Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers

Abstract

Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed de novo assembly of the V. mandarinia transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. After assembly, a total of 66,837 unigenes were clustered, 40,887, 44,455, and 22,390 of which showed homologous matches against the PANM, Unigene, and KOG databases, respectively. A total of 15,675 unigenes were assigned to Gene Ontology terms, and 5,132 unigenes were mapped to 115 KEGG pathways. The zinc finger domain (C2H2-like), serine/threonine/dual specificity protein kinase domain, and RNA recognition motif domain were among the top InterProScan domains predicted for V. mandarinia sequences. Among the unigenes, we identified 534,922 cDNA simple sequence repeats as potential markers. This is the first transcriptomic analysis of the wasp V. mandarinia using Illumina HiSeq 4000. The obtained datasets should promote the search for new genes to understand the physiological attributes of this wasp.

Figure 1

Sequence annotation of unigenes obtained from V. mandarinia transcriptome assembly and clustering. A three-way Venn diagram plot shows the unique and overlapped transcripts from unigene annotation hits (BLASTX; E-value ≤ 1E − 5) against PANM-DB, Unigene, and KOG databases, respectively.

Figure 2

Summary of homology search of assembled unigenes of V. mandarinia against PANM-DB. (a) Score distribution of BLASTX hits for each unigene with a cutoff E-value of 1E − 5. (b) E-value distribution of BLASTX hits for each unigene with a cutoff E-value of 1E − 5. (c) Identity distribution of BLASTX hits for each unigene. (d) Similarity distribution of BLASTX hits for each unigene. (e) Distribution of hit and nonhit sequences as compared with the length of unigenes.

Figure 3

Top-hit species distribution for V. mandarinia unigenes against PANM-DB. The top-hit species belonging to class Insecta and order Hymenoptera are shaded black. The top-hit insect species not belonging to order Hymenoptera are shown by green bars. The top-hit species not belonging to class Insecta are shown by blue bars.

Figure 4

Clusters of Orthologous Groups (KOG DB) based functional analysis of V. mandarinia unigenes. The unigenes on the basis of KOG DB analysis are classified to metabolism, cellular processes and signaling, information storage and processing, and poorly characterized gene categories.

Figure 5

The GO term classification for V. mandarinia unigenes. (a) The three-way Venn diagram analysis of unigenes classified into biological process, cellular component, and molecular function categories. (b) The number of unigenes assigned to the number of GO term annotations.

Figure 6

Gene Ontology classifications of assembled unigenes from V. mandarinia. (a) Biological processes, (b) molecular function, and (c) cellular components. The number of unigenes ascribed to each subcategory for each classification has been indicated.

Figure 7

Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway assignment for assembled unigenes from V. mandarinia. The unigenes have been categorized to metabolism, genetic information processing, environmental information processing, and organismal systems pathways.

Figure 8

The number of simple sequence repeats (SSRs) discovered in the unigenes of V. mandarinia classified based on motif sequence types.