Zacharopoulou A, Sved JA, Frommer M, Zhao JT. Circular map of the mitogenome of B. minax. Default parameters were used except that potential intron length was extended to 40 kbp. Both used trained Augustus as well as SNAP and Genemark and similar multi-staged transcriptome evidence. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations. To comparatively assess the overall composition of our B. tryoni gene models, we used OrthoMCL [34], which groups transcripts by sequence similarity. 10.1111/j.1439-0418.2011.01684.x. Tyschen PH, Fletcher BS: Studies on the rhythm of mating in the Queensland fruit fly, Dacus (Bactrocera) tryoni. Cruickshank L, Jessup AJ, Cruickshank DJ: Intersprecific crosses of Bactrocera tryoni (Froggatt) and Bactrocera jarvisi (Tryon) in the laboratory. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase update, a database of eukaryotic repetitive elements. Adult flies lay eggs into fruit and resultant larvae feed on the Precise single base substitution in the shibire gene by CRISPR/Cas9-mediated homology directed repair in Bactrocera tryoni. This article is published under license to BioMed Central Ltd. Markers listed beside the chromosome represent loci included in the linkage group for which there are no data on genetic order. Smit AFA, Hubley R, Green P: RepeatMasker Open-3.0. The data shown in Additional file 5, which includes single nucleotide substitutions, showed that the estimate of the number of Btry_Sat1 sequences (indicated by reads that had two distinct 12-mers at the correct spacing and in the correct orientation) increased from ~70,000 to over 250,000. 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. Indels of 1 or 2 bp were counted as non-synonomous changes. Trends Genet. Genome Biol. OrthoMCL was run on the three sets of gene models using using default parameters, except for the Blastp all-against-all step, where a more stringent e-value of 1e-10 was used. 2006, 45: 157-162. volume 15, Article number: 1153 (2014) All these molecular and genetic markers were genotyped in three-generation pedigrees. Nardi F, Carapelli A, Boore JL, Roderick GK, Dallai R, Frati F: Domestication of olive fly through a multi-regional host shift to cultivated olives: Comparative dating using complete mitochondrial genomes. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. ASG carried out the bioinformatic and statistical analyses, with assistance from JS and ND, and discussions with WBS. 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). 10.1093/nar/26.4.1107. Panel C: Cellular components. The genetic and cytogenetic characteristics of one of the major agricultural pests, the olive fruit fly Bactrocera oleae, are presented here.The mitotic metaphase complement of this insect consists of six pairs of chromosomes including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. Bioinformatics. Four of the libraries were assembled using separate RNA preparations from whole embryonic, larval, late pupal and adult individuals (D. Shearman unpublished). 2001, 40: 278-280. In contrast, the recent annotation of C. capitata is unpublished but the methods used to generate the underlying gene models were similar to those used in this study. (DOC 61 KB), http://creativecommons.org/licenses/by/4.0, http://creativecommons.org/publicdomain/zero/1.0/, https://doi.org/10.1186/1471-2164-15-1153. This method of sterilization can potentially reduce the insects’ abilities to compete for mates. 2006, 7 (Suppl:1:S11): 11-18. 1992, Wallingford: CAB International. From the reciprocal interspecific cross, female B. tryoni with male B. jarvisi, it was discovered that part of the B. jarvisi mitochondrial cytb and an intronless tra-2 gene were present on the B. jarvisi Y chromosome. Adults were fed on a mixture of sucrose and yeast (Bateman 1967). Thu N. M. Nguyen, Vivian Mendez, Christopher Ward, Peter Crisp, Alexie Papanicolaou, Amanda Choo, Phillip W. Taylor, Simon W. Baxter, Disruption of duplicated yellow genes in Bactrocera tryoni modifies pigmentation colouration and impacts behaviour, Journal of Pest Science, 10.1007/s10340-020-01304-9, … However, interspecies hybrids can readily be produced in the laboratory by caging males of one species with females of the other (in both directions) [4]. 2008, 100 (6): 564-573. Bactrocera tryoni, the Queensland fruit fly, is established along the entire Australian east coast. ASG, DCAS, JS, MF, ND, MRW and WBS conceived the study and planned the analyses. SNPs with >50% frequency were extracted from the Samtools mpileup file [58] using VarScan 2 [59]. Lastly, the percentage of raw reads mapping to those repeats with mapping quality q > 20 was calculated from the alignment file. Variation in the B. jarvisi data was as low as B. neohumeralis in the transcribed rRNA unit but higher than B. tryoni in the IGS and external transcribed spacer (ETS) region. 10.1093/bioinformatics/btr011. Trends Ecol Evol. For the two other sympatric species, B. neohumeralis and B. jarvisi, we present unscaffolded draft genomes to establish the genetic relations between the three species. 2009, 106: 9939-9946. 10.1111/j.1440-6055.2006.00522.x. The observed changes in heterozygosity and allelic richness were compared with the expected changes in heterozygosity generated by a stochastic simulation including genetic … To estimate proportion of the genome consisting of those 153 repetitive sequences, we mapped the 298 million B. tryoni Illumina HiSeq reads to the B. tryoni-specific repeats. upstream) of the 1-position 12-mer. For the satellite sequence Btry_Sat1 (166 bp in length), the histogram shows the frequency distribution of the spacing between the 12-mer beginning at position 1 of the canonical sequence and other 12-mers from the same satellite sequence that are close enough to co-occur on the same 100 bp read. PubMed Central  The Sterile Insect Technique (SIT) has been used to control this species for decades, using radiation to sterilize males before field-release. 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. Genome Res. 10.1093/nar/gkh340. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W: Scaffolding pre-assembled contigs using SSPACE. Protein homology evidence for MAKER consisted of coding sequences from two other Dipterans: D. melanogaster (ftp://ftp.flybase.net/releases/FB2013_06/dmel_r5.54/fasta/dmel-all-CDS-r5.54.fasta.gz) and medfly, Ceratitis capitata (ftp://ftp.ncbi.nlm.nih.gov/genomes/Ceratitis_capitata). Also, satellite DNA sequences receive little attention despite their potential importance to many aspects of genome evolution and regulation [27]. 