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Genome level analysis of Pteromalus puparum transcriptome: Preface

2019; Wiley; Volume: 103; Issue: 2 Linguagem: Inglês

10.1002/arch.21641

1520-6327

Yonggyun Kim,

Insect-Plant Interactions and Control

The healthy combination of advanced sequencing technology, powerful bioinformatics tools, and dedicated work has led to complete sequences and annotations of a rapidly expanding list of known insect genomes. This Special Issue of Archive of Insect Biochemistry and Physiology celebrates the first genome-level analysis of an endoparasitoid insect, Pteromalus puparum, recently completed by the group of Professor Gong-yin Ye. Using combined Illumina and PacBio sequencing, the assembled genome size is 338.1 Mb, with contig length N50 38.7 kb and scaffold length N50 1.2 Mb. This species is a particularly good choice for a genome project. Pteromalus is a species-rich genus, with 485 species globally, most of which 371 are known from Europe (Baur, 2015). P. puparum has high reproductive fitness, with numerous hosts including Papilionidae (e.g., Papilio polytes, P. polyxenens asterius, P. xuthus), Pieridae (e.g., Colias philodice, Eurema lisa, Pieris brassicae, P. protodice, Pieris rapae), Nymphalidae species (e.g., Agraulis vanillae, Limenitis archippus, Nymphalis antiopa, Polygonia satyrus, Vanessa atalanta, V. cardui, V. caryae), Geometridae (e.g., Lambdina fiscellaria), Coleophoridae (e.g., Coleophora fuscedinella), Psychidae (e.g., Thridopterys ephemeraeformis), Braconidae (e.g., Bracon gelechiae, Rogas stigmator), Ichneumonidae (e.g., Hyposoter fugitivus, Phobocampe clisiocampae, Polistiphaga fulva), Pteromalidae (e.g., Dibrachys cavus), Vespidae (e.g., Polistes fuscatus; Peck, 1963). It is a gregarious insect that deposits about 70 eggs per gram host (Takagi, 1986). Pupae of the butterfly P. rapae are major hosts, which P. puparum parasitizes on an almost global scale, in North America, Europe, Africa, and Asia including China. It contributes significant natural control of P. rapae pupae (Blunck, 1957; Hu, 1983; Muggeridge, 1943; Barlett et al., 1978). For example, the average percentage of parasitism caused by this wasp was 58.97% in the winter season, 62.35% in June with the high parasitism of more than 90% in Hangzhou, East China (Hu, 1983, 1984). With such a broad biogeography and host range, the P. puparum genome is a molecular resource of very high international value. Here, this special issue reports seven functional groups of transcriptomes based on a whole genome. Insects express a wide range of neuropeptides that signal and coordinate many physiological and behavioral processes. Adipokinetic hormone, for example, acts in mobilizing lipid reserves for energy metabolism. Xu et al. (ARCH 21625) identified 36 genes encoding neuropeptide precursor proteins and 33 genes encoding neuropeptide receptors. Compared with free-living insect species, P. puparum features a relatively small number of genes encoding neuropeptide precursors, as seen, also, in another endoparasitoid, Cotesia vestalis. They may be related to endoparasitoid life histories. Wang et al. (ARCH 21628) remind of the biological significance of insect cuticle, as an exoskeleton, restrictor of water loss, attachment sites for muscles and, again in host defense, a barrier to invaders. They identify 84 genes encoding cuticle proteins assorted into six gene families, the Rebers and Riddiford Conensus family (Baur, 2015), two genes in TWDL, six in CPF, eight in CPAP3, three in Apidermin and three encoding low-complexity proteins. The three Apidermin genes are known solely in Hymenoptera. Yang et al. (ARCH 21629) report on 202 genes that mediate immune signaling. These include recognition molecules, signal moieties and effector proteins that operate in the well-known signal pathways, Toll, IMD, JAK/STAT, and JNK. The core value of this report is drawing attention to the point that parasitoids are subject to immune challenges from host defense, microbes, and other invaders and they are prepared to mount vigorous defenses to these challenges. Biogenic amines such as octopamine, tyramine, dopamine, serotonin, and acetylcholine regulate various physiological processes in insects. Qi et al. (ARCH 21632) identified seven genes encoding their biosynthetic enzymes and 16 genes encoding G protein-coupled receptors associated with biogenic monoamines. Subsequent expression analyses proposed three octopamine and serotonin receptors that would play crucial roles in mediating secretion of venom materials from the salivary gland. MicroRNAs (miRNAs) are small RNAs that do not encode proteins but regulate expression of other protein-encoding messenger RNAs. Although there are reports of miRNAs in insects, this is a rich research area with a great deal of discovery to come. Xiao et al. (ARCH 21633) identified 254 mature miRNAs. Their expression varies among life stages and sexes. This paper opens a new door onto understanding miRNA actions in gene expression in an endoparasitoid and insects generally. Xu et al. (ARCH 21634) report on genes encoding glutathione S-transferases (GSTs), a family of enzymes that catabolize a very wide range of xenobiotic compounds, many of which are toxic, into harmless products. Their catalytic action involves a binding site for reduced glutathione and a second site for hydrophobic substrates in physical proximity. Xu et al. identified genes encoding 20 GSTs, 19 cytosolic, and 1 microsomal, slightly more than the 16 human GSTs. The P. puparum GSTs vary in numbers of exons and introns and in numbers and locations of binding sites. GST is present in prokaryotes and eukaryotes, and with a very long evolutionary history, we expect the discovery of new biological roles for GSTs in parasitoids and organisms generally. Several signal transduction pathways influence lifespan and some of the genes in these pathways are called "longevity-associated genes." Xiong et al. (ARCH 21635) report on 114 genes tentatively identified as longevity-associated. Many of these genes are associated with various signaling pathways, such as the insulin/insulin growth factor-1, phosphoinositide-3-kinase–protein kinase B, mitogen-activated protein kinase/extracellular-signal-regulated kinase, and mammalian target of rapamycin pathways, among others. This is a hypothesis-generating paper, opening a valuable corridor for understanding lifespan in parasitoids, which may have practical applications in producing large populations of adult parasitoids for deployment in biological control programs. Finally, I hope this special issue would be interesting and meaningful in understanding functional genes associated with various insect physiological processes in a whole-genome level.