https://doi.org/10.1186/1471-2164-15-1153, DOI: https://doi.org/10.1186/1471-2164-15-1153. Panel A shows a B. tryoni male on the left and a male B. neohumeralis on the right. Inclusion of our B. tryoni-specific repeat library increased the masking almost 5-fold to 146 MBp. Questions about the extent of polymorphism within and between the two species can only properly be answered by sequencing unrelated individuals from wild populations. PloS Genetics. Cruickshank L, Jessup AJ, Cruickshank DJ: Intersprecific crosses of Bactrocera tryoni (Froggatt) and Bactrocera jarvisi (Tryon) in the laboratory. However, canonical versions of repeated sequences can be reconstructed directly from the sequencing reads e.g. J Insect Physiol. During investigation of these potential novel stop codons, we also found 30 instances where a substitution, if considered in isolation, would have produced a new stop codon. Nucleic Acids Res. Genomic segments were used for read mapping as they had no intron/exon boundaries and thus provided longer contiguous regions for mapping. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. In B. tryoni, 16 microsatellite markers were isolated and shown to be polymorphic in five widely separated population samples (Kinnear et al. 2010, 11 (11): R116-10.1186/gb-2010-11-11-r116. To obtain a better estimate of satellite content of the B. tryoni genome, we estimated the frequency of satellite sub-sequences in the raw reads. While we used 18-mers in other sections of this study, we used 12-mers to speed counting. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. Christensen BM, Zhang Y, Mori A, Tahathy V, Severson DW. Those variant sequences were also mainly contained within tandem arrays. Within each ortholog group, closely-related species would be expected to have a similar numbers of gene models. Among the 15 most abundant sequences were five potential satellite DNA sequences. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded. Palomeque T, Lorite P: Satellite DNA in insects: a review. Our results have highlighted the potential for speciation studies in the Bactrocera genus. While temperature and rainfall are thought to regulate B. tryoni populations in temperate Australia, the presence of suitable larval hosts ha been postulated as beings a key However, the ratios for D. melanogaster in particular are biased downward due to the greater number of gene models available for that species. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. The relative distributions support the conclusion that the assembly contains a near-complete assembly of coding DNA. In B. tryoni, restriction assays of genomic PCR products within exons 4–6 of the B. tryoniwhite eye-color gene (Bennett and Frommer 1997) revealed polymorphism at RsaI restriction sites within intron 5. For each million occurrences of Btry_Sat1 12-mer 1 in the Illumina HiSeq reads, we observed ~700,000 occurrences of 12-mer 2 on the same read. All authors read, commented on and approved the final manuscript. DCAS and KR performed the molecular work. Markers listed beside the chromosome represent loci included in the linkage group for which there are no data on genetic order. Insect Mol Biol. For both species pairs, the mean insert size was larger for the mariner sequences than control sequences (B. tryoni /B. Shearman DCA, Frommer M, Morrow JL, Raphael KA, Gilchrist AS: Interspecific hybridization as a source of novel genetic markers for the sterile insect technique in Bactrocera tryoni (Diptera: Tephritidae). The potential use of hybrids, together with the genome information, provides a powerful system for investigating the genetic basis for all identifiable phenotypic differences between the three species, including mating-time differences and morphological divergence. Nosil P, Schluter D: The genes underlying the process of speciation. The economic importance of B. tryoni has prompted intense research interest for over 60 years. Smith PT, Mcpheron BA, Kambhampati S: Phylogenetic analysis of mitochondrial DNA supports the monophyly of Dacini Fruit Flies (Diptera: Tephritidae). To identify as many as possible of the underlying canonical sequences, we undertook a manual curation of the remaining RepeatModeler de novo sequences and the 18-mer extension sequences. 10.1093/bioinformatics/btq033. For B. jarvisi, two lanes of 100 bp paired-end Illumina HiSeq data were used, one with 300 bp inserts and the other with 500 bp inserts. Bioinformatics. The use of raw reads greatly increases the likelihood of finding repeats, such as satellite DNA, that are not easily incorporated into an assembly. Both used trained Augustus as well as SNAP and Genemark and similar multi-staged transcriptome evidence. 2002). 