The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications

Shen, Jinhui; Cong, Qian

doi:10.1016/j.mgene.2015.05.002

Cited by 21 publications

(22 citation statements)

References 97 publications

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“…The A+T-rich control region is most variable in sequence and length and contains several direct repeats of about 360 bp present in all six species. Among Hesperiidae with available mitogenomes 6, 10, 11, 13, 14, 17– 24 these repeats are unique to Megathymini. The repeats cause difficulty with mitogenome assembly and their number remains uncertain.…”

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Mitogenomes of Giant-Skipper Butterflies reveal an ancient split between deep and shallow root feeders

et al. 2017

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Background: Giant-Skipper butterflies from the genus Megathymus are North American endemics. These large and thick-bodied Skippers resemble moths and are unique in their life cycles. Grub-like at the later stages of development, caterpillars of these species feed and live inside yucca roots. Adults do not feed and are mostly local, not straying far from the patches of yucca plants. Methods: Pieces of muscle were dissected from the thorax of specimens and genomic DNA was extracted (also from the abdomen of a specimen collected nearly 60 years ago). Paired-end libraries were prepared and sequenced for 150bp from both ends. The mitogenomes were assembled from the reads followed by a manual gap-closing procedure and a phylogenetic tree was constructed using a maximum likelihood method from an alignment of the mitogenomes. Results: We determined mitogenome sequences of nominal subspecies of all five known species of Megathymus and Agathymus mariae to confidently root the phylogenetic tree. Pairwise sequence identity indicates the high similarity, ranging from 88-96% among coding regions for 13 proteins, 22 tRNAs and 2 rRNA, with a gene order typical for mitogenomes of Lepidoptera. Phylogenetic analysis confirms that Giant-Skippers (Megathymini) originate within the subfamily Hesperiinae and do not warrant a subfamily rank. Genus Megathymus is monophyletic and splits into two species groups. M. streckeri and M. cofaqui caterpillars feed deep in the main root system of yucca plants and deposit frass underground. M. ursus, M. beulahae and M. yuccae feed in the yucca caudex and roots near the ground, and deposit frass outside through a "tent" (a silk tube projecting from the center of yucca plant). M. yuccae and M. beulahae are sister species consistently with morphological similarities between them. Conclusions: We constructed the first DNA-based phylogeny of the genus Megathymus from their mitogenomes. The phylogeny agrees with morphological considerations.

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Mitogenomes of Giant-Skipper Butterflies reveal an ancient split between deep and shallow root feeders

et al. 2017

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“…We concerted our efforts to find real life biological projects where the utility of correctors is demonstrated by practical use. In contradiction to what we found in the articles accompanying each corrector, some real life projects use the correctors for additional applications like mithocondrial genome correction [139] and RNA-seq [140,141,142,143] [185] Hector/454 shall see in section "Testing", it has a good level of correction. As a general rule, Illumina data should be handled by Illumina-only correctors since they should be better tuned for the technology than their general counterparts.…”

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confidence: 66%

Improved Error Correction of NGS Data

Alic¹

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SummaryThe work done for this doctorate thesis focuses on error correction of Next Generation Sequencing (NGS) data in the context of High Performance Computing (HPC).Due to the reduction in sequencing cost, the increasing output of the sequencers and the advancements in the biological and medical sciences, the amount of NGS data has increased tremendously. Humans alone are not able to keep pace with this explosion of information, therefore computers must assist them to ease the handle of the deluge of information generated by the sequencing machines. Since NGS is no longer just a research topic (used in clinical routine to detect cancer mutations, for instance), requirements in performance and accuracy are more stringent. For sequencing to be useful outside research, the analysis software must work accurately and fast. This is where HPC comes into play. NGS processing tools should leverage the full potential of multi-core and even distributed computing, as those platforms are extensively available. Moreover, as the performance of the individual core has hit a barrier, current computing tendencies focus on adding more cores and explicitly split the computation to take advantage of them.This thesis starts with a deep analysis of all these problems in a general and comprehensive way (to reach out to a very wide audience), in the form of an exhaustive and objective review of the NGS error correction field. We dedicate a chapter to this topic to introduce the reader gradually and gently into the world of sequencing. It presents real problems and applications of NGS that demonstrate the impact this technology has on science. The review results in the following conclusions: the need of understanding of the specificities of NGS data samples (given the high variety of technologies and features) and the need of flexible, efficient and accurate tools for error correction as a preliminary step of any NGS postprocessing.As a result of the explosion of NGS data, we introduce MuffinInfo. It is a piece of software capable of extracting information from the raw data produced by the sequencer to help the user understand the data. MuffinInfo uses HTML5, therefore it runs in almost any software and hardware environment. It supports custom statistics to mould itself to specific requirements. MuffinInfo can reload the results of a run which are stored in JSON format for easier integration with third party applications. Finally, our application uses threads to perform the calculations, to load the data from the disk and to handle the UI.In continuation to our research and as a result of the single core performance limitation, we leverage the power of multi-core computers to develop a new error correction tool. The error correction of the NGS data is normally the first step of any analysis targeting NGS. As we conclude from the review performed within the frame of this thesis, many projects in different real-life applications have opted for this step before further analysis. In this sense, we propose MuffinEC, a multi-technology (Illu...

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“…To phylogenetically place Burara striata within Hesperiidae with available mitogenomes 7–9,12–14,21–25 , we constructed RAxML 26 maximum likelihood tree rooted with Pterourus glaucus (Papilionidae) mitogenome 12 (Fig 1b). The resulting tree topology is consistent with previous phylogenetic studies 4,5,25,27 : Coeliadinae are the sister to all other Hesperiidae; Euschemon is a sister to the rest of Hesperiidae except Coeliadinae; relationship between Eudaminae and Pyrginae is unresolved; and Heteropterinae are the sister to Hesperiinae.…”

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The complete mitochondrial genome of a skipper Burara striata (Lepidoptera: Hesperiidae)

Zhang

Cong

Shen

et al. 2017

Mitochondrial DNA Part B

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We assembled a complete mitogenome of an Asian skipper butterfly Burara striata (Hesperiidae, Coeliadinae), the first representative of the genus Burara, from next generation sequencing reads. The 15327 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A+T rich region. Its gene order is typical for mitogenomes of Lepidoptera. Phylogenetic analysis places Burara striata as a sister to Hasora, and Choaspes as a sister to both of these genera.

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The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications

Cited by 21 publications

References 97 publications

Mitogenomes of Giant-Skipper Butterflies reveal an ancient split between deep and shallow root feeders

Mitogenomes of Giant-Skipper Butterflies reveal an ancient split between deep and shallow root feeders

Improved Error Correction of NGS Data

The complete mitochondrial genome of a skipper Burara striata (Lepidoptera: Hesperiidae)

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