Genome and Evolutionary Analysis of Nosema ceranae: A Microsporidian Parasite of Honey Bees

Abstract

Microsporidia comprise a phylum of single cell, intracellular parasites and represent the earliest diverging branch in the fungal kingdom. The microsporidian parasite Nosema ceranae primarily infects honey bee gut epithelial cells, leading to impaired memory, suppressed host immune responses and colony collapse under certain circumstances. As the genome of N. ceranae is challenging to assembly due to very high genetic diversity and repetitive region, the genome was re-sequenced using long reads. We present a robust 8.8 Mbp genome assembly of 2,280 protein coding genes, including a high number of genes involved in transporting nutrients and energy, as well as drug resistance when compared with sister species Nosema apis. We also describe the loss of the critical protein Dicer in approximately half of the microsporidian species, giving new insights into the availability of RNA interference pathway in this group. Our results provided new insights into the pathogenesis of N. ceranae and a blueprint for treatment strategies that target this parasite without harming honey bees. The unique infectious apparatus polar filament and transportation pathway members can help to identify treatments to control this parasite.

Molecular Detection and Differentiation of Arthropod, Fungal, Protozoan, Bacterial and Viral Pathogens of Honeybees

“…Contradictions observed have resulted in scrutinizing the specificity, sensitivity, and reliability of available PCR assays and in the design of further improved ones [ 14 , 168 ]. The sequencing of N. ceranae and N. apis genomes has allowed us to identify several additional molecular targets that have been applied in molecular diagnostics ( Table 2 ) [ 174 , 175 , 176 ]. As an example, an N. ceranae / N. apis duplex PCR based on species-specific differences in the highly conserved rpb1 (DNA-dependent RNA polymerase II) gene resulted in higher reliability of results than simple PCR protocols based on the 16S rRNA gene [ 14 ].…”

Spillover and genome selection of the gut parasite Nosema ceranae between honey bee species

“…For genetic diversity analysis, a DNA library for F0 spores, three DNA libraries for F1_native spores (F1_native_1, F1_native_2 and F1_native_3) and three DNA libraries for F1_novel spores (F1_novel_1, F1_novel_2 and F1_novel_3) were sequenced. DNA sequencing reads were aligned to the N. ceranae genome (Ncer 3.0, GCA_004919615.1) using BWA with default parameters ( Li and Durbin, 2009 ; Huang et al., 2021 ). The SNVs were identified and annotated using the Picard-GATK-SNPEFF pipeline ( Van der Auwera et al., 2013 ).…”

Transcriptome of Nosema ceranae and Upregulated Microsporidia Genes during Its Infection of Western Honey Bee (Apis mellifera)

“…Previous studies have examined the gene expression profile and corresponding differentially expressed genes of N. ceranae -infected A. mellifera [ 28 , 29 , 30 ]. However, few studies have emphasized either the comprehensive gene expression of N. ceranae during its infection of A. mellifera or the common DEGs, which are important to N. ceranae for completing its life cycle [ 31 ]. Moreover, the genome of N. ceranae has been studied and reported for a better understanding of the architecture, regulation, and evolution of this pathogen [ 31 , 32 ].…”

“…However, few studies have emphasized either the comprehensive gene expression of N. ceranae during its infection of A. mellifera or the common DEGs, which are important to N. ceranae for completing its life cycle [ 31 ]. Moreover, the genome of N. ceranae has been studied and reported for a better understanding of the architecture, regulation, and evolution of this pathogen [ 31 , 32 ]. From our previous study, the identification of N. ceranae -specific genes during its infection of A. mellifera by suppressive subtractive hybridization (SSH) has been performed [ 33 ], but comprehensive data on the gene expression profile during the infection process are still unavailable.…”