Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava

Meta-Analysis of Immune Induced Gene Expression Changes in Diverse Drosophila melanogaster Innate Immune Responses

Simple Summary

Organisms can be infected by a wide range of pathogens, including bacteria, viruses, and parasites. Following infection, the host mounts an immune response to attempt to eliminate the pathogen. These responses are often specific to the type of pathogen and mediated by the expression of specialized genes. We have characterized the expression changes induced in host Drosophila fruit flies following infection by multiple types of pathogens, and identified a small number of genes that show expression changes in each infection. This includes genes that are known to be involved in pathogen resistance, and others that have not been previously studied as immune response genes. These findings provide new insight into transcriptional changes that accompany Drosophila immunity. They may suggest possible roles for the differentially expressed genes in innate immune responses to diverse classes of pathogens, and serve to identify candidate genes for further empirical study of these processes.

Abstract

Organisms are commonly infected by a diverse array of pathogens and mount functionally distinct responses to each of these varied immune challenges. Host immune responses are characterized by the induction of gene expression, however, the extent to which expression changes are shared among responses to distinct pathogens is largely unknown. To examine this, we performed meta-analysis of gene expression data collected from Drosophila melanogaster following infection with a wide array of pathogens. We identified 62 genes that are significantly induced by infection. While many of these infection-induced genes encode known immune response factors, we also identified 21 genes that have not been previously associated with host immunity. Examination of the upstream flanking sequences of the infection-induced genes lead to the identification of two conserved enhancer sites. These sites correspond to conserved binding sites for GATA and nuclear factor κB (NFκB) family transcription factors and are associated with higher levels of transcript induction. We further identified 31 genes with predicted functions in metabolism and organismal development that are significantly downregulated following infection by diverse pathogens. Our study identifies conserved gene expression changes in Drosophila melanogaster following infection with varied pathogens, and transcription factor families that may regulate this immune induction.

Genome assemblies of three closely related leaf beetle species (Galerucella spp.)

Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here, we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla, and G. tenella. The three assemblies have a genome size ranging from 460 to 588 Mbp, with N50 from 31,588 to 79,674 kbp, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.

Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand

Among the fish of the genus Oryzias, two species are frequently used as model animals in biological research. In Thailand, Oryzias mekongensis is usually found in natural freshwater near the Mekong Basin in the northeast region, while O. songkhramensis inhabits the Songkhram Basin. For differential morphological identification, the coloured bands on the dorsal and ventral margins of the caudal fin are used to distinguish O. mekongensis from O. songkhramensis. However, these characteristics are insufficient to justify species differentiation, and little molecular evidence is available to supplement them. This study aimed to investigate the molecular population and transcriptome profiles of adult O. mekongensis and O. songkhramensis. In the molecular tree based on cytochrome b sequences, O. mekongensis exhibited four clades that were clearly distinguished from O. songkhramensis. Clade 1 of the O. mekongensis population was close to the Mekong River and lived in the eastern portion of the upper northeast region. Clade 2 was far from the Mekong River and inhabited the middle region of the Songkhram River. Clade 3 was positioned to the west of the Songkhram River, and clade 4 was to the south of the Songkhram River Basin. After RNA sequencing using an Illumina HiSeq 2500 platform, the gene category annotations hardly differentiated the species and were discussed in the text. Based on the present findings, population dispersal of these Oryzias species might be associated with geographic variations of the upper northeast region. Molecular genetics and transcriptome profiling might advance our understanding of the evolution of teleost fish.