pest exceed 1billion USD annually. This troublesome pest has been especially problematic in many parts of China since the 1970s, where the only successful form of control has been the use of insecticides. However, *Plutella xylostella* has developed a robust resistance to many chemical and biological pesticides, including organophosphates, pyrethroids, agricultural antibiotics, and *Bacillus thuringiensis* Berliner (*Bt*) toxins, one of the most successful microbial insecticides used worldwide for suppressing pest populations, especially lepidopterans [@B2].

*Plutella xylostella* has been studied extensively as a model system for insect physiology and insecticide resistance, including cuticle function [@B3], chemosensory proteins [@B4], hormonal regulation [@B5], insect immunity and defense [@B6], [@B7], [@B8], insect-plant interaction [@B9], and the mechanistic study of insecticide resistance [@B10], [@B11], especially against *Bt* toxins [@B12]. The target site for *Bt* toxins is believed to be the midgut, a dynamic tissue which plays a vital role in metabolism, digestion, and detoxification. In Lepidoptera, previous studies have focused on the role of proteases, lipases and carbohydrases in digestion, and carboxylesterases, glutathione-s-transferases and cytochrome P450s in xenobiotic metabolism in the midgut [@B13], [@B14], [@B15]. With the advent of genomics and its "omics" tools, current research looked more closely at the physiological and toxicological changes at a global level instead of focusing on individual genes in the midgut. Meunier *et al* studied the transcriptional responses of spruce budworm, *Choristoneura fumiferana,* larval midgut when challenged with a Cry1Ab*Bt* toxin at a sublethal concentration [@B16]. Eum *et al* investigated the immune-inducible genes in *P. xylostella* using ESTs and cDNA microarray [@B7]. Etebari *et al* documented the host-parasitoid interactions in *P. xylostella* larvae using an Illumina-based transcriptome profiling technique [@B8]. Most recently, He *et al* preformed the most comprehensive transcriptome analysis covering several developmental stages and different susceptible levels of *P. xylostella*to chlorpyrifos and fipronil, respectively [@B17]. For non-model organisms, without a fully sequenced genome, a robust EST database is essential for any downstream "omics"-based analyses, especially for the RNAseq. The time- and tissue-specific nature of transcriptome sequencing offers an unparalleled opportunity to investigate the temporal and spatial changes of gene expressions related to a specific biological question. Although a whole body transcriptome is currently available [@B8], [@B17], tissue-specific gene expression profiles in *P. xylostella* are lacking.

In this study, we used the second generation Illumina sequencing platform to provide a comprehensive view of the genes expressed in the larval midgut of a *Bt* resistant *P. xylostella*. We generated over three billion bases of high-quality DNA sequences and investigated the potential roles of these predicted proteins involved in various physiological and toxicological processes in *P. xylostella*larval midgut. In our effort to analyze the midgut transcriptome of *P. xylostella*, we focused on genes potentially involved in insecticide resistance, digestion, immune and defensive response, and peritrophic membrane integrity. This transcriptome sequencing effort has dramatically increased the number of known genes for this insect model and provides an invaluable resource for the subsequent RNAseq analysis as well as for *P. xylostella* genome annotation.

RESULT AND DISCUSSION
=====================

Sequencing summary
------------------

To obtain an overview of the transcriptional profile of the midgut of the diamond back moth, *Plutella xylostella* (Lepidoptera: Plutellidae), a cDNA sample was prepared and sequenced using the Illumina sequencing platform. After cleaning and quality checks to remove the low quality reads, we obtained 39 million reads with an average length of 90bp from one plate of sequencing. To facilitate sequence assembly, these raw reads were assembly and resulted in 213,674 contigs with Trinity [@B18] (Table [1](#T1){ref-type="table"}). The average size of a contig was 189bp and further assembled into 63,312 unigenes with an average size of 416bp, including 3,333 unigenes (5.26%) which are over 1,000bp in length (Table [1](#T1){ref-type="table"}; Figure [1](#F1){ref-type="fig"}). The N50 of all contigs and unigenes are 262bp and 499bp, respectively. The size distribution of these contigs and unigenes are shown in Figure [1](#F1){ref-type="fig"}. The resultant parameters are comparable to a recent whole body transcriptomic sequencing efforts to inventory genes differentially expressed among developmental stages and between insecticide resistant and susceptible *P. xylostella* \[Table [1](#T1){ref-type="table"}\]. To examine the quality of newly assembled *P. xylostella* midgut transcriptome, we selected 5 unigenes randomly for the RT-PCR validation. The resultant PCR products were visualized on 1% agarose gel first and then cleaned for the direct sequencing. The identity of these PCR products (4/5) was confirmed by the conventional Sanger sequencing.

