Identification, Diversity and Evolution of MITEs in the Genomes of Microsporidian Nosema Parasites

Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous DNA transposons, which are widespread in most eukaryotic genomes. However, genome-wide identification, origin and evolution of MITEs remain largely obscure in microsporidia. In this study, we investigated structural fe...

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Published in:PloS one 2015-04, Vol.10 (4), p.e0123170-e0123170
Main Authors: He, Qiang, Ma, Zhenggang, Dang, Xiaoqun, Xu, Jinshan, Zhou, Zeyang
Format: Article
Language:English
Subjects:
Amplification
Deoxyribonucleic acid
Divergence
DNA
DNA Transposable Elements
European honeybee
Evolution
Fungal Proteins - genetics
Genetic aspects
Genetic polymorphisms
Genome, Fungal
Genomes
Genomics
Homology
Introns
Microsporidia
Mites
Nosema - genetics
Nosema antheraeae
Nosema bombycis
Nosema ceranae
Open Reading Frames
Parasites
Phylogeny
Polymorphism, Genetic
RNA, Fungal - genetics
Sequence Analysis, DNA
Species
Transposons
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Summary:Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous DNA transposons, which are widespread in most eukaryotic genomes. However, genome-wide identification, origin and evolution of MITEs remain largely obscure in microsporidia. In this study, we investigated structural features for de novo identification of MITEs in genomes of silkworm microsporidia Nosema bombycis and Nosema antheraeae, as well as a honeybee microsporidia Nosema ceranae. A total of 1490, 149 and 83 MITE-related sequences from 89, 17 and five families, respectively, were found in the genomes of the above-mentioned species. Species-specific MITEs are predominant in each genome of microsporidian Nosema, with the exception of three MITE families that were shared by N. bombycis and N. antheraeae. One or multiple rounds of amplification occurred for MITEs in N. bombycis after divergence between N. bombycis and the other two species, suggesting that the more abundant families in N. bombycis could be attributed to the recent amplification of new MITEs. Significantly, some MITEs that inserted into the homologous protein-coding region of N. bombycis were recruited as introns, indicating that gene expansion occurred during the evolution of microsporidia. NbS31 and NbS24 had polymorphisms in different geographical strains of N. bombycis, indicating that they could still be active. In addition, several small RNAs in the MITEs in N. bombycis are mainly produced from both ends of the MITEs sequence.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0123170