ORIGINAL ARTICLE Evolution of mitochondrial gene content: loss of genes, tRNAs and introns between Gossypium harknessii and other plants Binbin Lei • Shuangshuang Li • Guozheng Liu • Zhiwen Chen • Aiguo Su • Pengbo Li • Zhaohu Li • Jinping Hua Received: 29 April 2012 / Accepted: 11 May 2013 Ó Springer-Verlag Wien 2013 Abstract Mitochondrion is a kind of cell organelle known as the engine house of the cells in the performance of the production of energy in the form of ATP, and the regulation of cellular metabolism in programmed cell death. Plant mitochondria are involved in the formation of cytoplasm male sterility and the mechanism of restoration. Its genomes offer useful information in analysis of the evolution dynamics. The mitogenomes (mitochondrial genomes) of 2074A, a cytoplasmic male sterile line of Gossypium harknessii cytoplasm, was sequenced by Solexa strategy and assembled by SOAP de novo. Combined with public data, the sequences of nine mitochondrial functional genes in 20 taxa were used to reconstruct phylogenetic trees and further to demonstrate the variations of mitoge- nomes in higher plants. The sequence size, genome com- position, and the number of genes varied in mitogenomes, while the genes related to oxidative respiratory chain remain conserved. In examined mitogenomes, the number of protein-coding genes of higher plants varied from 24 to 42. And gene conservatism was quite different. Gene gain or loss entirely existed widely; genes insertion and loss of intron (s), and some altered as pseudogenes were checked; loss of tRNAs and insertion of cp-DNA transferring hap- pened frequently; and syntenic gene clusters were found. More than 50 % of intergenic regions were mainly accu- mulated by repeats and non-coding sequences. The variable mitogenomes existed conservatism, but it demonstrated that the linear relationship was not parallel to that in mi- togenomes of different species in evolution. The mitoge- nome of 2074A harbored 56 functional genes and changed quite a lot in sequences, while there were a few linear gene clusters and conserved flanking sequences of functional genes. Generally, the information was helpful for under- standing the results in mitogenome evolution. Keywords Mitogenome Á Evolution Á Gene loss Á Conservatism Á Gossypium harknessii Introduction The mitochondria and chloroplast are both maternal inheritance organelles in angiosperms, while it is different in gymnosperms (such as coniferous) (Zhong et al. 2011). Mitochondria, the morphologically distinctive semiauton- omous organelle with double-member of eukaryotes, served as manufacturers of cellular ATP during oxidative phosphorylation. Plant mitogenome has been characterized in low rate of point evolution (Palmer et al. 2000), high rates of rearrangement, genome growth, and shrinkage (Hao and Palmer 2009), and foreign DNA incorporation (Rice and Palmer 2006; Liu et al. 2011). Along with the development and application of next-sequencing technol- ogy, so far there are 63 mitogenomes of plant released in NCBI database (Fujii et al. 2010; Rodriguez-Moreno et al. 2011; Davila et al. 2011; Ma et al. 2012), which contained 25 eudicots, 11 momocots, and other land plants, such as B. Lei and S. Li contributed equally to this work. Electronic supplementary material The online version of this article (doi:10.1007/s00606-013-0845-3) contains supplementary material, which is available to authorized users. B. Lei Á S. Li Á G. Liu Á Z. Chen Á A. Su Á P. Li Á Z. Li Á J. Hua (&) College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, People’s Republic of China e-mail: jinping_hua@cau.edu.cn 123 Plant Syst Evol DOI 10.1007/s00606-013-0845-3