Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches

Abstract

Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp) genome sequences of G. raimondii are already available but not mitochondria. Here, we assembled the complete mitochondrial (mt) DNA sequence of G. raimondii into a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes. We also identified four larger repeats (63.9 kb, 10.6 kb, 9.1 kb, and 2.5 kb) in this mt genome, which may be active in intramolecular recombination in the evolution of cotton. Strikingly, nearly all of the G. raimondii mt genome has been transferred to nucleus on Chr1, and the transfer event must be very recent. Phylogenetic analysis reveals that G. raimondii, as a member of Malvaceae, is much closer to another cotton (G. barbadense) than other rosids, and the clade formed by two Gossypium species is sister to Brassicales. The G. raimondii mt genome may provide a crucial foundation for evolutionary analysis, molecular biology, and cytoplasmic male sterility in cotton and other higher plants.

Figure 1

The circular mitochondrial genome of G. raimondii. Genes shown outside of the circle are transcribed clockwise, whereas genes on the inside are transcribed counterclockwise. Genes belonging to different functional groups are color-coded. GC content is represented on the inner circle by the dark gray plot.

Figure 2

Frequency distribution of repeat lengths in the G. raimondii mt genome. The number of repeat lengths is shown by gray boxes, and the number represents the specific frequency of each repeat length.

Figure 3

Distribution of tRNA genes in higher plant mt genomes. Deep gray and light gray boxes indicate the number of cp-derived tRNAs and mt-native tRNAs, respectively.

Figure 4

K _a/K _s values of 36 protein-coding genes of G. raimondii, C. papaya, and P. tremula. Deep gray and light gray boxes indicate K _a/K _s ratio of C. papaya versus G. raimondii and P. tremula versus G. raimondii, respectively.

Figure 5

RNA-editing sites in the G. raimondii mt genome. Results are based on the PREP sites with the cut-off value of 0.6. The number of RNA-editing sites of each gene is shown by gray boxes.

Figure 6

Maximum likelihood tree based on 23 conserved protein-coding genes of 30 representative higher plant mt genomes. Numbers on each node are bootstrap support values. Marchantia polymorpha was used as outgroup. The yellow, red, blue, green, and baby blue circles represent the asterid, rosid, monocot, Gymnospermae, and Bryophyta classes, respectively. The black circle indicated G. raimondii, belonging to rosids.