Functional annotation
---------------------

For annotation, the unigenes were first searched using BLASTx against the non-redundant (nr) NCBI protein database with a cut-off E-value of 10^-5^. Using this approach, 28,768 genes (45.4% of all unigenes sequences) returned above the cut-off BLAST hits ([Additional file 1](#SM1){ref-type="supplementary-material"}: Table S1). Without a fully sequenced *P. xylostella* genome, more than half (54.6%) of the 63,312 assembled sequences could not be matched to known genes. The E-value distribution of the top hits in the nr database showed that 26.5% of the mapped sequences exhibit strong homology (smaller than 1.0E-45), whereas 73.5% of the homolog sequences have an E-value ranged between 1.0E-5 to 1.0E-45 (Figure [2](#F2){ref-type="fig"}A). For species distribution, 17.6% of the unigenes sequences have top matches (first hit) trained with sequences from the red flour beetle (*Tribolium castaneum*), followed by the ants (14.4%), mosquitoes (14.3%), fruitflies (12.4%), silkworm (*Bombyx mori*) (11.0%), and other Lepidoptera species (6.87%) (Figure [2](#F2){ref-type="fig"}B). There are 335 unigene sequences (1.15%) with the highest homology to genes from *P. xylostella* and the majority of these hits match to cytochrome P450 and trypsin-like serine proteinase (data not shown).

Functional classification and pathway analysis
----------------------------------------------

GO assignments were used to classify the functions of the predicted *P. xylostella* midgut genes. Based on sequence homology, 11,092 unigene sequences can be categorized into 49 functional groups ([Additional file 1](#SM1){ref-type="supplementary-material"}: Table S3, Figure [3](#F3){ref-type="fig"}). In each of the three main categories (biological process, cellular component and molecular function) of the GO classification, "Cell", "Cellular process", "Cell part", "Binding" and "Metabolic process" are the dominant terms. In contrast, few genes fall into terms of "Cell killing" and "Translation regulator activity", "Synapse part" and "Virion" (Figure [3](#F3){ref-type="fig"}).

To further evaluate the completeness of our transcriptome library and the effectiveness of our annotation process, we searched the annotated sequences for genes involved in the Cluster of Orthologous Groups (COG, <http://www.ncbi.nlm.nih.gov/COG/>) classifications. In total, out of 28,768 nr hits, 15,557 unigene sequences (54.1%) have a COG classification (Figure [4](#F4){ref-type="fig"}). Among the 25 COG categories, "General function prediction only cluster" (2605, 16.7%) represents the largest group, followed by "Replication, recombination and repair" (1347, 8.66%), and "Translation, ribosomal structure and biogenesis" (1159, 7.45%). "Nuclear structure" (12, 0.077%), "Extracellular structures" (18, 0.12%), and "RNA processing and modification" (99, 0.64%) are the least represented categories (Figure [4](#F4){ref-type="fig"}).

To identify the biological pathways that are active in *P. xylostella* midgut, 28,768 annotated sequences were mapped to the reference canonical pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG) [@B19]. In total, 16,732 sequences were assigned to 226 KEGG pathways. The pathways with most representation by the unique sequences are Metabolic pathways (3226 members), Spliceosome (705 members), and Purine metabolism (628 members) ([Additional File 1](#SM1){ref-type="supplementary-material"}: Table S4). These annotations provide a valuable resource to study specific physiological processes, functions, and pathways involved in the *P. xylostella* midgut.

Putative SNPs and SSRs
----------------------

There were a total of 4,953 putative single nucleotide polymorphisms (SNPs) wherein 2,013 were transversions and 2940 were transitions, respectively (Table [2](#T2){ref-type="table"}, [Additional file 1](#SM1){ref-type="supplementary-material"}: Table S5). Additionally, 2,351 simple sequence repeats (SSRs or microsatellites) were identified, of which 60% were dinucleotide repeats, followed by 37.5% trinucleotide and 2.1% tetranucleotide repeats (Table [3](#T3){ref-type="table"}, [Additional file 1](#SM1){ref-type="supplementary-material"}: Table S6). Molecular markers, SNPs and SSRs, identified in this study lay a foundation for the better understanding of the adaptation and ecology of *P. xylostella* [@B20]. The identity of predicted molecular markers, however, needs to be validated in future research to exclude false positives and sequencing errors.