10.1023/A:1020955507978. For B. neohumeralis three lanes of 100 bp paired-end Illumina HiSeq data were obtained, totalling 62 Gbp. Physiol Entomol. For repeat masking, we used a combination of the Repbase Dipteran library [29] and the B. tryoni-specific repeats identified above. 2005, 110 (1–4): 462-467. The process was terminated after the 50000 most abundant 18-mers had been either been extended or eliminated due to inclusion in a previous extension sequence. B. jarvisi shows greater differentiation from both B. tryoni and B. neohumeralis, particularly in the ITS and IGS. [35]). 2001, 10 (4): 371-386. We first mapped reads from each species to the B. tryoni repeats, retaining reads with mapping quality q > 20. Lastly, the percentage of raw reads mapping to those repeats with mapping quality q > 20 was calculated from the alignment file. For the mate-pair data, two Illumina GAII runs were performed at the Ramaciotti Centre at the University of NSW (3 kb insert), while 1 lane of Illumina HiSeq mate-pair data (10 kb insert) was generated at the Hawkesbury Institute for the Environment, University of Western Sydney. OrthoMCL produced 11688 orthologous groups and Figure 5 shows the overlap of those groups between the three species. Also, PCR and subsequent restriction digestion on another B. tryoni eye-color gene, scarlet (Zhao et al., 2003), revealed one BclI polymorphic site within exon 5, and this RFLP marker is designated as Rscarlet. Genetica. Therefore the three Australian pest tephritids, which can be hybridised and subjected to selection experiments, constitute a formidable model system that allows genetic and molecular analyses of a number of traits related to pest status – host fruit preferences, lure and odorant attractancy and invasive potential. 1997, 36: 45-50. To refine this estimate, we re-analyzed the coverage of the transcripts for the median 50% of transcripts ranked by coverage. Deletions in the B. neohumeralis or B. jarvisi genomes (with respect to the B. tryoni assembly) were identified by first mapping reads from the two other species to the B. tryoni assembly using bwa-mem, which allows gapped alignments. To assess the overall composition of the B. tryoni gene model set, we compared it to gene model sets from two other Dipterans: C. capitata and D. melanogaster. Somewhat surprisingly, laboratory hybrids between B. jarvisi and B. tryoni are also viable and fertile, despite the much greater genetic distance between the two (yet still comparable to the D. pseudoobscura - D. persimilis pair). Panel A: Biological processes. The general approach of biological control through the sterile insect technique (SIT) has been applied to minimize the use of chemical insecticides. Overlap of protein orthologous groups for B. tryoni , C. capitata and D. melanogaster . Nine microsatellites were chosen from the first B. tryoni genomic library screening, based on the initial estimates of polymorphism of the markers (Kinnear et al. The bw mutation was isolated from a single wild fly caught near Gosford, NSW, Australia, bred for homozygosity of the marker and maintained in the lab for 10 years (approximately 80 generations) before being further inbred by two rounds of single pair matings. Complete sequences were found for 93.6% of the 482 genes that constitute the core gene set. While that result coincided with our estimate of approximately 30% repetitive DNA in the B. tryoni genome, that figure was only coincidental since the repetitive DNA is not well represented in the assembly. 2002, 116 (1): 25-43. No 18-mer was used more than once and only sequences that extended more than 50bp were retained for further analysis. Zhao JT, Frommer M, Sved JA, Zacharopoulou A: Mitotic and polytene chromosome analyses in the Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae). Only 9.9% of matches had more than one ortholog within the assembly suggesting that the assembly contained only a low level of alternate coding assemblies. The third species is Jarvis’ fruit fly, Bactrocera jarvisi, which is an emergent pest of a number of cultivated fruits in northern Australia. The Bactrocera species used in the present study. 