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The complete mitochondrial genome sequence of an annual wild tobacco Nicotiana attenuata.

ABSTRACT: Nicotiana attenuata (N. attenuata) is a species of wild tobacco, which is a predominant ecological model native to North America. Here, we first assembled the complete mitochondrial (mt) DNA sequence of N. attenuata into a circular genome of length 394,341?bp, including 40 protein-coding genes, 4 rRNA genes, and 23 tRNA genes. A neighbour-joining phylogenetic tree was constructed based on the complete mt genome of N. attenuata and other 27 plant species to assess their phylogenic relationship and evolution. The complete mt genome of N. attenuata would be useful for the further analyses of Nicotiana species.

SUBMITTER: Xu Y

PROVIDER: S-EPMC7799719 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome sequence of an annual wild tobacco Nicotiana attenuata.

Xu Yiqing Y Zhang Fuquan F Hu Kun K

Mitochondrial DNA. Part B, Resources 20171207 2

Nicotiana attenuata (N. attenuata) is a species of wild tobacco, which is a predominant ecological model native to North America. Here, we first assembled the complete mitochondrial (mt) DNA sequence of N. attenuata into a circular genome of length 394,341 bp, including 40 protein-coding genes, 4 rRNA genes, and 23 tRNA genes. A neighbour-joining phylogenetic tree was constructed based on the complete mt genome of N. attenuata and other 27 plant species to assess thei ...[more]

PMID: 33474038

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Project description:Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now.We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites.The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de/ .

Project description:BACKGROUND: The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY: DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS: For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.

Dataset Information

The complete mitochondrial genome sequence of an annual wild tobacco Nicotiana attenuata.

Publications

The complete mitochondrial genome sequence of an annual wild tobacco <i>Nicotiana attenuata</i>.

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