http://orcid.org/0000-0001-5665-9312
Abstract
The complete mitogenome of Saccharum spp. hybrid ROC22 (a modern sugarcane cultivar) was sequenced and analyzed in the present study. Our results revealed that, unlike most plants, the complete mitogenome of sugarcane contains two distinct circular chromosomes, Chromosome 1 and Chromosome 2. The length of Chromosome 1 is 300,837 bp with the GC content of 43.93%, and the length of Chromosome 2 is 144,755 bp with the GC content of 43.57%. Apart from 16 tRNAs and six rRNAs non-coding genes, there are 20 protein-coding genes in Chromosome 1, including six nad genes, four rps genes, three atp genes, three ccm genes, two cox genes, one mat gene and one mtt gene. Chromosome 2 contains 18 genes, including five tRNA genes and 13 protein-coding genes (four nad genes, three rps genes, two atp genes, one ccm gene, one cob gene, one cox gene and one rpl gene). Phylogenetic analysis indicated that Saccharum spp. hybrid ROC22 is close with Saccharum officinarum Khon Kaen 3 and Sorghum bicolor species.
Sugarcane (Saccharum spp. hybrids) is the most important sugar-producing crop and raw biofuel material in the world (Zhou et al. Citation2018), which belongs to the grass family Gramineae. The major commercial sugarcane cultivars are all complex interspecies hybrids with allopolyploidy and aneuploidy with a huge genome (Zhou et al. Citation2014; Garsmeur et al. Citation2018). ROC22 (a Saccharum spp. hybrid from ROC5 × 69–463) is the most widely planted commercial variety during the past two decades in China, which accounts for about 60% of the total sugarcane cultivated area (Su et al. Citation2019). In this study, we described the characterization of the complete mitogenome of ROC22 and explored its phylogenetic relationship within Gramineae, which is expected to facilitate future studies on population genetic structure, phylogenetic relationships and genetic improvement in sugarcane.
The sugarcane cultivar ROC22 were harvested from the experimental station of Fujian Agriculture and Forestry University, Fuzhou, Fujian Province (geographic coordinates: 26° 9′ 8″ N, 119° 24′24″ E), China. ROC22 was stored in the Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University. Mitochondrial DNA (mtDNA) extraction and purification from fresh yellowing seedlings using an improved protocol, similarity to that reported by Chen et al. (Citation2011). The mitochondrial genome of ROC22 were sequenced by Illumina Hiseq XTen and PacBio Sequel platform, and assembled using a combination of the PacBio Sequel data and the Illumina Hiseq data by SPAdes v3.10.1 (Antipov et al. Citation2016). The genome sequences were annotated using GeSeq (Tillich et al. Citation2017). The complete mitochondrial genome sequence has been submitted to SRA with the accession number of SRR11358605.
Two distinct circular chromosomes, named Chromosome 1 and Chromosome 2, are contained in the complete mitogenome of sugarcane. The length of Chromosome 1 is 300,837 bp with the GC content of 43.93%, and the length of Chromosome 2 is 144,755 bp with the GC content of 43.57%. There are 20 protein-coding genes in Chromosome 1, including six nad genes, four rps genes, three atp genes, three ccm genes, two cox genes, one mat gene and one mtt gene. In addition, 16 tRNAs and six rRNAs non-coding genes are included in Chromosome 1. All coding gene sequences on Chromosome 1 start with ATG except for nad1, which starts with ACG. ccmC, ccmFn, matR, mttB, nad6, nad7 and rps1 terminate with TAG; atp1, ccmB, rps13 and rps2 terminate with TGA; atp4, atp8, cox1, cox2, nad1, nad9 and rps7 terminate with TAA, while nad2 and nad5 terminate with CGG and GTA, respectively. Chromosome 2 contains 18 genes, including five tRNA genes and 13 protein-coding genes (four nad genes, three rps genes, two atp genes, one ccm gene, one cob gene, one cox gene and one rpl gene). All the coding genes of Chromosome 2 begin with ATG except for nad2, which begins with TTG. atp9, rps3 and cob terminate with TAG, while ccmFc, rps12, cox3 and nad4 terminate with TGA, and the other five genes (rpl16, atp6, nad3, rps4, nad2 and nad5) terminate with TAA.
To conduct phylogenetic analysis of Saccharum spp. hybrid ROC22, the whole mitchondrial genome sequences of Saccharum spp. hybrid ROC22 and the other eight species (Oryza sativa, NC_011033.1; Zea mays, NC_007982.1; Sorghum bicolor, NC_008360.1; Triticum aestivum, NC_037304.1; Hordeum vulgare, IBSC_v2.dna. Mt: 1:525599:1 REF; Saccharum officinarum Khon Kaen 3, LC107874.1 and LC107875.1; Arabidopisis thaliana, NC_037304.1 and Brassica napus, NC_008285.1) were compared. A Maximum Likelihood phylogenetic tree was constructed using PhyML v3.0 with 1000 bootstrap replications (http://www.atgc-montpellier.fr/phyml/). It is revealed that the phylogenetic relationship of Saccharum spp. hybrid ROC22 is very close to the two species in the family Gramineae: S. officinarum Khon Kaen 3 and S. bicolor. Meanwhile, the Saccharum spp. hybrid ROC22 is phylogenetically distant from A. thaliana and B. napus, which are the species of family Cruciferae (). The complete mitogenome sequence provided herein would help understand Saccharum evolution and will contribute to further analysis of genetic diversity and molecular markers on Saccharum.
Figure 1. Maximum likelihood tree based on the complete mitochondrial genome sequences of nine species. The numbers on the branches are bootstrap values. The number at each node is the bootstrap probability. The number after the species name is the GenBank accession number. Asterisk, the genome sequence in this study.
Data availability
The data that support the findings of this study are available. Raw data sequences of Saccharum spp. hybrid ROC22 mitchondrial genome are available in NCBI SRA with the accession number of SRR11358605 (BioProject: PRJNA63602) at the URL (https://dataview.ncbi.nlm.nih.gov/objects?linked_to_id=SRR11358605&archive=biosample). The mitogenome of seven species as following are available in the public domain NCBI (Oryza sativa, Zea mays, Sorghum bicolor, Triticum aestivum, Saccharum officinarum Khon Kaen 3, Arabidopisis thaliana, and Brassica napus; the URL https://www.ncbi.nlm.nih.gov/) and the mitogenome of Hordeum vulgare is available in ensembl (http://asia.ensembl.org/index.html).
Disclosure statement
No potential conflict of interest was reported by the author(s).
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References
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