Abstract
BackgroundWe recently characterized HAmo SINE and its partner LINE in silver carp and bighead carp based on hybridization capture of repetitive elements from digested genomic DNA in solution using a bead-probe [1]. To reveal the distribution and evolutionary history of SINEs and LINEs in cyprinid genomes, we performed a multi-species search for HAmo SINE and its partner LINE using the bead-probe capture and internal-primer-SINE polymerase chain reaction (PCR) techniques.ResultsSixty-seven full-size and 125 internal-SINE sequences (as well as 34 full-size and 9 internal sequences previously reported in bighead carp and silver carp) from 17 species of the family Cyprinidae were aligned as well as 14 new isolated HAmoL2 sequences. Four subfamilies (type I, II, III and IV), which were divided based on diagnostic nucleotides in the tRNA-unrelated region, expanded preferentially within a certain lineage or within the whole family of Cyprinidae as multiple active source genes. The copy numbers of HAmo SINEs were estimated to vary from 104 to 106 in cyprinid genomes by quantitative RT-PCR. Over one hundred type IV members were identified and characterized in the primitive cyprinid Danio rerio genome but only tens of sequences were found to be similar with type I, II and III since the type IV was the oldest subfamily and its members dispersed in almost all investigated cyprinid fishes. For determining the taxonomic distribution of HAmo SINE, inter-primer SINE PCR was conducted in other non-cyprinid fishes, the results shows that HAmo SINE- related sequences may disperse in other families of order Cypriniforms but absent in other orders of bony fishes: Siluriformes, Polypteriformes, Lepidosteiformes, Acipenseriformes and Osteoglossiforms.ConclusionsDepending on HAmo LINE2, multiple source genes (subfamilies) of HAmo SINE actively expanded and underwent retroposition in a certain lineage or within the whole family of Cyprinidae. From this perspective, HAmo SINE should provide useful phylogenetic makers for future analyses of the evolutionary relationships among species in the family Cyprinidae.
Highlights
We recently characterized HAmo short interspersed repetitive elements (SINE) and its partner long interspersed repetitive elements (LINE) in silver carp and bighead carp based on hybridization capture of repetitive elements from digested genomic DNA in solution using a bead-probe [1]
We characterized a couple of SINE and LINE, designated HAmo SINE and its partner LINE, in silver carp and bighead carp based on hybridization capture of repetitive elements from digested genomic DNA in solu
125 internal sequences corresponding to different individual HAmo-SINE copies from the 17 cyprinid genomes were isolated and characterized. Four subfamilies and their different patterns of polyA insertion and short tandem duplication in tRNA-unrelated region Sixty-seven full-size sequences and 125 internal-SINE sequences [1] from 17 species of the family Cyprinidae were aligned
Summary
We recently characterized HAmo SINE and its partner LINE in silver carp and bighead carp based on hybridization capture of repetitive elements from digested genomic DNA in solution using a bead-probe [1]. Retrotransposons are widely distributed among eukaryotic genomes and occupy a substantial fraction of genome. These repeats increase in number by retroposition, which involves transcription of their genomic copies followed by reverse transcription of an RNA intermediate and results in cDNAs reintegration into the genome host [2,3,4]. We characterized a couple of SINE and LINE, designated HAmo SINE and its partner LINE, in silver carp and bighead carp based on hybridization capture of repetitive elements from digested genomic DNA in solu-. We found that HAmo SINEs was active and amplified recently in the genomes of these two young species utilizing the enzymatic machinery for retroposition of HAmoL2 [1]
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