Natural selection maintains the transcribed LTR retrotransposons in Nosema bombycis.
Eight intact LTR retrotransposons (Nbr1-Nbr8) have been previously characterized from the genome of Nosema bombycis, a eukaryotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements (Nbr9-Nbr14) identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions (Nbr12), deletions (Nbr11) and in-frame stop codons in coding regions (Nbr9) were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bombycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbr11 is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbr11 retrotransposon. Unlike other transposable elements, Nbr11 has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection.
Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400715, China.
Heng
H
Xiang
Guoqing
G
Pan
Ruizhi
R
Zhang
Jinshan
J
Xu
Tian
T
Li
Wenle
W
Li
Zeyang
Z
Zhou
Zhonghuai
Z
Xiang
D000595:Amino Acid Sequence; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D016818:Nosema / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D018626:Retroelements; D012641:Selection, Genetic; D016415:Sequence Alignment; D020079:Terminal Repeat Sequences; D014158:Transcription, Genetic
D005656:Fungal Proteins; D018626:Retroelements