33 research outputs found

    Structure of the intergenic spacers in chicken ribosomal DNA

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    International audienceAbstractBackgroundRibosomal DNA (rDNA) repeats are situated in the nucleolus organizer regions (NOR) of chromosomes and transcribed into rRNA for ribosome biogenesis. Thus, they are an essential component of eukaryotic genomes. rDNA repeat units consist of rRNA gene clusters that are transcribed into single pre-rRNA molecules, each separated by intergenic spacers (IGS) that contain regulatory elements for rRNA gene cluster transcription. Because of their high repeat content, rDNA sequences are usually absent from genome assemblies. In this work, we used the long-read sequencing technology to describe the chicken IGS and fill the knowledge gap on rDNA sequences of one of the key domesticated animals.MethodsWe used the long-read PacBio RSII technique to sequence the BAC clone WAG137G04 (Wageningen BAC library) known to contain chicken NOR elements and the HGAP workflow software suit to assemble the PacBio RSII reads. Whole-genome sequence contigs homologous to the chicken rDNA repetitive unit were identified based on the Gallus_gallus-5.0 assembly with BLAST. We used the Geneious 9.0.5 and Mega software, maximum likelihood method and Chickspress project for sequence evolution analysis, phylogenetic tree construction and analysis of the raw transcriptome data.ResultsThree complete IGS sequences in the White Leghorn chicken genome and one IGS sequence in the red junglefowl contig AADN04001305.1 (Gallus_gallus-5.0) were detected. They had various lengths and contained three groups of tandem repeats (some of them being very GC rich) that form highly organized arrays. Initiation and termination sites of rDNA transcription were located within small and large unique regions (SUR and LUR), respectively. No functionally significant sites were detected within the tandem repeat sequences.ConclusionsDue to the highly organized GC-rich repeats, the structure of the chicken IGS differs from that of IGS in human, apes, Xenopus or fish rDNA. However, the chicken IGS shares some molecular organization features with that of the turtles, which are other representatives of the Sauropsida clade that includes birds and reptiles. Our current results on the structure of chicken IGS together with the previously reported ribosomal gene cluster sequence provide sufficient data to consider that the complete chicken rDNA sequence is assembled with confidence in terms of molecular DNA organization

    Radioactive 26Al and massive stars in the Galaxy

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    Gamma-rays from radioactive 26Al (half life ~7.2 10^5 yr) provide a 'snapshot' view of ongoing nucleosynthesis in the Galaxy. The Galaxy is relatively transparent to such gamma-rays, and emission has been found concentrated along the plane of the Galaxy. This led to the conclusion1 that massive stars throughout the Galaxy dominate the production of 26Al. On the other hand, meteoritic data show locally-produced 26Al, perhaps from spallation reactions in the protosolar disk. Furthermore, prominent gamma-ray emission from the Cygnus region suggests that a substantial fraction of Galactic 26Al could originate in localized star-forming regions. Here we report high spectral resolution measurements of 26Al emission at 1808.65 keV, which demonstrate that the 26Al source regions corotate with the Galaxy, supporting its Galaxy-wide origin. We determine a present-day equilibrium mass of 2.8 (+/-0.8) M_sol of 26Al. We use this to estimate that the frequency of core collapse (i.e. type Ib/c and type II) supernovae to be 1.9(+/- 1.1) events per century.Comment: accepted for publication in Nature, 24 pages including Online Supplements, 11 figures, 1 tabl

    DNA metabarcoding, an efficient way to detect non-native cerambycid beetles in trapping collections?

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    Individual sorting and identification of thousands of insects collected in mass trapping biosurveillance programs is a labor intensive and time-consuming process. Metabarcoding, which allows for the simultaneous identification of multiple individuals in a single mixed sample, has the potential to expedite this process. However, detecting all the species present in a bulk sample can be challenging, especially when under-represented non-native specimens were intercepted. In this study, we quantified the effectiveness of metabarcoding at detecting exotic species within six different mock communities including or not native and non-native species of European xylophagous cerambycid beetles. Although we did not observe significant differences in the total number of species detected between MinION, Illumina, and IonTorrent sequencing technologies, a greater number of individuals was detected and identified to species using MinION, including the detection of three non-native cerambycids. The three sequencing technologies also showed similar results in detecting and identifying closely related species and species at low abundance. The capture method appears to greatly influence sample preservation and detection. Indeed, individuals captured in traps containing monopropylene and water had both lower DNA concentration leading to lower species detection rates compared to individuals killed using just an insecticide without any collection medium

    DNA metabarcoding, an efficient way to detect non-native cerambycid beetles in trapping collections?

    No full text
    Individual sorting and identification of thousands of insects collected in mass trapping biosurveillance programs is a labour intensive and time-consuming process. Metabarcoding, allows for the simultaneous identification of multiple individuals in a single mixed sample and has the potential to expedite this process. However, detecting all the species present in a bulk sample can be challenging, especially when under-represented non-native specimens are intercepted. In this study, we quantified the effectiveness of DNA metabarcoding at detecting exotic species within six different mock communities of native and non-native species of European xylophagous cerambycid beetles. The main objective is to compare three different sequencing technologies (MinION, Illumina, and IonTorrent) to evaluate which one is the most suitable in this context. Although we did not observe significant differences in the total number of species detected between the three sequencing technologies, MinION detected a greater number of species on field-like samples. All three sequencing technologies achieved in detecting and identifying closely related species and species at low abundance. The capture method of insects in the field greatly influences sample preservation and detection. Individuals captured in traps containing monopropylene and water had lower DNA concentration, leading to lower species detection rates compared to individuals killed using just an insecticide without any collection medium

    Molecular biosurveillance of wood-boring cerambycid beetles using DNA metabarcoding

    No full text
    Individual sorting and identification of thousands of insects collected in mass trapping biosurveillance programs is a labor intensive and time-consuming process. Metabarcoding, which allows for the simultaneous identification of multiple individuals in a single mixed sample, has the potential to expedite this process. However, detecting all the species present in a bulk sample can be challenging. In this study, we quantified the effectiveness of metabarcoding at detecting all species in six different mock communities of xylophagous cerambycid beetles. No significant differences in the number of species detected were observed between MinION, Illumina, and IonTorrent sequencing technologies. However, a greater number of individuals was detected and identified to species using MinION. In addition, the proportion of reads assigned to the species level was higher with Illumina technology. The three sequencing technologies also showed similar results in detecting and identifying closely related species and species at low abundance. The capture method greatly influences sample preservation and detection. Indeed, individuals captured using monopropylene and water had both lower DNA concentration and species detection rates compared to individuals killed using just an insecticide without any collection medium
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