Putative transcription factors
------------------------------

Of the 63,312 unigene sequences, 31,978 unigenes sequences with an open reading frame longer than 150 bp were used for the transcription factor (TF) prediction. After the HMMER search with 75 TF families from the *Drosophila* Transcription Factor Database (<http://www.flytf.org/>), 1107 unigenes were predicted as putative TF ([Additional file 1](#SM1){ref-type="supplementary-material"}: Table S7). Among them, the pfam family for "Zinc finger, C2H2 type" represents the largest TF family (407, 36.8%), followed by "Ras family" (77, 6.96%), and "Zinc-finger associated domain (zf-AD)" (67, 6.05%). (Table [4](#T4){ref-type="table"}, [Additional file 1](#SM1){ref-type="supplementary-material"}: Table S7).

Genes putatively involved in insecticide resistance
---------------------------------------------------

*Plutella xylostella* has developed resistance to various synthetic and biological pesticides, and has been an important model system to study the molecular mechanisms underlying the development of insecticide resistance. Sequences encoding enzymes potentially involved in xenobiotic detoxification and the targets of the major classes of synthetic insecticides were extracted and compared with sequences from the NCBI protein database. Genes potentially associated with the *Bt* toxicity and resistance in the *P. xylostella* larval midgut are listed in Figure [5](#F5){ref-type="fig"}, including alkaline cadherin, phosphatase, aminopeptidase, chymotrypsin, proteinase/protease, trypsin, ABC transporter, and glycosphingolipid. Among them, chymotrypsin was identified from the *P. xylostella* for the first time. In total, we obtained 28 chymotrypsin and 53 ABC transporter related sequences. After removing redundant sequences, we identified 18 different chymotrypsin sequences ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S8) and 35 ABC transporter sequences ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S9). The number of genes of interest obtained in this larval midgut transcriptome is comparable to a whole body sequencing effort (Figure [5](#F5){ref-type="fig"}), reflecting the tissue (spatial)-specific nature of transcriptome sequencing approach. Recently, an ABCC2 gene in *Heliothis virescens* was genetically linked to the Cry1Ac resistance. A loss-of-function mutation in ABCC2 led to the loss of Cry1Ac binding to membrane vesicles, suggesting ABC transporters may play a key role in the mode of action of *Bt* toxins [@B21]. Moreover, Baxter *et al* (2011) cloned an ABCC2 gene in *P. xylostella*, and genetically mapped it onto a locus controlling the *Bt* Cry1Ac resistance [@B12].

ESTs potentially involved in the insecticide metabolic resistance are summarized in Table [5](#T5){ref-type="table"}, including conventional detoxification enzymes such as cytochrome P450 monooxygenase, carboxylesterase and glutathione S-transferase; and putative insecticide targets, including neuropeptide receptor, glutamate receptor and ryanodine receptor. Based on the closest BLAST hits in the NCBI nr database, transcripts encoding putative P450s were assigned to appropriate CYP clades and families (Table [6](#T6){ref-type="table"}). Specifically, among 156 P450 unigenes annotated in the NCBI nr database, 74 contained CYP family information and 41 GST unigenes annotated in the NCBI nr database, 23 contained GST class information. The remaining 74 P450 unigenes were subdivided into 4 clades and 13 families, including 3 families of CYP304, CYP305 and CYP306 in CYP2 clade, 6 families of CYP6, CYP321, CYP337, CYP347, CYP354 and CYP366 in CYP3 clade, 1 CYP4 family in CYP4 clade, and 3 families of CYP301, CYP314 and CYP333 in mitochondrial CYP clade (Table [6](#T6){ref-type="table"}). The majority of annotated P450s belonged to the CYP3 clade (41/74), and followed by CYP4 (13/74), mitochondrial (13/74), and CPY2 (7/74). At the family level, CYP6 (26) and CYP4 (13) are the most abundant P450 families. Four genes (CYP6B8, CYP6B9, CYP6B28 and CYP6B27) have been identified from *Helicoverpa zea*in the CYP6 family, which are associated with xenobiotics resistance [@B22], [@B23].

Meanwhile, the remaining 23 GST unigenes were subdivided into 5 classes, among which the *Omega*class was the main group (10/23) which is identified in some Lepidopteran species, for example, *Spodoptera litura* [@B24], *Bombyx mori* [@B25], but absent in *Trialeurodes vaporariorum*[@B26], *Acyrthosiphon pisum* and *Myzus persicae*[@B27]. Furthermore, glutamate receptors are synaptic receptors located primarily on the membranes of neuronal cells and mediate neuronal communication at synapses throughout vertebrate and invertebrate nervous systems [@B28]. Ryanodine receptors (RyRs) are the major cellular mediator of calcium-induced calcium release in animal cells. Diamide insecticides control insects by the activation of RyRs which leads to uncontrolled calcium release in muscle [@B29]. In this study, unigenens encoding the glutamate receptor (10) and ryanodine receptor (22), respectively, were identified. After consolidating the redundant sequences, we assembled 8 different glutamate receptor sequences ([Additional file 1](#SM1){ref-type="supplementary-material"}: Table S2) and 9 ryanodine receptor sequences ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S10).

