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• W2955502307 abstract "Pyrococcus furiosus DSM 3638 is a model organism for hyperthermophilic archaea with an optimal growth temperature near 100 °C. The genome was sequenced about 18 years ago. Recent publications suggest that in contrast to other Pyrococcus species, the genome of P. furiosus DSM 3638 is prone to genomic rearrangements. Therefore, we re-sequenced the genome using third generation sequencing techniques. The new de novo assembled genome is 1,889,914 bp in size and exhibits high sequence identity to the published sequence. However, two major deviations were detected: (1) The genome is 18,342 bp smaller than the NCBI reference genome due to a recently described deletion. (2) The region between PF0349 and PF0388 is inverted most likely due an assembly problem for the original sequence. In addition, numerous minor variations, ranging from single nucleotide exchanges, deletions or insertions were identified. The total number of insertion sequence (IS) elements is also reduced from 30 to 24 in the new sequence. Re-sequencing of a two-year-old “lab culture” using Nanopore sequencing confirmed the overall stability of the P. furiosus DSM 3638 genome even under normal lab conditions without taking any special care. To improve genome annotation, the updated DNA sequence was combined with an RNA sequencing approach. Here, RNAs from eight different growth conditions were pooled to increase the number of detected transcripts. Furthermore, a differential RNA-Seq approach was employed for the identification of transcription start sites (TSSs). In total, 2515 TSSs were detected and classified into 834 primary (pTSS), 797 antisense (aTSS), 739 internal and 145 secondary TSSs. Our analysis of the upstream regions revealed a well conserved archaeal promoter structure. Interrogation of the distances between pTSSs and aTSSs revealed a significant number of antisense transcripts, which are a result of bidirectional transcription from the same TATA box. This mechanism of antisense transcript production could be further confirmed by in vitro transcription experiments. We assume that bidirectional transcription gives rise to non-functional antisense RNAs and that this is a widespread phenomenon in archaea due to the architecture of the TATA element and the symmetric structure of the TATA-binding protein." @default.
• W2955502307 created "2019-07-12" @default.
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• W2955502307 date "2019-07-12" @default.
• W2955502307 modified "2023-10-17" @default.
• W2955502307 title "Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the Pyrococcus furiosus DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription" @default.
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• W2955502307 cites W1968199899 @default.
• W2955502307 cites W1980484671 @default.
• W2955502307 cites W1985886752 @default.
• W2955502307 cites W1988784578 @default.
• W2955502307 cites W1992223935 @default.
• W2955502307 cites W1992987210 @default.
• W2955502307 cites W2003188984 @default.
• W2955502307 cites W2004494938 @default.
• W2955502307 cites W2011780260 @default.
• W2955502307 cites W2021341670 @default.
• W2955502307 cites W2025889710 @default.
• W2955502307 cites W2055559156 @default.
• W2955502307 cites W2062896692 @default.
• W2955502307 cites W2072084446 @default.
• W2955502307 cites W2074053727 @default.
• W2955502307 cites W2074471151 @default.
• W2955502307 cites W2084618810 @default.
• W2955502307 cites W2095297536 @default.
• W2955502307 cites W2103441770 @default.
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• W2955502307 cites W2110753148 @default.
• W2955502307 cites W2111766142 @default.
• W2955502307 cites W2111918410 @default.
• W2955502307 cites W2113943239 @default.
• W2955502307 cites W2117885750 @default.
• W2955502307 cites W2121139063 @default.
• W2955502307 cites W2131271579 @default.
• W2955502307 cites W2134840548 @default.
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• W2955502307 cites W2139544568 @default.
• W2955502307 cites W2139762065 @default.
• W2955502307 cites W2139898631 @default.
• W2955502307 cites W2147797592 @default.
• W2955502307 cites W2151605074 @default.
• W2955502307 cites W2153992812 @default.
• W2955502307 cites W2155943701 @default.
• W2955502307 cites W2157009395 @default.
• W2955502307 cites W2160121221 @default.
• W2955502307 cites W2162900837 @default.
• W2955502307 cites W2166200063 @default.
• W2955502307 cites W2169456326 @default.
• W2955502307 cites W2171445712 @default.
• W2955502307 cites W2172232888 @default.
• W2955502307 cites W2195724570 @default.
• W2955502307 cites W2229252416 @default.
• W2955502307 cites W2254859047 @default.
• W2955502307 cites W2296941811 @default.
• W2955502307 cites W2371465739 @default.
• W2955502307 cites W2470052926 @default.
• W2955502307 cites W2513021116 @default.
• W2955502307 cites W2589372192 @default.
• W2955502307 cites W2591367881 @default.
• W2955502307 cites W2594270742 @default.
• W2955502307 cites W2726242383 @default.
• W2955502307 cites W2726257503 @default.
• W2955502307 cites W2737196618 @default.
• W2955502307 cites W2742189960 @default.
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• W2955502307 doi "https://doi.org/10.3389/fmicb.2019.01603" @default.
• W2955502307 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6640164" @default.
• W2955502307 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/31354685" @default.
• W2955502307 hasPublicationYear "2019" @default.
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