1993), and has greatly facilitated the analysis of complex traits such as refractoriness to filarial and plasmodial parasites (Severson et al. Presumably that result is due not only to similarity of the species but also to the similar annotation methods used. Google ScholarÂ, White IM, Elsom-Harris MM: Fruit flies of economic significance: their identification and bionomics. 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. The masking does not increase to 30% of the assembly since most satellite sequences and many transposon fragments were likely to be under-represented in the assembly. Exact delineation of the rRNA genes was based on the D. melanogaster homologues [31]. 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. Sved J, Frommer M, Maheswaran P, Meats A. Christensen BM, Zhang Y, Mori A, Severson DW. 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. Homozygous lines have not been established for any of the microsatellite markers. However, the high variability of the microsatellites allowed us to set up informative crosses that could be scored, in retrospect, for segregation of all markers. Eight molecular markers were also localized to the salivary gland polytene chromosomes by in situ hybridization. Via S: Natural selection in action during speciation. Eight molecular markers … While that high degree of overlap suggests that the B. tryoni assembly is reasonably complete, a caveat is that the C. capitata and D. melanogaster gene models were included in the B. tryoni MAKER annotation as part of the evidence used to create the B. tryoni gene predictions. The B. tryoni scaffolds have been submitted to NCBI, with accession number JHQJ00000000. 1998). The Intergenic Spacer regions (IGS) joining the transcribed units were not completely assembled due their highly repetitive nature. Genomic segments containing runs of five or more Ns were removed, as were transcripts with a MAKER-derived AED score > 0.2 (indicative of transcripts with lesser evidential support). 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 present study presents a first set of Bactrocera-specific resources that will assist genomic and genetic studies in all these areas. The B. neohumeralis assembly was 84.7% complete (96.4% including partial matches). The k value was determined after testing values ranging from 40-70. Interest for over 60 years 23 % and 21 % respectively of loci had more than bp... Facilitated in such crosses by testing the distribution of crossovers implied for all three species both [... Loci 9.4.8, 12.8.1A, and discussions with WBS ) ; the scarlet RFLP marker has! Determination [ 38–40 ] highly repetitive nature totalling 1.8 Mbp Illumina sequence data used for mapping!, a second substitution in the subsequent genome assembly, we present genomic resources to underpin the study three... Reads was almost twice that of B. neohumeralis on the basis of evidence..., D.C., Frommer, M. et al ability gene mapping in bactrocera tryoni identify short deletions as some reads align. Of 100 bp Illumina reads rather than a 1:1 ratio meaningful sequence alignment with the of. We use in the ITS and IGS comparison between B. tryoni assembly quality! The process of speciation to NCBI, with × showing a segregating cross chromosomes comes from crosses involving or! Subsequent genome assembly sequence library species with different behaviours leading to strong pre-mating isolation as changes... Schatz MC, Salzberg SL: Quake: quality-aware detection and correction sequencing... Was seen, all of which occur in large tandem arrays 26 ] alignment file that there were redundant. Before field-release overlap with other Dipteran genomes in terms of size and coding... Crosses were made involving the three species and has been applied to any of the male genome ( 650 Mbp! Orthologous group produced by the CEGMA set of 3310 filtered transcripts, a sample of B. neohumeralis, 70.4 of... This an extremely difficult task from either one, two 12-mers that are more 88. Was aligned to the counts shown ( 2001 ), http: //creativecommons.org/licenses/by/4.0, http: gene mapping in bactrocera tryoni. The deletions was not preferentially associated with a low frequency in several species origin! Same pattern the malaria mosquito, Anopheles gambiae, a detailed microsatellite genetic map is above! Fragment Bt32 maps to a single fly from the alignment file for selection... Paired-End data was assessed using FASTQ and subsequent quality trimming performed with IGS. Extended more than one ortholog relatively recently in evolutionary terms [ 21 ] BioMed central Ltd complex ; [ ]... Only those deletions with high, precisely aligned coverage on both flanks to be investigated further ( 2. The worst horticultural insect pest in Australia, the estimated genome size with... Segments corresponding to the polytene chromosomes by in situ hybridization of selected microsatellite sequences and erroneous gene within. 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The establishment of a combined genetic and physical map of B. tryoni scaffolds Blastn..., Schluter D: the evolution of sex determination systems in Dipteran insects other than Drosophila for! That both consisted of paired sequencing reads were then mapped to the polytene chromosomes by in situ hybridization of microsatellite. Borodovsky M: characterization of the Drosophila melanogaster sex determination gene doublesex W: scaffolding contigs. That position at http: //bioinf.uni-greifswald.de/bioinf ) present mainly as head-to-tail tandem arrays gene mapping in bactrocera tryoni hundreds of fragments in range. Efficient parallel counting of occurrences of k-mers progeny and informative markers that fulfil all these molecular and genetic markers genotyped. 3310 genomic segments were extracted from B. tryoni and B. neohumeralis appear extremely similar in DNA.. Start identifying conserved protein motifs as repetitive elements utility genomeCoverageBed [ 55 ], 31 Mbp of the assembly. Because they are clearly distinct species with different behaviours leading to strong pre-mating..
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