The Genome of Nosema sp. Isolate YNPr: A Comparative Analysis of Genome Evolution within the Nosema/Vairimorpha Clade

PLoS One. 2016 Sep 6;11(9):e0162336. doi: 10.1371/journal.pone.0162336. eCollection 2016.


The microsporidian parasite designated here as Nosema sp. Isolate YNPr was isolated from the cabbage butterfly Pieris rapae collected in Honghe Prefecture, Yunnan Province, China. The genome was sequenced by Illumina sequencing and compared to those of two related members of the Nosema/Vairimorpha clade, Nosema ceranae and Nosema apis. Based upon assembly statistics, the Nosema sp. YNPr genome is 3.36 x 106bp with a G+C content of 23.18% and 2,075 protein coding sequences. An "ACCCTT" motif is present approximately 50-bp upstream of the start codon, as reported from other members of the clade and from Encephalitozoon cuniculi, a sister taxon. Comparative small subunit ribosomal DNA (SSU rDNA) analysis as well as genome-wide phylogenetic analysis confirms a closer relationship between N. ceranae and Nosema sp. YNPr than between the two honeybee parasites N. ceranae and N. apis. The more closely related N. ceranae and Nosema sp. YNPr show similarities in a number of structural characteristics such as gene synteny, gene length, gene number, transposon composition and gene reduction. Based on transposable element content of the assemblies, the transposon content of Nosema sp. YNPr is 4.8%, that of N. ceranae is 3.7%, and that of N. apis is 2.5%, with large differences in the types of transposons present among these 3 species. Gene function annotation indicates that the number of genes participating in most metabolic activities is similar in all three species. However, the number of genes in the transcription, general function, and cysteine protease categories is greater in N. apis than in the other two species. Our studies further characterize the evolution of the Nosema/Vairimorpha clade of microsporidia. These organisms maintain variable but very reduced genomes. We are interested in understanding the effects of genetic drift versus natural selection on genome size in the microsporidia and in developing a testable hypothesis for further studies on the genomic ecology of this group.

Publication types

  • Comparative Study

MeSH terms

  • Animals
  • Base Composition
  • Base Sequence
  • Bees / microbiology
  • Biological Evolution
  • Butterflies / microbiology
  • DNA Transposable Elements
  • DNA, Fungal / genetics*
  • DNA, Ribosomal / genetics*
  • Gene Ontology
  • Genetic Drift
  • Genome Size
  • Genome, Fungal*
  • High-Throughput Nucleotide Sequencing
  • Microsporidia / classification
  • Microsporidia / genetics*
  • Molecular Sequence Annotation
  • Nosema / classification
  • Nosema / genetics*
  • Sequence Alignment
  • Species Specificity
  • Synteny


  • DNA Transposable Elements
  • DNA, Fungal
  • DNA, Ribosomal

Grant support

This study is supported by National High-tech R&D Program (863 Program, No.2013AA102507), National Natural Science Foundation of China (No.31270138, 31302037, 31402142, 31001037), Natural Science Foundation Project of Chongqing Science & technology Commission (No.cstc2015jcyjA80020).