title: Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation.
abstract: BACKGROUND
  Microsporidian Nosema bombycis has received much attention because the pébrine disease of domesticated silkworms results in great economic losses in the silkworm industry. So far, no effective treatment could be found for pébrine. Compared to other known Nosema parasites, N. bombycis can unusually parasitize a broad range of hosts. To gain some insights into the underlying genetic mechanism of pathological ability and host range expansion in this parasite, a comparative genomic approach is conducted. The genome of two Nosema parasites, N. bombycis and N. antheraeae (an obligatory parasite to undomesticated silkworms Antheraea pernyi), were sequenced and compared with their distantly related species, N. ceranae (an obligatory parasite to honey bees).
  
  
  RESULTS
  Our comparative genomics analysis show that the N. bombycis genome has greatly expanded due to the following three molecular mechanisms: 1) the proliferation of host-derived transposable elements, 2) the acquisition of many horizontally transferred genes from bacteria, and 3) the production of abundnant gene duplications. To our knowledge, duplicated genes derived not only from small-scale events (e.g., tandem duplications) but also from large-scale events (e.g., segmental duplications) have never been seen so abundant in any reported microsporidia genomes. Our relative dating analysis further indicated that these duplication events have arisen recently over very short evolutionary time. Furthermore, several duplicated genes involving in the cytotoxic metabolic pathway were found to undergo positive selection, suggestive of the role of duplicated genes on the adaptive evolution of pathogenic ability.
  
  
  CONCLUSIONS
  Genome expansion is rarely considered as the evolutionary outcome acting on those highly reduced and compact parasitic microsporidian genomes. This study, for the first time, demonstrates that the parasitic genomes can expand, instead of shrink, through several common molecular mechanisms such as gene duplication, horizontal gene transfer, and transposable element expansion. We also showed that the duplicated genes can serve as raw materials for evolutionary innovations possibly contributing to the increase of pathologenic ability. Based on our research, we propose that duplicated genes of N. bombycis should be treated as primary targets for treatment designs against pébrine. The genome data and annotation information of N. bombycis and N.antheraeae were submitted to GenBank (Accession numbers ACJZ01000001 -ACJZ01003558).
authors.affiliation: State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Pan
authors.forename: Jinshan
authors.initials: J
authors.lastname: Xu
authors.forename: Tian
authors.initials: T
authors.lastname: Li
authors.forename: Qingyou
authors.initials: Q
authors.lastname: Xia
authors.forename: Shao-Lun
authors.initials: SL
authors.lastname: Liu
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.forename: Songgang
authors.initials: S
authors.lastname: Li
authors.forename: Chunfeng
authors.initials: C
authors.lastname: Li
authors.forename: Handeng
authors.initials: H
authors.lastname: Liu
authors.forename: Liu
authors.initials: L
authors.lastname: Yang
authors.forename: Tie
authors.initials: T
authors.lastname: Liu
authors.forename: Xi
authors.initials: X
authors.lastname: Zhang
authors.forename: Zhengli
authors.initials: Z
authors.lastname: Wu
authors.forename: Wei
authors.initials: W
authors.lastname: Fan
authors.forename: Xiaoqun
authors.initials: X
authors.lastname: Dang
authors.forename: Heng
authors.initials: H
authors.lastname: Xiang
authors.forename: Meilin
authors.initials: M
authors.lastname: Tao
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Li
authors.forename: Junhua
authors.initials: J
authors.lastname: Hu
authors.forename: Zhi
authors.initials: Z
authors.lastname: Li
authors.forename: Lipeng
authors.initials: L
authors.lastname: Lin
authors.forename: Jie
authors.initials: J
authors.lastname: Luo
authors.forename: Lina
authors.initials: L
authors.lastname: Geng
authors.forename: LinLing
authors.initials: L
authors.lastname: Wang
authors.forename: Mengxian
authors.initials: M
authors.lastname: Long
authors.forename: Yongji
authors.initials: Y
authors.lastname: Wan
authors.forename: Ningjia
authors.initials: N
authors.lastname: He
authors.forename: Ze
authors.initials: Z
authors.lastname: Zhang
authors.forename: Cheng
authors.initials: C
authors.lastname: Lu
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Keeling
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Zhonghuai
authors.initials: Z
authors.lastname: Xiang
authors.forename: Zeyang
authors.initials: Z
authors.lastname: Zhou
mesh_terms: D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics* / Q000469:parasitology; D004251:DNA Transposable Elements; D020440:Gene Duplication; D022761:Gene Transfer, Horizontal; D023281:Genomics; D006790:Host-Parasite Interactions / Q000235:genetics*; D016814:Microsporidia / Q000235:genetics* / Q000472:pathogenicity; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data
chemical_list: D004251:DNA Transposable Elements