Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.
Project description:Spodoptera litura (Lepidoptera: Noctuidae), which has a strong and rapid reproductive capacity, is a polyphagous pest with great destruction to many crops, causing economic loss to agricultural production worldwide. Its two testes began to fuse into a single one during the larva-to-pupa metamorphosis, which was favorable to the sperms development in our previous study. But the mechanism of testicular fusion is still unknown. In this study, we analyzed long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in the testes by high-throughout RNA-seq to explore the mechanism of testicular fusion in S. litura. In total, 2,150 lncRNAs, 2,742 target mRNAs and 347 miRNAs were identified in the testes from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 0-day-old pupae (P0D) (after fusion). It was found that a large number of DElncRNAs, DEmRNAs and a little number of DEmiRNAs were up-regulated from L6D4 to L6D6 when the testes began to fuse, a little number of DElncRNAs, DEmRNAs and a large number of DEmiRNAs were down-regulated from L6D6 to P0D after the testicular fusion. The GO terms and KEGG pathway enrichment analysis of DElncRNAs target DEmRNAs showed that ECM remodeling enzymes: stromelysin, A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTs) and inducible metalloproteinase inhibitor protein (IMIPs), ECM-intergrin interaction pathway and cell adhesion molecules (integrin, cadherin) may be involved in the testicular fusion. The DElncRNA-DEmiRNA-DEmRNA regulatory network related to ECM remodeling enzymes and its signal pathway may play important roles in cell adhesion when the testicular fusion occured. Our study will provide comprehensive information to study the mechanism of testicular fusion, and especially, will promote the functional study of non-coding RNAs (lncRNAs and miRNAs) during the testicular fusion in S. litura.