Dataset Information

The mitochondrial genome of Atrocalopteryx melli Ris, 1912 (Zygoptera: Calopterygidae) via Ion Torrent PGM NGS sequencing.

ABSTRACT: The mitochondrial genome of Atrocalopteryx melli was sequenced and assembled via Next-Generation Sequencing (NGS) and iteratively assembly process with a reference seed. This genome is 15,562?bp long and A?+?T biased (71%), with 37 genes arranged in common order of Odonata. All protein-coding genes are initiated by typical "ATN" codon, and 9 genes are terminated with a complete stop codon, except nad4, nad5, cox2, and cox3, which are terminated with an incomplete codon "T(aa)". The S5 intergenic spacer is absent in this genome, supporting that lacking of S5 as a specific character for damselflies. The A?+?T rich region of A. melli is 267?bp longer than that of A. atrata. This mitogenome provides new molecular information for understanding of A. melli and Atrocalopteryx.

SUBMITTER: Xu S

PROVIDER: S-EPMC7800031 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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The mitochondrial genome of <i>Atrocalopteryx melli</i> Ris, 1912 (Zygoptera: Calopterygidae) via Ion Torrent PGM NGS sequencing.

Xu Shaolin S Guan Zhaoying Z Huang Qi Q Xu Lei L Vierstraete Andy A Dumont Henri J HJ Lin Qiuqi Q

Mitochondrial DNA. Part B, Resources 20180111 1

The mitochondrial genome of <i>Atrocalopteryx melli</i> was sequenced and assembled via Next-Generation Sequencing (NGS) and iteratively assembly process with a reference seed. This genome is 15,562 bp long and A + T biased (71%), with 37 genes arranged in common order of Odonata. All protein-coding genes are initiated by typical "ATN" codon, and 9 genes are terminated with a complete stop codon, except nad4, nad5, cox2, and cox3, which are terminated with an incomplete codon "T(aa)". The S5 int ...[more]

PMID: 33474087

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Project description:BackgroundMassively parallel sequencing (MPS) technologies have the capacity to sequence targeted regions or whole genomes of multiple nucleic acid samples with high coverage by sequencing millions of DNA fragments simultaneously. Compared with Sanger sequencing, MPS also can reduce labor and cost on a per nucleotide basis and indeed on a per sample basis. In this study, whole genomes of human mitochondria (mtGenome) were sequenced on the Personal Genome Machine (PGMTM) (Life Technologies, San Francisco, CA), the out data were assessed, and the results were compared with data previously generated on the MiSeqTM (Illumina, San Diego, CA). The objectives of this paper were to determine the feasibility, accuracy, and reliability of sequence data obtained from the PGM.Results24 samples were multiplexed (in groups of six) and sequenced on the at least 10 megabase throughput 314 chip. The depth of coverage pattern was similar among all 24 samples; however the coverage across the genome varied. For strand bias, the average ratio of coverage between the forward and reverse strands at each nucleotide position indicated that two-thirds of the positions of the genome had ratios that were greater than 0.5. A few sites had more extreme strand bias. Another observation was that 156 positions had a false deletion rate greater than 0.15 in one or more individuals. There were 31-98 (SNP) mtGenome variants observed per sample for the 24 samples analyzed. The total 1237 (SNP) variants were concordant between the results from the PGM and MiSeq. The quality scores for haplogroup assignment for all 24 samples ranged between 88.8%-100%.ConclusionsIn this study, mtDNA sequence data generated from the PGM were analyzed and the output evaluated. Depth of coverage variation and strand bias were identified but generally were infrequent and did not impact reliability of variant calls. Multiplexing of samples was demonstrated which can improve throughput and reduce cost per sample analyzed. Overall, the results of this study, based on orthogonal concordance testing and phylogenetic scrutiny, supported that whole mtGenome sequence data with high accuracy can be obtained using the PGM platform.

Project description:The emergence of benchtop sequencers has made clinical genetic testing using next-generation sequencing more feasible. Ion Torrent's PGM™ is one such benchtop sequencer that shows clinical promise in detecting single nucleotide variations (SNVs) and microindel variations (indels). However, the large number of false positive indels caused by the high frequency of homopolymer sequencing errors has impeded PGM™'s usage for clinical genetic testing. An extensive analysis of PGM™ data from the sequencing reads of the well-characterized genome of the Escherichia coli DH10B strain and sequences of the BRCA1 and BRCA2 genes from six germline samples was done. Three commonly used variant detection tools, SAMtools, Dindel, and GATK's Unified Genotyper, all had substantial false positive rates for indels. By incorporating filters on two major measures we could dramatically improve false positive rates without sacrificing sensitivity. The two measures were: B-Allele Frequency (BAF) and VARiation of the Width of gaps and inserts (VARW) per indel position. A BAF threshold applied to indels detected by UnifiedGenotyper removed ~99% of the indel errors detected in both the DH10B and BRCA sequences. The optimum BAF threshold for BRCA sequences was determined by requiring 100% detection sensitivity and minimum false discovery rate, using variants detected from Sanger sequencing as reference. This resulted in 15 indel errors remaining, of which 7 indel errors were removed by selecting a VARW threshold of zero. VARW specific errors increased in frequency with higher read depth in the BRCA datasets, suggesting that homopolymer-associated indel errors cannot be reduced by increasing the depth of coverage. Thus, using a VARW threshold is likely to be important in reducing indel errors from data with higher coverage. In conclusion, BAF and VARW thresholds provide simple and effective filtering criteria that can improve the specificity of indel detection in PGM™ data without compromising sensitivity.

Dataset Information

The mitochondrial genome of Atrocalopteryx melli Ris, 1912 (Zygoptera: Calopterygidae) via Ion Torrent PGM NGS sequencing.

Publications

The mitochondrial genome of <i>Atrocalopteryx melli</i> Ris, 1912 (Zygoptera: Calopterygidae) via Ion Torrent PGM NGS sequencing.

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