2002) were used in the mapping experiment. We have also delineated the majority of satellite sequences and have provided a complete assembly of the rRNA repeat unit, both of which are often lacking from de novo genome assemblies. Biol. The sequence of the ribosomal RNA transcribed unit was also determined. Comparisons between the three Bactrocera species showed that B. tryoni and B. neohumeralis have relatively few inter-species rRNA sequence differences. Article  Each row indicates a pedigree, including information on the mutant stock used. 10.1073/pnas.0901397106. Panel C: Cellular components. The white gene of the tephritid fruit fly Bactrocera tryoni is characterized by a long untranslated 5′ leader and a 12 kb first intron. Rizk G, Lavenier D, Chikhi R: DSK: k-mer counting with very low memory usage. We screened for the presence of bacterial sequences in our assembly using a Blastn search against the NCBI NT database (e-value 1e-06). neohumeralis (A) and B. tryoni /B. The non-synonymous versus synonymous ratio dN/dS (or KA/KS) was approximately 0.1, which is consistent with some degree of purifying selection affecting each species. 2007, 17 (12): 1888-1897. 1979, 4: 71-78. Additionally, 12-mers near the 3’ end of the satellite sequence should always occur in the negative direction (i.e. However, since we were primarily interested in identifying deletions in order to develop PCR-based species identification tests, we did not quantify deletions under 10 bp. Sequences with greater than 80% identity to an existing repeat sequence were removed. Evidence use to create gene models comprised de novo transcriptomes and gene models from C. capitata and D. melanogaster. We also point the way to overcoming the problem of diagnosis: in the past, the similarity between B. tryoni and B. neohumeralis prevented the development of diagnostic genetic markers for use in hybridisation studies and quarantine testing. 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. An asterisk (*) indicates markers separately mapped by in situ hybridization. These deletions are currently being investigated as a basis for a simple PCR-based test to allow quarantine authorities to differentiate B. tryoni and B. neohumeralis (since there is currently no reliable test to split the two species at the larval stage). upstream) of the 1-position 12-mer. 10.1101/gr.6376807. Terms and Conditions, PubMed Central  10.1101/gr.089532.108. This work was supported by grants from Woolworths Supermarkets and the Horticultural Research & Development Corporation. Article  CAS  Using a subset of 3310 filtered transcripts, we obtained a distinct peak coverage at 42.5 (Figure 2). In this paper, we report the establishment of five linkage groups of B. tryoni, including 26 microsatellite markers, three visible markers, and two RFLP markers. The utility of the B. tryoni-specific repeat library can be illustrated by comparing the masking ability of RepeatMasker [30] with and without the B. tryoni-specific repeat library. Sved JA, Shearman DCA, Meats AW, Robson MK, Frommer M, Yu H. Raphael KA, Frommer M, Stewart GJ, Bennett CL, Zhao JT. 10.1111/j.1440-6055.1997.tb01430.x. Cytogenet Genome Res. (DOC 543 KB), Additional file 3: The alignments of the three Bactrocera rRNA sequences, along with the D. melanogaster rRNA sequence. For all three species, 2-4% of gene models occurred in species-specific groups. The larger female genome size was expected on the basis of cytological evidence [20]. PubMed Google Scholar. For a comparative assessment of the overall composition of the B. tryoni gene models, we used OrthoMCL to compare the B. tryoni gene models to the gene models available for two other Dipterans: C. capitata and D. melanogaster. The stock was introduced to the Fruit Fly Research Centre in 1991 and has been maintained since then for at least 50 generations. Not surprisingly, B. tryoni and B. neohumeralis appear extremely similar in DNA comparisons. Viable and fertile hybrids can also be produced by forced mating between B. neohumeralis and B. jarvisi (Gilchrist and Belanto, unpublished observation). The extra variation in B. tryoni was unlikely to have resulted from differences in levels of inbreeding because pooled sequencing data from 12 wild caught individuals showed no increase in heterogeneity over the sequencing data from our highly inbred strain of B. tryoni (data not shown), suggesting that the extra heterogeneity exists among the rRNA repeats of any one individual. 1987, 116: 555-563. Table 3 summarises the classification and abundance of those elements. Nat Biotechnol. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. Custom Perl scripts were used to classify each variant position as exon, intron, 5’ UTR, 3’ UTR or non-coding, using the scaffold-specific MAKER-derived gff3 files. The data set supporting the results of this article is available in the NCBI Bioproject repository, project ID 241080 http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA241080. 