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.

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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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    Biochimie 07/2015; 117. DOI:10.1016/j.biochi.2015.06.027 · 2.96 Impact Factor
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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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    Genome Biology and Evolution 11/2014; 6(12). DOI:10.1093/gbe/evu253 · 4.23 Impact Factor
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    • "dactylifera was not included because individual gene expression levels were not reported) showed a weak correlation among species (Supplementary Fig. 4), suggesting that the transcriptional regulation of plant mitogenomes has evolved via lineage-specific diversification of an ancestral pattern. Although none of these studies used biological replicates, the consistency of results between tissues and treatments from P. pinnata (Supplementary Fig. 5) and P. dactylifera (see Fig. S2 in Fang et al., 2012) suggests that the variance detected by deep transcriptome sequencing is biological rather than methodological in nature. "
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