Horizontal Transfers Of Transposable Elements In The Silkworm Genome

Transposable elements (TEs) are DNA fragments that can move from one place toanother place in their host genomes. They are dividedinto two classes based on theirtransposition mechanisms. RNA elements transpose using a “copy-and-paste” process.However, DNA elements transpose generally by a “cut-and-paste” process. As more andmore genomes are currently sequenced, it has been found that TEs account for a greatproportion of eukaryotic genomes. In addition, recent studies have shown that TEs playimportant roles on genome size, chromosome structure, genome rearrangement, newgene generation and regulation of neighboring gene structure and expression and so on.They also provide the raw material for evolution of biological complexity. Therefore,TEs are becoming hot spot in genomics and functional genomics research.As a model of Lepidopteran insects, the silkworm (Bombyx mori) is the onlyknown completely-domesticated insect and a good material for genetics research.Genome-wide screening of TEs of the silkworm has shown that TEs constituteapproximately35%of the silkworm genome. In the sequenced insect genomes,transposon content of the silkworm is the second most, which was just below the Aedesaegypti47%. However, the origin and evolution history of silkworm genomic TEs arestill unknown. In this study, several molecular biological analyses were applied toanalyze characteristics and evolutionary history of the silkworm hAT, Chapaev andMITEs. Meanwhile, the origin of the recombination-activating gene1(RAG1) was alsoanalyzed in detail. The main conclusions are as follows:①Characteristic and evolutionary histroy of a novel hAT transposon in the silkwormand triatomine bug (Rhodnius prolixus): A hAT transposon was identified in thesilkworm and triatomine bug through the homology-based strategy. Structure andphylogenetic analysis confirmed that they represent a new family of hAT. Meanwhile, itgenerated a MITE, Bm-MITE15, in the silkworm genome. Highly conservation ofBm-MITE15copy sequences and its insertion/deletion polymorphism in the differentstrains of silkworm suggested that Bm-MITE15might have activity in silkworm genome.Finally, through phylogeny, codon preference, purified selection and transposondistribution analyses confirmed that this novel transposon has horizontally transferredinto the silkworm and triatomine bug. It concluded that the new hAT transposon couldbe used as useful and efficient molecular tools in triatomine transgenic. ②Horizontal transfer of the Chapaev transposons in different species: Insertionbiased analysis found that all Chapaev3transposons generated TWA (W:A/T) TSDduring the process of their transposition. The nucleotide adjacent to the apparent TSDwas always an “A” on the5′-end and a“T” on the3′-end. Then, three members of theChapaev3transposon (Merrow, Garfield and Conan) were analyzed in detail in thisstudy. First, to rule out false positive, PCR, cloning and sequencing was performed inthis study, and it confirmed that the transposons did exist in these species. Then,orthologous loci, insertion time, codon preference, purifying selection, transposondistribution and host geographical distribution analyse confirmed that they invaded intotheir hosts by horizontal transfers. Among them, polydnavirus may be carriers ofhorizontal transmission of Chapaev transposon among these species. In addition,host-parasite interaction is conducive to their horizontal transfer of Chapaevtransposons.③Origin of recombination activating gene1(RAG1): Through sequence analysisof Chapaev, Transib and RAG1and their evolutionary relationships, we put forward twokinds of possible models about the origin of RAG1.1. RAG1represents a chimera thatarose by fusion of a Chapaev N-term domain to a Transib core region;2. RAG1isderived from a group of transposase which was neither from Transib superfamily norfrom Chapaev superfamily, but a common ancestor of them.④Characteristics and evolutionary history of six miniature inverted-repeattransposable elements (MITEs) in the silkworm and triatomine bug: MITEs describedhere were strikingly similar to each other in the silkworm and triatomine bug. Theyshowed similar TIRs, high sequence identities, and similar targets for integration. Allthese data indicated that each family identified in both species originated from the sameancestral transposon and could be recognized as the same transposon evolving in twovery different genomic backgrounds. Potential autonomous elements responsible for thespread were found using the homology-based strategy and extensive analysis. Theywere present in six invertebrate genomes. Further analysis showed that theseautonomous elements have been horizontally transferred into their hosts.Based on theabove results, this study puts forward a model about the origin and evolution of MITEsin the silkworm. The detailed process is as follows:1. an ancestor transposon was firstlyintroduced into the ancestor of Lepidopteran insects by Horizontal transfer. It isspeculated that the twisted-wing parasites may be the candidate vectors for thesetransfers;2. Then, many internal deletion copies (including MITEs) of this autonomous element are generated; Finally, the silkworm MITEs are obtained from its ancestorthrough vertical inheritance.⑤Novel_NA may represent a new class of MITEs: The characteristics ofnon-autonomous nature, small size, and high copy number for Novel_NA transposonidentified in this study implied that it might be a short interspersed element (SINE)-likeor MITE-like element. Then, sequence characteristic and secondary structure analysesdemonstrated that Novel_NA was a MITE-like element. We speculate that Novel_NA,HzMINE-2and DINE-1may represent a new class of MITEs in insects.The above results show that the silkworm autonomous transposon (hAT andChapaev) have been horizontally transferred into its genome. However, thenon-autonomous transposon MITEs have been vertically inherited into silkwormgenome. These results will help us to better understand the evolutionary history andorigins of transposons in the silkworm. In addition, the results also showed that theRAG1may have two kinds of origin models:1. RAG1represents a chimera of Chapaevand Transib transposons;2. Chapaev, Transib and RAG1were derived from a commonancestor. These results will help us to be a more comprehensive understanding of the"RAG transposon" model and contribution of transposons in the origin of genes.