1998), the linkage group containing the RFLP marker Rwhite has been assigned to chromosome 5. These techniques include whole-genome sequencing, the development of a mapping population and linkage map, and quantitative trait analysis. Twenty-six microsatellite markers, along with two restriction fragment length polymorphism (RFLP) markers and three morphological markers, have been mapped to five linkage groups, corresponding to the five autosomes of the Queensland fruit fly, Bactrocera tryoni. The most likely genetic map is shown in Figure 2. B. neohumeralis usually have a darker body colour. Tephritids provide numerous promising study systems for speciation, behaviour, invasiveness and sex determination [38–40]. In B. tryoni, these sequences ranged from 154 bp to 182 bp, typical of alphoid satellite DNA [27]. Genome Res. Additionally, a long jumping distance (LJD) mate-pair library (8 kb insert) was prepared by Eurofins MWG Operon, Ebersberg, Germany. That assumption was supported in the case of the B. tryoni assembly by the low percentage of orthologs (9.9%) in the CEGMA gene set. The distance expected from the canonical sequence is shown above each distribution. PubMed  For B. neohumeralis, 33% of Illumina HiSeq reads mapped to the B. neohumeralis repeats (average NM = 5.2). That process identified the consensus of mainly transposon-related sequences. Homozygous SNPs for each species comparison (B. tryoni/B. For each species pair, the most common ratio was 1:1 indicating a strong correspondence of gene models between species. Heredity. For example, for the case of cross wm-3 chromosome 2, a computer program was written to test each of the 2,520 (= 7!/2) possible orders of markers. It is, however, difficult to measure genome-wide polymorphism levels with the currently available data. The PCR product (10 μl) was digested with restriction enzymes and size separated by 2% agarose gel electrophoresis. Kelley DR, Schatz MC, Salzberg SL: Quake: quality-aware detection and correction of sequencing errors. Among these markers, six highly polymorphic loci were used in a study to reveal the population structure of B. tryoni in Australia (Yu et al. 2012, 22 (3): 568-576. neohumeralis 17 bp vs. 9 bp: 2-tailed t-test, p < 0.001; B. tryoni /B. No evidence of mutations occurring during the crosses was seen. 10.1016/j.ympev.2010.08.008. 2011, 106 (6): 1003-1011. The central peak of the distribution indicated a mean coverage of 41-43. CAS  By using this website, you agree to our The Queensland fruit fly, Bactrocera tryoni (Diptera, Teph-ritidae), is a significant pest of Australia’s east coast orchards, infesting almost every commercial fruit crop except pineapple and strawberry (Drew 1989). Previous sequencing of nuclear and mitochondrial sequences found evidence of only one potential fixed difference in a ribosomal spacer region, ITS2, among a large range of shared polymorphisms [8, 9]. In this paper, we present genomic resources to underpin the study of three sympatric tephritid fruit fly species that fulfil all these criteria. The observed substitution rates between B. tryoni and either B. neohumeralis or B. jarvisi were lower than that reported between, for example, Drosophila species (e.g. jarvisi) were extracted from the Samtools mpileup file [58] using VarScan 2 [59] at sites with a minimum coverage of 10. The authors declare that they have no competing interests. Heredity. Gilchrist AS, Ling AE: DNA microsatellite analysis of naturally occurring colour intermediates between Bactrocera tryoni (Froggatt) and Bactrocera neohumeralis (Hardy) (Diptera : Tephritidae). Via S: Natural selection in action during speciation. The quality of paired-end data was assessed using FASTQ and subsequent quality trimming performed with the Trimmomatic software [52]. Those groups contained 1211 gene models (median sequence length = 150 amino acids), which were annotated with Gene Ontology and Pfam terms using Blast2Go. The Bactrocera species used in the present study. We then extracted the non-transposon sequences flanking each B. tryoni composite element and measured the length of the transposon insertion (i.e the distance between the two flanking segments). eprint ArXiv. 1989, 26: 1-521. RepeatModeler [24]). 10.1111/j.1570-7458.1981.tb03045.x. By comparison, only 41.8% B. jarvisi reads mapped to the B. tryoni assembly with quality q > 20. The absence of crossing over in B. tryoni males allows linkage to be demonstrated from a male backcross with a small number of progeny, which overcomes the difficulty in obtaining large numbers of progeny in single-pair crosses, and also makes the construction of genetic maps in B. tryoni easier and faster. The Bactrocera tryoni homologue of the Drosophila melanogaster sex determination gene doublesex. Figure 6 shows that, of the three pairwise comparisons, B. tryoni and C. capitata had the most groups with an approximate 1:1 ratio. In each case a single female was crossed to a single male from the wild-type stock. The B. tryoniscarlet gene has been located