Putative digestive enzymes
--------------------------

The lepidopteran midgut plays key roles in the nutrient digestion and allocation. Digestive enzymes identified from this sequencing effort include trehalase, carboxypeptidase, dipeptidyl-peptidase, α-amylase, glucosidase and lipase (Table [5](#T5){ref-type="table"}), chymotrypsin, proteinase/protease, aminopeptidase, and trypsin (Figure [5](#F5){ref-type="fig"}). Trehalase plays a pivotal role in various physiological processes, including flight metabolism [@B30], chitin synthesis [@B31], and cold tolerance [@B32] through the hydrolysis of trehalose, a principal hemolymph sugar in insects which is an indispensable substrate for energy production and macromolecular biosynthesis [@B33]. Trehalase was divided into the soluble (Tre-1) and the membrane-bound (Tre-2) trehalases [@B34]. In total, 11 trehalose related sequences were obtained. After consolidating the redundant sequences, we identified 8 different trehalase sequences containing Tre-1 and Tre-2 ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S11).

The most abundant digestive enzymes in this study are carboxypeptidase and aminopeptidase, a group of specialized exopeptidases that break down dietary proteins into amino acids and small peptides. Current studies of insect digestive exopeptidases have been focused primarily on aminopeptidases due to the fact that midgut aminopeptidases may serve as the receptors for *Bt* endotoxins [@B35]-[@B38]. In this study, a wealth of aminopeptidases and carboxypeptidases were uncovered, and these finding will undoubtedly facilitate the future research on *P. xylostella* midgut exopeptidases.

Candidate genes involved in the immune and defense response
-----------------------------------------------------------

Although the insect midgut has traditionally been viewed as a tissue primarily involved in digestion and detoxification, several studies have also placed increasing emphasis on the immune responsiveness of this tissue [@B39]-[@B41]. Some immune responses induced by the presence of microbes in food can be transmitted from insect parent to their offspring [@B41], [@B42]. Recent studies have identified a significant number of immune- and metabolic-related genes in the midgut. Transcriptomic analysis on parasitized versus non-parasitized *P. xylostella* larvae led to the identification of *Ds*IV, a gene expressed by ichnoviruses, a symbiotic polydnaviruses associated with ichneumonid parasitoids, *Diadegma semiclausum*[@B8]. *Ds*IV plays a major role in host immune suppression and developmental regulation. In our *P. xylostella* larval midgut EST database, the most abundant immune response genes are putative serine proteinase inhibitors or serpins. After consolidating the original 64 unigenes, we identified 21 different serpin sequences ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S12). Among them, 5 correspond to the existing *P. xylostella* serpins (3 serpin-1, 1 serpin-2, and 1 serpin-3) [@B43], and the remaining 16 unigenes are novel serpins ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S12).

Among the 6 different PGRPs identified in this study ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S13), two match the known *P. xylostella* PGRPs, and the other four are new genes (PGRP-LC, PGRP-SC2, PGRP-D and PGRP-B). Based on the InterProScan analysis, these new PGRPs all possess a conserved amidase-like domain (IPR002502), a typical active site for PGRPs. Further analysis shows that *P. xylostella* PGRP-B is very similar to PGRP-B from the Eri silkworm, *Samia cynthia ricini*[@B44], and PGRP-LB from the fruit fly,*Drosophila melanogaster* [@B45]. Both of these PGRPs are constitutively expressed in the larval midgut. PGRP-LC in *D. melanogaster*serves as a signal-transducing innate immune receptor [@B46], [@B47]. In *P. xylostella*, the functional characterization of PGRP-LC, -SC2, -D and -B homologues identified in this study could therefore be a logical first step to understand how peptidoglycan fragments are recognized by the lepidopteran immune system.

