A Complete Sequence and Transcriptomic Analyses of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome

University of Veterinary Medicine Hanover, Germany
PLoS ONE (Impact Factor: 3.23). 05/2012; 7(5):e37164. DOI: 10.1371/journal.pone.0037164
Source: PubMed


Based on next-generation sequencing data, we assembled the mitochondrial (mt) genome of date palm (Phoenix dactylifera L.) into a circular molecule of 715,001 bp in length. The mt genome of P. dactylifera encodes 38 proteins, 30 tRNAs, and 3 ribosomal RNAs, which constitute a gene content of 6.5% (46,770 bp) over the full length. The rest, 93.5% of the genome sequence, is comprised of cp (chloroplast)-derived (10.3% with respect to the whole genome length) and non-coding sequences. In the non-coding regions, there are 0.33% tandem and 2.3% long repeats. Our transcriptomic data from eight tissues (root, seed, bud, fruit, green leaf, yellow leaf, female flower, and male flower) showed higher gene expression levels in male flower, root, bud, and female flower, as compared to four other tissues. We identified 120 potential SNPs among three date palm cultivars (Khalas, Fahal, and Sukry), and successfully found seven SNPs in the coding sequences. A phylogenetic analysis, based on 22 conserved genes of 15 representative plant mitochondria, showed that P. dactylifera positions at the root of all sequenced monocot mt genomes. In addition, consistent with previous discoveries, there are three co-transcribed gene clusters-18S-5S rRNA, rps3-rpl16 and nad3-rps12-in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms.

    • "Extensive variation has been reported from the mt genome of the resurrection fern, Boea hygrometrica, relative to a complete absence of polymorphic sites across the cp genome (Zhang et al., 2012a,b). Similarly, much higher rates of polymorphism were recovered in the mt compared to the cp genomes for various cultivars of date palm (Yang et al., 2010;Fang et al., 2012). Mosses have notably conserved mt genomes in terms of gene order across the macroevolutionary tree of life (Liu et al., 2014). "
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    ABSTRACT: Bryophytes (mosses, liverworts, and hornworts) are diverse and ecologically and evolutionarily significant yet genomic scale data sets and analyses remain extremely sparse relative to other groups of plants, and are completely lacking at the infraspecific level. By sequencing the complete organellar genomes and nuclear ribosomal repeat from seven patches of a South American sub-Antarctic neo-endemic non-model moss, we present the first characterization of infraspecific polymorphism within and across the three genomic compartments for a bryophyte. Diversity within patches is accounted for by both intraindividual and interindividual variation for the nuclear ribosomal repeat and plastid genome, respectively. This represents the most extensive infraspecific genomic dataset generated for an early land plant lineage thus far and provides insight into relative rates of substitution between organellar genomes, including high rates of nonsynonymous to synonymous substitutions.
    No preview · Article · Dec 2015 · Molecular Phylogenetics and Evolution
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    • "It is as small as 6 kb in the Apicomplexan parasite Plasmodium [15], but reaches over 11 Mb in some Silene plant lineages [16]. In model and crop plant species the mtDNA is in the range of 200e700 kb, containing less than 60 known genes for proteins, transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) [17] [18] (Fig. 1). Besides identified genes, part of which include introns, the plant mtDNA contains stretches of sequences of nuclear or plastid origin, whereas more than half of its content is of unidentified origin and function. "
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    ABSTRACT: Originally focused on the nuclear and cytosolic compartments, the concept of regulation driven by non-coding RNAs (ncRNAs) is extending to mitochondria and chloroplasts. These organelles have distinct genetic systems that need coordination with cellular demands. In mammals, nuclear-encoded microRNAs were found associated with the mitochondria. Some of these contribute to the regulation of mitochondrial transcription and translation. Others were proposed to be stored in the organelles and to be released for regulation of nuclear transcripts. Further ncRNAs of various sizes derive from the mitochondrial genome and it was speculated that organelles host antisense or RNA interference pathways. Long ncRNAs mapping to the mitochondrial DNA seem to operate in the nucleus. Altogether, the origin and trafficking of ncRNAs categorized as mitochondrial in mammals raise questions far beyond the current knowledge. In protozoa, hundreds of guide RNAs specify editing events needed to generate functional messenger RNAs. Only few ncRNAs have been reported in plant mitochondria, but editing sites were revealed in non-coding regions of the organellar genome, suggesting that the corresponding transcripts have a function. Conversely, numerous ncRNA candidates were identified in chloroplasts, essentially mapping to the plastid genome. A synthetic view of the data with their functional implications is given here. Copyright © 2015. Published by Elsevier B.V.
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    • "The substitution matrix estimated from mtpt sequences (table 2) predicts an equilibrium GC content that is substantially higher than observed values at synonymous sites of mitochondrial genes but right in line with values from intergenic regions. This finding is supported by the observation that older mtpts have higher GC content (Fang et al. 2012), indicating that substitution biases bring the nucleotide composition of horizontally transferred sequences into balance with the rest of their new host genome over time (Lawrence and Ochman 1997). Therefore, our results suggest that selection on synonymous substitutions is strong enough to substantially alter nucleotide composition in mitochondrial protein genes. "
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    ABSTRACT: Angiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of non-adaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA (mtpts). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred since their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew towards nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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