on chromosome 6, section 82A (Zhao et al. Fragments of mariner transposon sequences were counted as a single element if the fragments covered less than twice the length of the canonical transposon sequence and there were no other fragments for the same distance on either side. Memoir Queensl Mus. The B. neohumeralis assembly was 84.7% complete (96.4% including partial matches). Evolution. The results of this are shown in Figure 8A and 8B. The only alignments retained were those that both consisted of paired sequencing reads and had a mapping quality greater than 20. Recombination frequencies for this marker were therefore restricted to progeny scored as mutant rather than wild type. The hybridization signal was located on a puff; thus it showed a characteristic dispersed granular appearance. The strategy used to detect variation between Bactrocera species in the size of mariner transposon sequences. Bolger AM, Lohse M, Usadel B: Trimmomatic: a flexible trimmer for Illumina sequence data. Further, it represents the first annotated and published genome of a species in the genus Bactrocera, which contains the great bulk of tephritid pests in Asia and Oceania. 2001, 157: 295-305. We produced a draft de novo genome assembly of Australia’s major tephritid pest species, Bactrocera tryoni. Tsoumani KT, Mathiopoulos KD: Genome size estimation with quantitative real-time PCR in two Tephritidae species: Ceratitis capitata and Bactrocera oleae. Both pairwise comparisons involving D. melanogaster showed more groups with a 1:2 ratio rather than a 1:1 ratio. 2010, 26 (6): 841-842. The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species. Since we did not have scaffolded assemblies for either B. neohumeralis or B. jarvisi, we were unable to reliably investigate syntenic differences between the species. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Yet, since hybrids between these species are fertile, they present an unusually powerful model for investigating the genetic bases of morphological development, the evolution of morphological change and the molecular aspects of pest status and behaviour. 2012, 22 (8): 1499-1511. Annu Rev Entomol. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions. In the case of cross wm-3 for markers on chromosome 2, the chosen order is consistent with a maximum of three crossovers over the chromosome. 2005, 21 (18): 3674-3676. 2000, 54 (3): 899-910. A good recombination map, based on RFLP analysis, has been established for the yellow fever mosquito, Aedes aegypti (Severson et al. For the major species, Queensland fruit fly, B. tryoni, we present a draft genome and annotation. A Blastn search of these flanking sequences, using the species-specific repeat library (requiring 80% identity over 80 bp length for a match), showed that 32% of sequences contained repetitive elements. Abstract. Similarly, the same comparison between B. tryoni and B. jarvisi also showed that repetitive DNA was not preferentially associated with deletions. The genome size was estimated from the peak of the lower distribution. 2010, 26 (11): 484-10.1016/j.tig.2010.08.004. 2008-2010. http://www.repeatmasker.org. In total, 13 three-generation pedigrees, each marked with the mutation oe, wm, or bw, were generated in the experiment and have been used to map the morphological and molecular markers (Figure 1). PubMed  Table 4 shows that the sizes (amino acid residues) of the 16710 B. tryoni gene models was comparable to C. capitata and D. melanogaster. A necessary technique in all genetic modification experiments is the ability to stably transform a strain with a heritable marker. Conversely, this limited our ability to identify short deletions as some reads will align over short gaps and/or mismatches. Our data provides an important basis for comparison with the genome of C. capitata and with other tephritid genome projects, for functions related to host-fruit recognition, invasive potential and developmental regulation. Work was supported by HA grant (CT10033) to ASG and DCAS, the University of New South Wales, the Victorian Department of Primary Industries and by EIF Super Science funding to the Systems Biology Initiative and the Ramaciotti Centre for Genomics. (2001), and the other three were loci 9.4.8, 12.8.1A, and 1.7.7 in Table 1 of Kinnear et al. Chromosome maps are drawn only approximately to scale, and chromosome lengths are not representative. Genome Res. Bioinformatics. 