The primary structure of defensin-like-1 protein genes (Unigene51045_mk) from *P. xylostella* midgut was compared with other lepidopteran defensins in [Additional file 2](#SM2){ref-type="supplementary-material"}: Figure S1. The amino acid alignments show a highly conserved six cysteine residues in these defensin-like proteins ([Additional file 2](#SM2){ref-type="supplementary-material"}: Figure S1). As part of the innate immune defense against pathogens, a group of 5 ESTs putatively encoding lysozymes were indentified in the *P. xylostella* larval midgut ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S14). The deduced amino acid sequence alignments show the alpha-lactalbumin motif (lysozyme C signature) in the *P. xylostella* lysozyme-like protein 1 (LLP1, Unigene58181_mk) ([Additional file 2](#SM2){ref-type="supplementary-material"}: Figure S2). However, the *P. xylostella* LLP1 lacks the catalytic residues Glu and Asp (marked with \* in [Additional file 2](#SM2){ref-type="supplementary-material"}: figure S2), which are conserved in classical lysozymes and necessary for their enzymatic activity [@B48]*.* In tasar silkworm, *Antheraea mylitta*, the lack of this critical residue is thought to account for the loss of muramidase activity [@B48], and the similar enzymatic consequences would therefore be hypothesized for the *P. xylostella* LLP1 homologue.

Genes putatively involved in the peritrophic membrane biosynthesis, metabolization and remodeling
-------------------------------------------------------------------------------------------------

The midgut is involved in the biosynthesis, degradation, and remodeling of the peritrophic matrix (PM), a permeable protein shield protecting the midgut epithelium and a likely target site for *Bt* toxins [@B49]. Fourteen chitin synthase related sequences were obtained; in which 8 unigenes correspond to the chitin synthase 1(Table [5](#T5){ref-type="table"}). *P. xylostella*chitin synthase 1 were found to express in all developmental stages [@B50]. After consolidating the redundant sequences, 4 different chitin synthase sequences (Unigene23722_mk, Unigene60458_mk, Unigene4562_mk, and Unigene12371_mk) were identified ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S15). Sequence comparisons of predicted amino acid sequence of the longest *P. xylostella*chitin synthase (Unigene4562_mk) with other lepidopteran chitin synthase are shown in [Additional file 2](#SM2){ref-type="supplementary-material"}: Figure S3. In addition, 9 putative chitin deacetylase sequences containing chitin deacetylase 1, 2, 4, 5a and 5b were consolidated from the initial pool of 21 unigenes by removing the redundant sequences ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S16).

Housekeeping genes
------------------

Normalization of target gene expression levels is a critical step in the qRT-PCR analysis, a molecular biology tool used extensively for the downstream functional characterization of the annotated candidate genes [@B51]. The use of reference genes as internal controls is the most common method for normalizing the qRT-PCR data [@B52]. In this study, referring to a list of human reference genes [@B53], 28,768 annotated unigenes were subjected to the housekeeping genes search. A total of 1808 unigenes grouped into 119 clusters were annotated as the putative reference genes ([Additional file 2](#SM2){ref-type="supplementary-material"}: Table S17). Among them, the most well represented housekeeping genes in the *P. xylostella*larval midgut are myosin (142, 7.85%), follows by ATPase (113, 6.25%) and proteasome (89, 4.92%). (Table [7](#T7){ref-type="table"}, [Additional file 2](#SM2){ref-type="supplementary-material"}: Table S17). To standardize the qRT-PCR analysis in *P. xylostella,*a parallel study is currently underway to select the appropriate reference genes from these newly annotated housekeeping genes.

MATERIALS AND METHODS
=====================

*Plutella xylostella* colony maintenance
----------------------------------------

The PXR colony has been maintained since 2005 and subjected to the laboratory selection with Cry1Ac at the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences.. *Plutella xylostella* colonies were provisioned with cabbage seedlings (*Brassica oleracea* L., cv Jingfeng 1), and kept at 26°C with a 12:12 (L: D) photoperiod.

RNA isolation and cDNA library construction for transcriptome analysis
----------------------------------------------------------------------

Fresh midgut tissue was dissected from 3rd instar *P. xylostella*. Midgut total RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer\'s instructions. The quality and integrity of resultant total RNA was checked on 1% agarose gel first, and further examined with a 2100 Bioanalyzer (Agilent Technologies) using a minimum RIN (RNA Integrated Number) value of 8. Poly (A)-containing RNA was then separated from total RNA using the Dynabeads® mRNA purification kit (Invitrogen), and the quality was checked on a denaturing gel. The cDNA library for transcriptome sequencing was prepared using the ScriptSeq™ mRNA-Seq Library Preparation Kit (Illumina, San Diego, CA) following manufacturer\'s recommendations.

