Complete mitochondrial genome sequence of the “copper moss” Mielichhoferia elongata reveals independent nad7 gene functionality loss
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Author and article information
Abstract
The mitochondrial genome of moss Mielichhoferia elongata has been sequenced and assembled with Spades genome assembler. It consists of 100,342 base pairs and has practically the same gene set and its order as in other known bryophyte chondriomes. The genome contains 66 genes including three rRNAs, 24 tRNAs, and 40 conserved mitochondrial proteins genes. Unlike the majority of previously sequenced bryophyte mitogenomes, it lacks the functional nad7 gene. The phylogenetic reconstruction and scrutiny analysis of the primary structure of nad7 gene carried out in this study suggest its independent pseudogenization in different bryophyte lineages. Evaluation of the microsatellite (simple sequence repeat) content of the Mielichhoferia elongata mitochondrial genome indicates that it could be used as a tool in further studies as a phylogenetic marker. The strongly supported phylogenetic tree presented here, derived from 31 protein coding sequences of 40 bryophyte species is consistent with other reconstructions based on a number of different data sets.
Cite this as
2018. Complete mitochondrial genome sequence of the “copper moss” Mielichhoferia elongata reveals independent nad7 gene functionality loss. PeerJ Preprints 6:e3465v2 https://doi.org/10.7287/peerj.preprints.3465v2note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This version takes into account all the remarks and corrections made by reviewers. The INTRODUCTION was improved, the main ideas, motivations, and context are more clearly communicated. The information regarding the life style/cycle of mosses, the general features and the current research progress in the mitochondrial genome of mosses were provided. The phrases about heavy metals tolerance mechanisms as a goal of a study were excluded. We excluded also phrases in INTRODUCTION and DISCUSSION about possible involvement of mitochondrial genome features in heavy metal tolerance. The information about nad7 gene function was added. The data about sample preparation and DNA isolation were provided. A number of CDS was corrected and a new list of them is inserted. All figures were redrawn and a new reference and an acknowledgment were added in this connection. One more grant was added in the Declaration. The manuscript was reviewed by Academic English Language Editing services and some typos were corrected.
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Supplemental Information
Mitogenome map of M. elongata (MF417767)
The phylogenetic tree based on nuclear rDNA region (5.8S rDNA - ITS 2 - 5‘-end of 26S rDNA). The alignment consists of 440 positions. The tree reconstruction was conducted in TREECON software (Van de Peer & De Wachter, 1994) using the Neighbor-Joining method (Saitou & Nei 1987) with 500 bootstrap replications. Bootstrap support values >50% are shown next to the branches. The evolutionary distances were computed using the Kimura method (1980) with gaps taken into account as it implemented in the TREECON package.
The alignment of nad7 genes from nine moss species
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Denis V Goruynov analyzed the data, wrote the paper, prepared figures and/or tables.
Svetlana V Goryunova analyzed the data, wrote the paper, reviewed drafts of the paper.
Oxana I Kuznetsova performed the experiments.
Maria D Logacheva conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools.
Irina A Milyutina performed the experiments, analyzed the data.
Alina V Fedorova performed the experiments.
Michael S Ignatov reviewed drafts of the paper, plants collection and identification.
Aleksey V Troitsky conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
The Mielichhoferia elongata mitochondrial genome sequence described here is accessible via GenBank accession number MF417767. According to standard practice, this number would be open to public immediately after paper publication.
Data Deposition
The following information was supplied regarding data availability:
The raw data has been uploaded as a Supplemental File.
Funding
This work was supported by the Russian Foundation for Basic Research (No 15-04-06027, and No15-04-06116). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
