Genome-wide identification and expression profiling of serine proteases and homologs in the diamondback moth, Plutella xylostella (L.)

Abstract

Background: Serine proteases (SPs) are crucial proteolytic enzymes responsible for digestion and other processes including signal transduction and immune responses in insects. Serine protease homologs (SPHs) lack catalytic activity but are involved in innate immunity. This study presents a genome-wide investigation of SPs and SPHs in the diamondback moth, Plutella xylostella (L.), a globally-distributed destructive pest of cruciferous crops.

Results: A total of 120 putative SPs and 101 putative SPHs were identified in the P. xylostella genome by bioinformatics analysis. Based on the features of trypsin, 38 SPs were putatively designated as trypsin genes. The distribution, transcription orientation, exon-intron structure and sequence alignments suggested that the majority of trypsin genes evolved from tandem duplications. Among the 221 SP/SPH genes, ten SP and three SPH genes with one or more clip domains were predicted and designated as PxCLIPs. Phylogenetic analysis of CLIPs in P. xylostella, two other Lepidoptera species (Bombyx mori and Manduca sexta), and two more distantly related insects (Drosophila melanogaster and Apis mellifera) showed that seven of the 13 PxCLIPs were clustered with homologs of the Lepidoptera rather than other species. Expression profiling of the P. xylostella SP and SPH genes in different developmental stages and tissues showed diverse expression patterns, suggesting high functional diversity with roles in digestion and development.

Conclusions: This is the first genome-wide investigation on the SP and SPH genes in P. xylostella. The characterized features and profiled expression patterns of the P. xylostella SPs and SPHs suggest their involvement in digestion, development and immunity of this species. Our findings provide a foundation for further research on the functions of this gene family in P. xylostella, and a better understanding of its capacity to rapidly adapt to a wide range of environmental variables including host plants and insecticides.

Fig. 1

Scaffold localization and gene structure of P. xylostella trypsin genes. (a) The four scaffolds with ≥ four trypsin genes. Genes names and the distance of two adjacent genes (kilobases, kb) are showed on the right and left of the bar, respectively. Scaffold numbers are presented at the top of each bar. (b) Gene structure of the P. xylostella trypsins located on the four scaffolds was shown in Fig. 1a. Values (0, 1, and 2) above each of the black lines indicate the intron phase. The scale line at the bottom shows the length of each gene

Fig. 2

Phylogenetic relationship of trypsins in P. xylostella and other insect species. The phylogenetic tree was constructed using MEGA 6.06 with neighbor joining approach based on Poisson model and pairwise deletion of gaps. The percentage bootstrap scores higher than 50 % are indicated on the nodes. The first two letters in each of the gene names represent the acronym of scientific name for a given species (Cf: Choristoneura fumiferana; Sn: Sesamia nonagrioides; Sf: Spodoptera frugiperda; Ms: Mythimna separate; Aa: Aedes aegypti; Ag: Anopheles gambiae; Px: Plutella xylostella; Nl: Nilaparvata lugens; Cq: Culex quinquefasciatus; On: Ostrinia nubilalis; Dm: Drosophila melanogaster; Ha: Helicoverpa armigera). P. xylostella trypsins are marked with red dots

Fig. 3

Phylogenetic relationship of chymotrypsins in P. xylostella and other Lepidoptera species. The phylogenetic tree was constructed using MEGA 6.06 with neighbor joining approach based on Poisson model and pairwise deletion of gaps. The percentage bootstrap scores higher than 50 % are indicated on the nodes. The first two letters in each of the gene names represent the acronym of scientific name for a given species (Px: Plutella xylostella; On: Ostrinia nubilalis; Ha: Helicoverpa armigera; Bm: Bombyx mori). P. xylostella chymotrypsins are marked with red dots

Fig. 4

Phylogenetic relationship of CLIPs in P. xylostella and other four insect species. The phylogenetic tree was constructed using MEGA 6.06 with neighbor joining approach based on Poisson model and pairwise deletion of gaps. The percentage bootstrap scores higher than 50 % are indicated on the nodes. The first two letters in each of the gene names represent the acronym of scientific name for a given species (Dm: Drosophila melanogaster; Bm: Bombyx mori; Ms: Manduca sexta; Am: Apis mellifica). P. xylostella CLIPs are marked with red triangles

Fig. 5

Domain architecture (a) and phylogenetic analysis of Nudel (b) and gastrulation defective (Gd) (c) using MEGA 6.06 with neighbor joining approach based on Poisson model and pairwise deletion of gaps. The sequences used for phylogenetic analysis of the Nudel gene in P. xylostella and other seven insect species were obtained from GenBank (NCBI) with accession numbers: Px003732 (PxNudel, Plutella xylostella), XP_001944581 (ApNudel, Acyrthosiphon pisum), XP_006559739 (AmNudel, Apis mellifica), NP_523947 (DmNudel, Drosophila melanogaster), XP_013138700 (PpNudel, Papilio polytes), XP_013190169 (AtNudel, Amyelois transitella), XP_001843380 (CqNudel, Culex quinquefasciatus) and XP_008201274 (TcNudel, Tribolium castaneum). The sequences used for phylogenetic analysis of the Gd gene in P. xylostella and other seven insect species were obtained from GenBank (NCBI) with accession numbers: Px006975 (PxGd, Plutella xylostella), KJ512078 (NlGd, Nilaparvata lugens), XP_003690498 (AfGd, Apis florea), XP_006563318 (AmGd, Apis mellifica), XP_003704669 (MrGd, Megachile rotundata), XP_003427708 (NvGd, Nasonia vitripennis), XP_004929031 (BmGd, Bombyx mori) and NP_511134 (DmGd, Drosophila melanogaster). P. xylostella Nudel and Gd are marked with red dots

Fig. 6

Expression profiling of the P. xylostella SP and SPH genes across different developmental stages. The log₂ RPKM values are presented by bar colors where the darker red represents higher expression values, the darker green represents lower expression values, and the gray represents missing values. E, eggs; L1, 1st-instar larvae; L2, 2nd-instar larvae; L3, 3rd-instar larvae; L4, 4th-instar larvae; P, pupae; AM, adult males; AF, adult females. The RPKM values are given in the Additional file 10: Table S3