WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants

Database, 2018, 1–9 doi: 10.1093/database/bay081 Database tool Database tool Longfei Chen1,# , Kun Lang1,2,# , Shoudong Bi2,# , Jiapeng Luo1 , Feiling Liu1 , Xinhai Ye1 , Jiadan Xu1 , Kang He1 , Fei Li1,*, Gongyin Ye1,* and Xuexin Chen1 1 Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China and 2 Anhui Agricultural University, 130 Changjiangxilu, Hefei, Anhui, 230036, China ∗ Corresponding author: Tel/Fax: +86-571-88982679; Email: Correspondence may also be addressed to Dr Gongyin Ye. Tel/Fax: +86-571-8898269; Email: # These authors contributed equally. Citation details: Chen,L., Lang,K., Bi,S. et al. WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants. Database (2018) Vol. 2018: article ID bay081; doi:10.1093/database/bay081 Received 24 March 2018; Revised 27 June 2018; Accepted 10 July 2018 Abstract Insect pests reduce yield and cause economic losses, which are major problems in agriculture. Parasitic wasps are the natural enemies of many agricultural pests and thus have been widely used as biological control agents. Plants, phytophagous insects and parasitic wasps form a tritrophic food chain. Understanding the interactions in this tritrophic system should be helpful for developing parasitic wasps for pest control and deciphering the mechanisms of parasitism. However, the genomic resources for this tritrophic system are not well organized. Here, we describe the WaspBase, a new database that contains 573 transcriptomes of 35 parasitic wasps and the genomes of 12 parasitic wasps, 5 insect hosts and 8 plants. In addition, we identified long non-coding RNA, untranslated regions and 25 widely studied gene families from the genome and transcriptome data of these species. WaspBase provides conventional web services such as Basic Local Alignment Search Tool, search and download, together with several widely used tools such as profile hidden Markov model, Multiple Alignment using Fast Fourier Transform, automated alignment trimming and JBrowse. We also present a collection of active researchers in the field of parasitic wasps, which should be useful for constructing scientific networks in this field. Database URL: http://www.insect-genome.com/waspbase/ © The Author(s) 2018. Published by Oxford University Press. Page 1 of 9 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. (page number not for citation purposes) WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants Page 2 of 9 Database, Vol. 2018, Article ID bay081 Introduction Data resources Genomes We collected the genome data of 12 parasitic wasps from the NCBI including Ceratosolen solmsi, Copidosoma floridanum, Cotesia vestalis, Diachasma alloeum, Fopius arisanus, Microplitis demolitor, Macrocentrus cingulum, Nasonia giraulti, Niphoparmena longicornis, Nasonia vitripennis, Orussus abietinus and Trichogramma pretiosum (Figure 1) (8, 9, 11). The gene annotation files were Figure 1. The design of WaspBase. The diagram shows the data and software used in WaspBase. obtained for nine parasitic wasps including C. solmsi (8), C. floridanum (10), D. alloeum, F. arisanus (4), M. demolitor (11), M. cingulum, N. vitripennis (9), O. abietinus and T. pretiosum. We then focused on these nine parasitic wasps with gene annotation information. There are nine insect hosts for these nine parasitic wasps, of which five have genome data and five have annotated genomes (12, 13). These five insect pests damage eight crops all of which have genome data, but six have annotation information (Figure 2). So, we collected a final genome data of nine parasitic wasps, five insect hosts and six plants (Table 1). The references reporting the interactions between parasitic wasps, insect hosts and plants were given in supplementary table S1. OGS The General Feature Format version 3 (Gff3) files containing annotation information were downloaded with the genome data, and the official gene sets (OGSs) were extracted from the genome based on the annotation in the Gff3 file. Then, the nucleotide sequences and protein sequences of annotated genes were produced (Table 2). Transcriptomes The raw data of 34 samples of parasitic wasps were downloaded from the NCBI SRA (Sequence Read Archive) database (https://www.ncbi.nlm.nih.gov/sra). We assembled 22 transcriptomes using Trinity and TopHat-Cufflinks with default parameters (26, 27). Together with 21 other Insects are the most widely distributed animal species on earth. Most insects are herbivores that cause huge yield losses when feeding on crops. Insects such as houseflies and mosquitos are vectors of pathogens that cause disease in humans and domesticated animals (1). To combat these insect pests, many methods have been developed, and some of which are used in agriculture. Insecticides are one of the main methods of pest control in agriculture. Unfortunately, overuse of insecticides causes serious environment pollution and food safety problems (2). Therefore, alternative, environment-friendly pest control methods should be developed. Biological control is an environment-friendly pest control method. Parasitic wasps are well-known biological control agents (3, 4) as they are effective natural enemies of many economically important insect pests. Parasitic wasps are a group of hymenopteran insects that lay eggs in or on the bodies of hosts (5). The wasp larvae feed on the host until pupation and eventually kill the host (6). However, pest control using parasitic wasps has some apparent disadvantages such as wasp development lagging behind pest outbreaks and low-control efficiencies. Understanding the antagonistic interactions between parasitic wasps and their hosts is an important task to improve control efficiencies (7). At present, the genomes of 34 parasitic wasps have been deposited in public databases such as National Center for Biotechnology Information (NCBI). In addition, the genomes of six hosts of these wasps and eight plants that are damaged by these insect hosts are available. Among these species, five parasitic wasps (4,8–11), six insect hosts (12–18) and six plants (19–24) were publicly reported. Though these data can be retrieved from NCBI, they are not well organized and thus have not been fully explored. Here, we collected the genome and transcriptome data of 34 parasitic wasps, 9 insect hosts and 8 plants from NCBI, i5k workspace@NAL (25) and InsectBase (7). Then, we constructed a database, which we named WaspBase, to serve as an integrated genomic resource for a tritrophic system of wasps, hosts and plants. Page 3 of 9 Database, Vol. 2018, Article ID bay081 available t (...truncated)