Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants

Xiaofang Liao,Yanhong Zhao,Dongmei Liu,Hong Wang,Peng Chen,Bujin Zhou,Xiangjun Kong,Muhammad Haneef Kashif,Ruiyang Zhou,Aziz Khan

doi:10.1038/s41598-018-30297-w

Xiaofang Liao, Yanhong Zhao + Show 8 more

Open Access

https://doi.org/10.1038/s41598-018-30297-w

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Abstract

Plant mitochondrial (mt) genomes are species specific due to the vast of foreign DNA migration and frequent recombination of repeated sequences. Sequencing of the mt genome of kenaf (Hibiscus cannabinus) is essential for elucidating its evolutionary characteristics. In the present study, single-molecule real-time sequencing technology (SMRT) was used to sequence the complete mt genome of kenaf. Results showed that the complete kenaf mt genome was 569,915 bp long and consisted of 62 genes, including 36 protein-coding, 3 rRNA and 23 tRNA genes. Twenty-five introns were found among nine of the 36 protein-coding genes, and five introns were trans-spliced. A comparative analysis with other plant mt genomes showed that four syntenic gene clusters were conserved in all plant mtDNAs. Fifteen chloroplast-derived fragments were strongly associated with mt genes, including the intact sequences of the chloroplast genes psaA, ndhB and rps7. According to the plant mt genome evolution analysis, some ribosomal protein genes and succinate dehydrogenase genes were frequently lost during the evolution of angiosperms. Our data suggest that the kenaf mt genome retained evolutionarily conserved characteristics. Overall, the complete sequencing of the kenaf mt genome provides additional information and enhances our better understanding of mt genomic evolution across angiosperms.

Highlights

Mitochondria are the main organelles responsible for plant energy metabolism and play an imperative role in supplying ATP via oxidative phosphorylation during development, reproduction and various biochemical processes in plants
The structure of first the complete kenaf mt genome sequence was determined, and phylogenetic analyses were performed for comparisons with angiosperm mt genomes
Despite the large size differences among the mt genomes of various higher plant species, these genomes share a similar set of functional genes, which is consistent with the results reported by Mower et al.[27]

Summary

Introduction

Mitochondria are the main organelles responsible for plant energy metabolism and play an imperative role in supplying ATP via oxidative phosphorylation during development, reproduction and various biochemical processes in plants. The noncoding regions vary and exhibit low conservation across species, which renders the sequencing of plant mt genomes, in angiosperms, extraordinarily difficult. Despite the great variation in size and physical mapping properties, plant mitochondria exhibit significant conservation in functional genes, including 37–83 protein coding, tRNA and rRNA genes[21]. The shuffling of mtDNA sequences by recombination, repeat sequences and most noncoding sequences plays an important role in mt genome evolution by changing the gene organization and creating chimeric genes[22,23]. In most plant mt genomes, many homologous sequences are derived from the chloroplasts and nucleus[6,9]. Horizontal gene (or DNA) transfers appear to be responsible for the integration of exogenous DNA and explain the complex structure of angiosperm mt genomes[24,25]. Our data provide basic information and a better understanding of the evolutionary processes of kenaf mt genome

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