Achilles, a New Family of Transcriptionally Active Retrotransposons from the Olive Fruit Fly, with Y Chromosome Preferential Distribution

Abstract

Sex chromosomes have many unusual features relative to autosomes. The in depth exploration of their structure will improve our understanding of their origin and divergence (degeneration) as well as the evolution of genetic sex determination pathways which, most often are attributed to them. In Tephritids, the structure of Y chromosome, where the male-determining factor M is localized, is largely unexplored and limited data concerning its sequence content and evolution are available. In order to get insight into the structure and organization of the Y chromosome of the major olive insect pest, the olive fly Bactrocera oleae, we characterized sequences from a Pulse Field Gel Electrophoresis (PFGE)-isolated Y chromosome. Here, we report the discovery of the first olive fly LTR retrotransposon with increased presence on the Y chromosome. The element belongs to the BEL-Pao superfamily, however, its sequence comparison with the other members of the superfamily suggests that it constitutes a new family that we termed Achilles. Its ~7.5 kb sequence consists of the 5’LTR, the 5’non-coding sequence and the open reading frame (ORF), which encodes the polyprotein Gag-Pol. In situ hybridization to the B. oleae polytene chromosomes showed that Achilles is distributed in discrete bands dispersed on all five autosomes, in all centromeric regions and in the granular heterochromatic network corresponding to the mitotic sex chromosomes. The between sexes comparison revealed a variation in Achilles copy number, with male flies possessing 5–10 copies more than female (CI range: 18–38 and 12–33 copies respectively per genome). The examination of its transcriptional activity demonstrated the presence of at least one intact active copy in the genome, showing a differential level of expression between sexes as well as during embryonic development. The higher expression was detected in male germline tissues (testes). Moreover, the presence of Achilles-like elements in different species of the Tephritidae family suggests an ancient origin of this element.

Identification of Y‐chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species

“…Expression of typo‐gyf transcripts was found among seven Bactrocera species we tested, and determining whether copy number expansions have occurred in these cases will provide insight into the origin of this duplication. There are documented examples of duplicated B. oleae Y‐chromosome sequences, including importin‐4 gene fragments (Gabrieli et al, ), and although not exclusively Y‐chromosomal, the long terminal repeat retrotransposon Achilles (Tsoumani et al, ). Further sequencing of Y‐chromosomes from a range of tephritids, determining copy number variation using genomic DNA or performing chromosomal in situ hybridization experiments, will help determine the extent to which typo‐gyf has been duplicated.…”

“…The Drosophila Y can acquire genes from other chromosomes, and different rates of gene gain occur within the genus (Tobler et al, 2017), which complicates comparative genomic studies attempting to identify Y-chromosome orthologues (Koerich et al, 2008). A range of methods have been used to identify Y-chromosome genes and sequences in nonmodel dipteran insects, including suppression subtractive hybridization (Salvemini et al, 2014), representational difference analysis (Gabrieli et al, 2011), Y-chromosome isolation with pulse field gel electrophoresis and sequencing (Tsoumani et al, 2015) and developing sex-specific genomic libraries (Hall et al, 2013;Koerich et al, 2016). However, First published online 21 June 2019. expressed Y-chromosome genes remain largely unknown among tephritid fruit flies.…”

“…Much of the empirical work on Y‐chromosome evolution has involved Drosophila species, which do share some features with mammals, including X–Y pairing during mitosis, low gene content and high levels of repetitive elements (Carvalho et al, ). Identifying active genes amongst repetitive sequences on Y‐chromosomes remains challenging (Tsoumani et al, ), but their identification can help understand factors contributing to sex determination and male fertility (Hall et al, ).…”

Cytogenetic Analysis of the South American Fruit Fly Anastrepha fraterculus (Diptera:Tephritidae) Species Complex: Construction of Detailed Photographic Polytene Chromosome Maps of the Argentinian Af. sp.1 Member

“…These characteristics support the heterochromatic nature of the sex chromosomes, a phenomenon that is common in the different genera of tephritids analyzed so far, namely Anastrepha , Bactrocera , Ceratitis , Dacus and Rhagoletis [ 10 , 65 , 69 – 76 ]. The heterochromatic nature of both sex chromosomes in tephritids is also evident by the abundance of highly repetitive DNA [ 77 – 79 ] and the limited number of genes, including the ribosomal DNA genes mapped on both sex chromosomes. This pattern of localization of the ribosomal genes is common to all tephritids analysed, such as C .…”

Transcribed sex-specific markers on the Y chromosome of the oriental fruit fly, Bactrocera dorsalis

“…Based on the highly heterochromatic and degenerate nature of the B. dorsalis Y chromosome [ 6 ], the enrichment of repetitive sequences and transposable elements (TEs) is expected. Enrichment of TEs on the highly heterochromatic Y chromosomes of other tephritids has been demonstrated [ 28 – 31 ]. Of particular interest is the presence of the non-LTR retrotransposon R1, which is also present on the X chromosome.…”