Sequence analysis
-----------------

The cDNA library was sequenced on the Illumina sequencing platform (GAII). The insert size of the library is approximately 200 bp and both ends of the cDNA were sequenced. Image deconvolution and quality value calculations were performed using the Illumina GA pipeline 1.3. The raw reads were cleaned by removing adaptor sequences, empty reads and low quality sequences (reads with unknown sequences \'N\'). The reads obtained were assembled using Trinity [@B18]. The result unigenes were used for the blast search and annotation against an NCBI nr database using an E-value cut-off of 10^-5^. Functional annotation by gene ontology terms (GO; <http://www.geneontology.org>) was analyzed by Blast2go software. The COG and KEGG pathway annotation were performed using Blastall software against Cluster of Orthologous Groups database and Kyoto Encyclopedia of Genes and Genomes database, respectively. The data sets are available at the NCBI Short Read Archive (SRA) with the accession number: SRX101299.

Identification of putative molecular markers
--------------------------------------------

SNPs were predicted using the Short Oligonucleotide Alignment Program 2 (SOAP2) software package \[SOAPsnp, 54\]). Briefly, all high quality reads were used for mapping with arbitrary criteria of at least 5 reads supporting the consensus or variant. The identification and localization of microsatellites were accomplished using a PERL5 script (*MIcroSAtellite* MISA) [@B55]. The script can identify both perfect and compound microsatellites, which are interrupted by certain number of bases.

Identification and classification of putative transcription factors
-------------------------------------------------------------------

ESTScan [@B56] was used to detect coding sequences in assembled EST sequences. Sequences that resulted in peptides longer than 50 amino acids were used to predict TFs. TF prediction was carried out according to He *et al* [@B57] with some modifications. The HMM profiles of 75 TF families were downloaded from the *Drosophila* Transcription Factor Database (<http://www.flytf.org/>) and PFAM [@B58]. An HMMER search with a threshold E-value of 0.01 was carried out and unique genes with significant hits to the HMM profiles were annotated as TFs.

SUPPLEMENTARY MATERIAL
======================

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Table S1-S7.

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Click here for additional data file.

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Figure S1-S3 and Table S8-S17.

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Click here for additional data file.

Authors are grateful to the two anonymous reviewers for their critical comments and suggestions. Special thanks go to Dr. John Obrycki (University of Kentucky) for his comments on an earlier draft. The current study was supported by the National Natural Youthful Science Foundation of China (Grant No. 30900948), the Special Fund for Agro-scientific Research in the Public Interest (201103021), the National Science and technology support task (2012BAD19B06), the National Basic Research and Development Program of China (2009CB119004), and the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P. R. China.

Author Contributions
====================

Conceived and designed the experiments: WX YYL XGZ YJZ. Performed the experiments: WX YYL. Analyzed the data: WX XGZ. Contributed reagents/materials/analysis tools: WX YYL XGZ YJZ. Wrote the paper: WX WF ZXY QJW SLW BYX XGZ YJZ.

![**Length distribution of assembled sequences in *P. xylostella* larval midgut transcriptome.**The average length of contig*(A) and unigene (B*) in *P. xylostella* larval midgut transcriptome were 84 and 416bp, respectively.](ijbsv08p1142g01){#F1}

![**E-value and species distribution of the top BLASTX hits**. The BLASTX search was carried out against the NCBI (National Center for Biotechnology Information) nr database. The search results were summarized based on the distribution of their E-value (A) and taxonomic status (B), respectively.](ijbsv08p1142g02){#F2}

![**Distribution of Gene Ontology (GO) terms in *P. xylostella* larval midgut transcriptome.**(A) Biological Process, (B) Cellular Component, (C) Molecular Function.](ijbsv08p1142g03){#F3}

![**Distribution of Clusters of Orthologous Groups (COG) in *P. xylostella* larval midgut transcriptome.**Among 28,768 nr hits, 8,583 sequences have a COG classification among the 25 categories.](ijbsv08p1142g04){#F4}

![**Genes putatively associated with *Bt* toxicity and resistance in *P. xylostella* larval midgut transcriptome.**Black bar represents the existing *P. xylostella* sequence available in the NCBI protein database (as of August 2011, red bar denotes the number of sequences obtained in a tissue-specific transcriptome (this study), and green bar includes the number of sequences acquired through a whole body transcriptome **[@B17]**.](ijbsv08p1142g05){#F5}

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Sequencing summary in *Plutella xylostella* larval midgut transcriptome

  Sequencing Summary                 Midgut specific transcriptome   Whole body transcriptome^a^
  ---------------------------------- ------------------------------- -----------------------------
  Total number of reads              39,764,230                      27,514,263-29,793,272
  Total base pairs (bp)              3,578,780,700                   4,127,139,450-4,468,990,800
  Average read length (bp)           90                              75^b^
  Total number of contig             213,674                         223,409-313,859
  Mean length of contigs (bp)        189                             153-161
  N50^d^ of contigs                  262                             152-168
  Total number of unigenes           63,312                          171,262^c^
  Mean length of unigenes            416                             436-468
  N50^d^ of unigenes                 499                             470-521
  Sequences with E-value \< 10^-5^   28,768 (45.4%)                  38,255 (22.3%)
  Reference                          this study                      [@B17]

^a^Whole body transcriptome included 6 libraries covering 4 developmental stages and 2 resistant 3rd instar larvae.

