Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina

Abstract

BackgroundTransposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications (e.g., in evolution) and applications (e.g., as transgenic tools). They also represent a major challenge for the assembly and annotation of genomic sequences. However, they are still largely unknown in non-model species.ResultsHere, we have annotated the repeats and transposable elements present in a 600 kb genomic region of the blowfly Calliphora vicina (Diptera: Calliphoridae) which contains most of the achaete-scute gene complex of this species. This is the largest genomic region to be sequenced and analyzed in higher flies outside the Drosophila genus. We find that the repeat content spans at least 24% of the sequence. It includes 318 insertions classified as 3 LTR retrotransposons, 21 LINEs, 14 cut-and-paste DNA transposons, 4 helitrons and 33 unclassified repeats.ConclusionsThis is the most detailed description of TEs and repeats in the Calliphoridae to date. This contribution not only adds to our knowledge about TE evolution but will also help in the annotation of repeats on Dipteran whole genome sequences.

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)

“…Outside of Drosophila, DINE-1 like elements have been identified in many lepidopteran [ 25 - 27 ], hemipteran [ 27 ], and dipteran [ 10 , 28 ] genomes (Additional file 1 : Table S1). These elements are also described from the genomes of sea urchin [ 24 ] and molluscs (Additional file 1 : Table S1) [ 22 , 23 , 29 ].…”

“…These elements are also described from the genomes of sea urchin [ 24 ] and molluscs (Additional file 1 : Table S1) [ 22 , 23 , 29 ]. DINE-1 like elements have attained high copy number in drosophilids [ 10 ] and other insect and invertebrate genomes (Additional file 1 : Table S1) [ 22 , 24 , 25 , 27 , 28 ]. In D. melanogaster DINE-1 elements are the most abundant TE (for review [ 30 ]) and constitute 9.2% (approximately 114 kbp) of the dot chromosome [ 21 ].…”

The genomes of a monogenic fly: views of primitive sex chromosomes

“…In Ca. vicina, the AS-C gene complex is flanked by repeats and transposable elements 55 . Additionally, within Diptera, the AS-C gene complex (which is made up of the genes achaete, scute, lethal of scute, and asense) is located on the X chromosomes in Drosophila and is involved in the sex-determining pathway wherein scute is an X chromosome signaling element 56 .…”

The achaete‐scute complex in Diptera: patterns of noncoding sequence evolution

“…All three genes are intronless and show the same orientation. All other ORFs correspond to transposable elements; these elements, which account for 24% of the sequence, have been described in detail in Negre & Simpson (). ac , sc and l'sc are grouped in a gene complex.…”

“…Only three fly genes were detected: sc , l'sc and ac . All other hits correspond to transposases, retrotranscriptases and other repeat sequences (described in Negre & Simpson, ).…”