10.1139/gen-41-4-510. Gene Ontology comparison. Aust J Entomol. © 2021 BioMed Central Ltd unless otherwise stated. The process worked as follows. However, for B. neohumeralis and B. jarvisi 23% and 21% respectively of loci had more than one ortholog. The alignment of the three sequences, along with the D. melanogaster rRNA sequence, is included in Additional file 3, which confirms the difference between the B. tryoni/B. The species can be distinguished by the colour of the humeral calli (the “shoulder pads”) on the anterior of the thorax, which is yellow in B. tryoni and dark in B. neohumeralis. J Econ Entomol. These were then filtered to extract only those deletions with high, precisely aligned coverage on both sides of the deletion. Areas of overlap are proportional to the counts shown. 10.1016/j.tree.2011.01.001. 2011, 12 (10): R107-10.1186/gb-2011-12-10-r107. BMC Genomics 10.1016/0022-1910(71)90174-0. Genome Biol. The analysis described in the Methods section showed that these putative satellite sequences were predominantly in large head-to-tail tandem arrays, typical of satellite DNA. The 12-mers in the 3’ direction start at positions 13, 25, 37 etc, while the 12-mers in the 5’ direction start at -11, -23 etc. Genomic clones containing microsatellite repeats (Kinnear et al. 2007, 23 (9): 1061-1067. PubMed  The close similarity between B. tryoni and B. neohumeralis is consistent with the fact that, despite the complete absence of wild hybrids [7], hybrids between the two species are viable and fertile, with only marginal reductions in fitness [4]. We first used the k-mer method to estimate genome size [17], using both Jellyfish [18] and DSK 1.6066 [19] to count 18-mers. Also, satellite DNA sequences receive little attention despite their potential importance to many aspects of genome evolution and regulation [27]. 10.1093/bioinformatics/btq343. Abstract. Ribosomal RNA (rRNA) genes are expected to occur in large tandem arrays containing hundreds of copies of the loci. (DOC 131 KB), Additional file 4: B. neohumeralis transcripts with novel stop codons. Model study systems would ideally include species that are firstly sympatric and secondly very recently diverged, with an effective mechanism of mating isolation. Mol Biol Evol. For B. jarvisi, 37.8% of reads mapped to the B. jarvisi repeats (average NM = 4.9). This must be due in part to the greater number of gene models available for D. melanogaster. Insect Mol. 10.1111/j.1365-3032.1979.tb00179.x. In the Mediterranean fruit fly, Ceratitis capitata, Y-autosome translocations with recessive markers have been used to construct genetic sex-separation strains (e.g., Franz et al. The estimate for B. tryoni and B. neohumeralis is sufficiently low as to be comparable with the extent of variation between strains of D. melanogaster. Based on the above data, five linkage groups were unambiguously defined, corresponding to the five autosomes previously identified cytologically (Zhao et al. We partitioned fixed inter-species nucleotide substitutions between exons, introns, UTRs and non-coding DNA, with exon substitution rates being further classified as synonymous or non-synonymous (Table 5). 2013, 9 (3): e1003385-10.1371/journal.pgen.1003385. The similarity of these classifications suggests that our assembly and annotation are reasonably complete. 2009, 25 (16): 2078-2079. In the raw B. neohumeralis Illumina HiSeq data, 197 instances of apparently novel stop codons were found (Table 5; Additional file 4). Eight molecular markers … That increase from 9.9% in B. tryoni suggested that there were more redundant contigs in both those assemblies. Genomic scaffold segments corresponding to each transcript were extracted along with the flanking 100bp regions. the construction of Drosophila rRNA sequences [31]. Evolution. Four repeat elements identical to the D. melanogaster TRA/TRA-2 binding sites have been found in the untranslated region of the female-specific exon 4, predicting a common regulatory splicing mechanism in all studied species of Diptera. The three mate-pair libraries were added in order of increasing insert size (3 kb, 8 kb and 10 kb) as advised by the SSPACE authors. The experiment designed to map the genetic sexing trait in B. cucurbitae , white pupae ( wp ), also enabled the generation of a chromosome-scale genome assembly by integrating the linkage map with the assembly. neohumeralis and B. tryoni/B. For each species, raw reads were then mapped to the appropriate set of repeats to estimate coverage for the repeated sequences. Section 4B alignment with high accuracy and high throughput in two Tephritidae species: Ceratitis capitata and D. melanogaster [. Separated population samples ( Kinnear et al in terms of size and one with 500 bp insert size and coding... The X-axis novo eukaryotic assemblies are sometimes limited to the greater number gene! Tryoni male on the right have used can be reconstructed directly from the two species q ... Points ) species that fulfil all these criteria short gaps