^b^Paired-end sequencing (75bp in each single-ended).

^c^171,262 non-redundant sequences from clustered results of all six libraries range from 54,869 to 73,194 unigenes.

^d^N50 size of contigs or unigenes was calculated by sorting all the sequences by their respective lengths, and then adding the length from longest to shortest until the summed length exceeded 50% of the total length of all sequences.

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Putative SNPs in *Plutella xylostella* larval midgut transcriptome

  SNP type       Number of Occurrence
  -------------- ----------------------
  Transition     2,940
  A-G            1,448
  C-T            1,492
  Transversion   2,013
  A-C            441
  A-T            564
  C-G            565
  G-T            443
  Total          4,953

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Microsatellite loci predicted in *Plutella xylostella* larval midgut transcriptome

  -------------------------------------------------------------------------------------------------------------------------
  No. of repeats   Di-\                 Tri-\                Tetra-\              Penta-\              Hexa-\
                   nucleotide repeats   nucleotide repeats   nucleotide repeats   nucleotide repeats   nucleotide repeats
  ---------------- -------------------- -------------------- -------------------- -------------------- --------------------
  5                1096                 624                  38                   2                    \-

  6                196                  186                  11                   \-                   \-

  7                51                   59                   \-                   \-                   \-

  8                29                   12                   \-                   \-                   \-

  9                16                   \-                   \-                   \-                   \-

  10               8                    \-                   \-                   \-                   \-

  11               14                   \-                   \-                   \-                   \-

  12               7                    \-                   \-                   \-                   \-

  15               \-                   1                    \-                   \-                   \-

  16               \-                   \-                   \-                   \-                   1

  Subtotal         1417                 882                  49                   2                    1
  -------------------------------------------------------------------------------------------------------------------------

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Top transcription factor (TF) families in *Plutella xylostella* larval midgut transcriptome^a^

  TF related pfam ID   Pfam domain description                 Number of occurrence in midgut
  -------------------- --------------------------------------- --------------------------------
  PF00096              Zinc finger, C2H2 type                  407
  PF00071              Ras family                              77
  PF07776              Zinc-finger associated domain (zf-AD)   67
  PF00651              BTB/POZ domain                          47
  PF00412              LIM domain                              30
  PF00046              Homeobox domain                         29
  PF00010              Helix-loop-helix DNA-binding domain     26
  PF00628              PHD-finger                              26
  PF00856              SET domain                              26
  PF05485              THAP domain                             24
  PF00505              HMG (high mobility group) box           23
  PF00439              Bromodomain                             21

^a^Drosophila transcription factor database was used as a reference for the TF domain family search in this study.

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Genes of interest in *Plutella xylostella* larval midgut transcriptome

  Genes                                                                     NCBI^a^   Midgut specific^b^   Whole body^c^
  ------------------------------------------------------------------------- --------- -------------------- ---------------
  ***Metabolic insecticide resistance and insecticide targets***                                           
  Cytochrome P450 monooxygenase                                             17        156                  235
  Carboxylesterase                                                          9         28                   40
  Glutathione S-transferase                                                 7         41                   40
  Acetylcholinesterase                                                      4         1                    5
  Nicotinic acetylcholine Receptor                                          25        1                    22
  GABA receptor                                                             6         2                    7
  Neuropeptide receptor                                                     1         43                   31
  Glutamate receptor                                                        0         10                   48
  G-protein coupled receptor                                                0         14                   8
  Ryanodine receptor                                                        0         22                   60
  Lipophorin receptor                                                       1         8                    6
  Sodium channel                                                            14        6                    13
  Chloride channel                                                          5         19                   21
  NADH dehydrogenase                                                        0         31                   44
  NADH oxidoreductase                                                       0         14                   27
  Catalase                                                                  0         20                   21
  Peroxidase                                                                0         21                   36
  Superoxide dismutase                                                      3         8                    11
  ***Nutrient digestion***                                                                                 
  Trehalase                                                                 0         11                   11
  Serine proteinase all types                                               5         45                   26
  Cysteine proteinase all types                                             0         9                    11
  Carboxypeptidase all types                                                0         71                   109
  Dipeptidyl-peptidase                                                      0         19                   20
  α-amylase                                                                 0         15                   10
  glucosidase                                                               0         62                   77
  Lipase                                                                    16        149                  153
  ***Innate immune defense***                                                                              
  Toll-like receptor (TLR)                                                  0         5                    4
  β-1,3-glucan                                                              0         13                   38
  β-1,3-glucanase                                                           1         8                    5
  Peptidoglycan recognition protein                                         2         10                   12
  Defensin                                                                  0         1                    0
  Lysozyme                                                                  0         7                    7
  Serine protease inhibitor (Serpin)                                        6         46                   78
  Transferrin                                                               1         14                   19
  ***Peritrophic membrane biosynthesis, metabolization and remodelling***                                  
  Chitin synthase                                                           2         14                   24
  Chitinase                                                                 3         38                   39
  Chitin deacetylase                                                        0         12                   9
  Peritrophin-like, Mucin-like                                              51        1                    46

