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

Choo, Amanda; Nguyen, Thu; Ward, Christopher; Chen, Isabel Y.; Sved, J. A.; Shearman, Deborah; Gilchrist, A. S.; Crisp, Peter A.; Baxter, Simon W.

doi:10.1111/imb.12602

Cited by 13 publications

(21 citation statements)

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“…The sequence of these scaffolds amounts to 1.7 Mb and provides a valuable resource for Y chromosome gene identification. Previously, 700 kb of Y chromosome was identified for Bactrocera tyroni using genotype-bysequencing data and whole-genome resequencing [117]. Y chromosomes, however, remain difficult to assemble.…”

Section: Discussionmentioning

confidence: 99%

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

et al. 2020

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Background: The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on the fruits thus destroying them. The lack of a high-quality genome and other genomic and transcriptomic data has hindered progress in understanding the fly's biology and proposing alternative control methods to pesticide use. Results: Genomic DNA was sequenced from male and female Demokritos strain flies, maintained in the laboratory for over 45 years. We used short-, mate-pair-, and long-read sequencing technologies to generate a combined male-female genome assembly (GenBank accession GCA_001188975.2). Genomic DNA sequencing from male insects using 10x Genomics linked-reads technology followed by mate-pair and long-read scaffolding and gapclosing generated a highly contiguous 489 Mb genome with a scaffold N50 of 4.69 Mb and L50 of 30 scaffolds (GenBank accession GCA_001188975.4). RNA-seq data generated from 12 tissues and/or developmental stages allowed for genome annotation. Short reads from both males and females and the chromosome quotient method enabled identification of Y-chromosome scaffolds which were extensively validated by PCR.

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Section: Discussionmentioning

confidence: 99%

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

et al. 2020

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“…Bactrocera dorsalis provides an additional example that tephritid Y chromosomes, despite their high degeneracy and heterochromatic nature, harbour transcribed sequences, in addition to the MoY factor. This had previously been shown for the Y chromosomes of B. oleae and B. tryoni [28,38]. These Y-linked sequences require further investigation at the functional level.…”

Section: Discussionmentioning

confidence: 53%

“…Gigyf is highly expressed in embryonic stages and codes for GIGYF protein that forms a complex with eukaryotic initiation factor 4E homologous protein to elicit translational repression and promotes target mRNA decay. Paralogues of the gyf gene were identified in another Bactrocera species, B. tryoni [38]. About 41 copies, referred to as typo-gyf, are present on the B. tryoni Y chromosome.…”

Section: Discussionmentioning

confidence: 99%

“…Another copy of the gene, gyf, is present on the X chromosome. Choo and colleagues [38] suggest that a duplication that gave rise to the Y-linked typo-gyf copies occurred in Bactrocera between 5.5 and 10.6 MYA, before the split that gave rise to among others, B. tryoni and B. dorsalis, but after the split that gave rise to B. oleae [38]. The extent of copy number expansion in B. dorsalis needs to be determined, but at least one X chromosome copy of the gyf gene (sequence NW_ 011875054.1) and at least two Y chromosome typo-gyf copies (of which contigs 2 and 3 are fragments) are present.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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Background The Oriental fruit fly, Bactrocera dorsalis, is a highly polyphagous invasive species with a high reproductive potential. In many tropical and subtropical parts of the world it ranks as one of the major pests of fruits and vegetables. Due to its economic importance, genetic, cytogenetic, genomic and biotechnological approaches have been applied to understand its biology and to implement the Sterile Insect Technique, currently a part of area-wide control programmes against this fly. Its chromosome complement includes five pairs of autosomes and the sex chromosomes. The X and Y sex chromosomes are heteromorphic and the highly heterochromatic and degenerate Y harbours the male factor BdMoY. The characterization of the Y chromosome in this fly apart from elucidating its role as primary sex determination system, it is also of crucial importance to understand its role in male biology. The repetitive nature of the Y chromosome makes it challenging to sequence and characterise. Results Using Representational Difference Analysis, fluorescent in situ hybridisation on mitotic chromosomes and in silico genome resources, we show that the B. dorsalis Y chromosome harbours transcribed sequences of gyf, (typo-gyf) a homologue of the Drosophila melanogaster Gigyf gene, and of a non-LTR retrotransposon R1. Similar sequences are also transcribed on the X chromosome. Paralogues of the Gigyf gene are also present on the Y and X chromosomes of the related species B. tryoni. Another identified Y-specific repetitive sequence linked to BdMoY appears to be specific to B. dorsalis. Conclusions Our random scan of the Y chromosome provides a broad picture of its general composition and represents a starting point for further applicative and evolutionary studies. The identified repetitive sequences can provide a useful Y-marking system for molecular karyotyping of single embryos. Having a robust diagnostic marker associated with BdMoY will facilitate studies on how BdMoY regulates the male sex determination cascade during the embryonic sex-determination window. The Y chromosome, despite its high degeneracy and heterochromatic nature, harbours transcribed sequences of typo-gyf that may maintain their important function in post-transcriptional mRNA regulation. That transcribed paralogous copies of Gigyf are present also on the X and that this genomic distribution is maintained also in B. tryoni raises questions on the evolution of sex chromosomes in Bactrocera and other tephritids.

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“…We have previously created a B. tryoni strain with a white eye phenotype, through a white gene knock out using the NHEJ pathway [10], demonstrating that the CRISPR/Cas9 technology is applicable to B. tryoni and could hence be used to produce a B. tryoni GSS. The generation of a functional GSS using CRISPR/Cas9 gene editing will require creating an efficient embryonic conditional lethal mutation such as a tsl mutation (usually through the HDR mechanism), followed by translocation or insertion of a functional copy of the gene into identified Y chromosome regions [11]. The aim of this study is to introduce a tsl mutation into the germline of B. tryoni using the CRISPR/Cas9 technology.…”

Section: Introductionmentioning

confidence: 99%

Precise single base substitution in the shibire gene by CRISPR/Cas9-mediated homology directed repair in Bactrocera tryoni

et al. 2020

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Background Pest eradication using the Sterile Insect Technique (SIT) involves high-density releases of sterilized males that mate with wild females and ultimately suppress the population. Sterilized females are not required for SIT and their removal or separation from males prior to release remains challenging. In order to develop genetic sexing strains (GSS), conditional traits such as temperature sensitive lethality are required. Results Here we introduce a known Drosophila melanogaster temperature sensitive embryonic lethal mutation into Bactrocera tryoni, a serious horticultural pest in Australia. A non-synonymous point mutation in the D. melanogaster gene shibire causes embryonic lethality at 29 °C and we successfully used CRISPR/Cas9 technology to recreate the orthologous shibire temperature sensitive-1 (shits1) mutation in B. tryoni. Genotypic analyses over three generations revealed that a high fitness cost was associated with the shits1 mutant allele and shits1 homozygotes were not viable at 21 °C, which is a more severe phenotype than that documented in D. melanogaster. Conclusions We have demonstrated the first successful use of CRISPR/Cas9 to introduce precise single base substitutions in an endogenous gene via homology-directed repair in an agricultural pest insect and this technology can be used to trial other conditional mutations for the ultimate aim of generating genetic sexing strains for SIT.

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

Cited by 13 publications

References 81 publications

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

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

Precise single base substitution in the shibire gene by CRISPR/Cas9-mediated homology directed repair in Bactrocera tryoni

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