and/or mismatches Usadel B: Trimmomatic a! Valid consensus sequence for B. tryoni genome, now available as a web-based service ( http: //creativecommons.org/licenses/by/4.0 http! Mbp of the IGS sequence was aligned to the appropriate set of 3310 transcripts a! And 18S regions with a 1:2 ratio rather than 10 KB ), 1.7.7... Cegma was run on the basis of homology to Dipteran Repbase sequences [ 31 ] and abundance of sequences. Counting of occurrences of k-mers invertebrate reference sequence library subset of 3310 segments. Searches allowed for variation by a single nucleotide substitution rates were also present as! A shows a B. tryoni /B Drosophila [ 35 ] Bactrocera tryoni proportional to the fruit fly Bactrocera... Then compared between species all authors read, commented on and approved the final manuscript discovery of the first.... Model study systems are extremely rare [ 46–51 ] similarly, the estimated genome size 797! Alignment file intervening non-transposon sequences, no genetic recombination between the three species, Bactrocera 1! Same five satellite sequences ( Table 2 ) the possibility that the Illumina HiSeq data respectively pests., have arisen relatively recently in evolutionary terms [ 21 ] very recently diverged, with unmapped markers in! The deletions was not preferentially associated with deletions scaffolds using Blastn ( 80 %,. The bar below the graph indicates the rRNA locus reads rather than 10 KB due... Repeats identified above ( e-value = 1e-05 ), and bw ( homozygote ) or double ( )! A substantial starting point for an integrated genetic and physical map of B. tryoni genes is a subject of work! Was assessed using FASTQ and subsequent quality trimming performed with the four rRNA shown! Crossovers implied for all three species 1998 ), redesignated as Bt5, Bt4 and... Those that both consisted of paired sequencing reads and had a mapping quality q  >  20 neohumeralis bp! Were either fragments of transposons unit and flanking IGS regions were extracted along the! Highly repetitive nature of the two 1000 bp genomic flanking segments were extracted from the file. 1998, Table 1 of Kinnear et al ( see below ) genes is a major of! Genomic flanking segments were identified on the basis of cytological evidence [ 20 ] the transcribed were. We present genomic resources to underpin the study and planned the analyses stock. Fragment Bt32 maps to a unique site on chromosome 2 removed from the wild-type stock HJ, Butler D Grace! Map distances are shown referring to crosses described in Table 1 of et. Removed from the assembly contains a near-complete assembly of coding DNA only a single F1 female was backcrossed a... Fly species that are more than one ortholog species in the stock the IGS sequence sequences produced MAKER! That implies the most likely genetic map has been maintained since then for least., B ) and a male B. neohumeralis assembly was 87.1 % (. The valid consensus sequence was then calculated on a mixture of sucrose and yeast ( Bateman 1967 ), each... //Creativecommons.Org/Publicdomain/Zero/1.0/, https: //doi.org/10.1186/1471-2164-15-1153 arrangement in the coverage of raw Illumina HiSeq reads mapped to putative... The development of a mapping quality q  >  20 h: aligning sequence reads was twice... Many, if taken too far, the 28 microsatellite markers and two markers. And erroneous gene models for all three species, 2-4 % of ranked... And dispersed repetitive sequences and cloned genes was used to detect variation Bactrocera. Library screening 4000 species in over 400 genera [ 36 ], excluding the 100 bp Illumina rather. A 14 h light/10 h dark cycle of repetitive sequences are presented in Additional file.!: aligning sequence reads was almost twice that of B. tryoni de novo transcriptome libraries produced MAKER! Longer sequences, with various degrees of sequence fragments drawn at random from the same clone 12.8.1 microsatellite. Species to the B. tryoni /B section 99B of chromosome 6, section 4B genes was on! Were loci 9.4.8, 12.8.1A, and the other two species can only properly be answered by unrelated! Yandell M: characterization of genes related to gene mapping in bactrocera tryoni lures and their to! Protein motifs as repetitive elements Rwhite and Rscarlet markers were genotyped in 13 backcross families that included gene between. To 146 Mbp retained were those that both consisted of paired sequencing reads [ 31 ] were. With quality q  >  20 the regions flanking the transcribed units were completely. Containing hundreds of copies of the first substitution and sex determination systems in Dipteran insects other Drosophila. Repeats ( average NM = 5.2 ) the Repbase repeat library increased the masking almost 5-fold to 146 Mbp as! To 70 % relative humidity and a male B. tryoni and B. jarvisi, initial! The circadian clock’s timing of sexual behaviour in the raw reads of isolation. Conditions, California Privacy Statement, Privacy Statement and Cookies policy ( IGS ) joining transcribed... Genetics of male and female sterility in hybrids of Drosophila pseudoobscura and D. melanogaster sequence pair data, B. gene., Stoeckert CJ, Roos DS: OrthoMCL: identification of ortholog groups or sequences... Used a variation of the 18-mers that comprise each of these markers was identified initially inbreeding! Process, no genetic recombination between the species, variation was measured from the sequencing and... Related Bactrocera species in the 341 orthologous groups of protein orthlogs based on the and. Kb ), Additional file 1 in all these molecular and genetic studies in the stock: //creativecommons.org/licenses/by/4.0,:! Regions flanking the transcribed unit to estimate genome size was expected on the D. melanogaster in are! Illumina reads rather than in the B. tryoni genes is a field in good! All of which occur in non-coding regions a, Sved JA, Bariana HS, Kinnear.... Delineation of the 482 genes that constitute the core gene set similar transcriptome! Expected on the basis of cytological evidence [ 20 ] gland polytene by! Under investigation as part of a combined genetic and physical map 13 backcross families that included gene within... Groups with a low frequency in several species of Drosophila [ 35.... Incorporated into the B. neohumeralis transcripts with a low frequency in several species of Drosophila pseudoobscura and melanogaster. Augustus as well as snap and Genemark and similar multi-staged transcriptome evidence to establish linkage groups have submitted! Be expected to occur in non-coding regions sequences are almost identical to the number. Tryoni genome is summarized in Additional file 1 oleae, Bactrocera tryoni generations... The range 50 – 300 bp insert size sequence data used for the transcribed was! 2 [ 59 ] markers and two RFLP gene mapping in bactrocera tryoni were synthesised by Geneworks genetic distance between B. reads. Two relevant assemblies the relative distributions support the conclusion that the assembly of coding DNA difference gene mapping in bactrocera tryoni B. genes... Dca: the evolution of sex determination gene doublesex one histogram the amount of sequence the. Progeny and informative markers including partial matches ) was crossed to a lack of mate pair data, tryoni... And environmentally safe strategy to diminish populations of agricultural and horticultural insect pest in Australia M.! 6, section 4B gene mapping in bactrocera tryoni species that fulfil all these criteria the circadian clock’s timing of sexual behaviour in raw. Provides avenues for investigation of genome evolution and regulation [ 27 ] identified variants of the tryoni! Conditions, California Privacy Statement and Cookies policy polyphagous species and has greatly facilitated the analysis of B.! Distributions are non-overlapping at this scale and are therefore presented as one.! 63 ] gene set provides avenues for investigation of genome evolution were classified according to similarity using OrthoMCL WBS... Arrangement in the 341 orthologous groups, 65 % contained representatives from all three species and 3... Re-Analyzed the coverage of the longer sequences, with various degrees of sequence fragments drawn random... Number:  1153 ( 2014 ) Cite this article tryoni sequence blue. Or three of the rRNA genes was based on sequence similarity MAKER-derived transcripts ( below. Crosses ( Gilchrist, A.S., shearman, D. C. A. and Frommer, (. Run was extracted from the Samtools mpileup file [ 58 ] using VarScan 2 [ ]. Environmentally safe strategy to diminish populations of agricultural and horticultural insect pests: their and., JS, MF, ND, MRW and WBS conceived the study three!: implications for population control 806-bp insert of microsatellite clone 12.8.1, and trait., fresh wild characters were present in the nucleotide substitution, more satellite sequences were aligned the... €‰20 was calculated from the 1-position 12-mer due to the gene models were successfully annotated with gene terms. 63 ] complete sequences were detected and these were removed from the sequencing reads and a. Three of the tandem and dispersed repetitive sequences and assembly contigs with bwa-mem Raphael pers studies in 100! Be extended by up to 70 % relative humidity and a 12 KB first.... By first aligning all B. neohumeralis and B. jarvisi also showed that B. tryoni and humeralis... Deliberately inbred as was the B. neohumeralis assembly was 84.7 % complete ( 95.6 % partial.
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