^a^Number of *Plutella xylostella* sequences available at the NCBI protein database (as of August 2011).

^b^Number of sequences obtained in a tissue-specific transcriptome (this study, in shade).

^b^Number of sequences obtained in a whole body transcriptome **[@B17]**.

###### 

Different CYPs P450 clans, families, and GSTs classes in midgut transcriptome of *Plutella xylostella*

  Detoxification enzymes                    \#Occurrence   Family members with corresponding number
  ----------------------------------------- -------------- --------------------------------------------------------------------------------------------------------------------------------------
  **CYPs P450**                                            
  ***Cyp2 clade*(3 families)**                             
  CYP304                                    04             CYPCCCIVA1(1) , CYPCCCIVF2(3)
  CYP305                                    01             CYPCCCVB1(1)
  CYP306                                    02             CYPCCCVIA1(2)
  ***Cyp3 clade*(6 families)**                             
  CYP6                                      26             CYPVIAB13(5), CYPVIAB5(4), CYPVIAE27(1), CYPVIAE32(5), CYPVIAE9(1), CYPVIAN5(5), CYPVIBK1(1), CYPVIBQ4(1), CYPVIK1(3)
  CYP321                                    06             CYPCCCXXIA1(3), CYPCCCXXIB1(3)
  CYP337                                    02             CYPCCCXXXVIIA1(1), CYPCCCXXXVIIB1(1)
  CYP347                                    01             CYPCCCXLVIIA1(1)
  CYP354                                    04             CYPCCCLIVA5(4)
  CYP366                                    02             CYPCCCLXVIA1(2)
  ***Cyp4 clade*(1 family)**                               
  CYP4                                      13             CYPIV(1), CYPIVAB2(1), CYPIVCG1(1), CYPIVG11(1), CYPIVG4(1), CYPIVG47(2), CYPIVM1(2), CYPIVM2(1), CYPIVM5(1), CYPIVM7(1), CYPIVV2(1)
  ***Mitochondrial CYP clade*(3 family)**                  
  CYP301                                    02             CYPCCCIA1(1), CYPCCCIB1(1)
  CYP314                                    05             CYPCCCXIVA1(5)
  CYP333                                    06             CYPCCCXXXIIIA3(2), CYPCCCXXXIIIB10(1), CYPCCCXXXIIIB11(3)
  **GSTs classes**                                         
  Delta                                     2              Delta(1), Delta3(1)
  Epsilon                                   3              Epsilon2(1), Epsilon4(1), Epsilon6(1)
  Omega                                     10             Omega1(7),Omega2(1), Omega3(2)
  Theta                                     4              Theta(3), Theta1(1)
  Zeta                                      4              Zeta(2), Zeta1(2)

###### 

Top 20 housekeeping genes in *Plutella xylostella* larval midgut transcriptome

  Gene                                         Number of occurrence
  -------------------------------------------- ----------------------
  myosin                                       142
  ATPase                                       113
  proteasome                                   89
  splicing factor                              84
  longation factor                             70
  lectin                                       54
  dynein                                       50
  eukaryotic translation initiation factor 3   49
  tubulin                                      40
  protein kinase C                             38
  collagen                                     38
  chitinase                                    38
  clathrin                                     37
  glycoprotein                                 36
  ubiquitin specific protease (USP)            31
  NADH dehydrogenase (ubiquinone)              31
  ATP synthase                                 29
  coatomer protein complex                     27
  sorting nexin (SNX)                          26
  actin                                        24

[^1]: \* These authors contributed equally.

[^2]: Competing Interests: The authors have declared that no competing interest exists.
