The Complete Mitochondrial Genome of <i>Gossypium hirsutum</i> and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

<div><p>Background</p><p>Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (<i>Gossypium hirsutum</i> L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes.</p><p>Methodology/Principal Findings</p><p>We utilized 454 technology for sequencing and combined with Fosmid library of the <i>Gossypium hirsutum</i> mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on <i>Cycas taitungensis</i> and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of <i>G. hirsutum</i> was obtained. The completed <i>G.hirsutum</i> mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes.</p><p>Conclusion</p><p>The <i>G. hirsutum</i> mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.</p>