Comparative Analysis of Chloroplast Genome in <i>Saccharum</i> spp. and Related Members of ‘<i>Saccharum</i> Complex’
High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-07-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/14/7661 |
| Summary: | High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘<i>Saccharum</i> Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of <i>Saccharum</i> (among them, <i>S. robustum</i>, <i>S. sinense</i>, and <i>S. barberi</i> firstly reported in this study) and 2 sugarcane relative species, <i>Tripidium arundinaceum</i> and <i>Narenga porphyrocoma</i>. The plastid phylogenetic signal demonstrated that <i>S. officinarum</i> and <i>S. robustum</i> shared a common ancestor, and that the cytoplasmic origins of <i>S. sinense</i> and <i>S. barberi</i> were much more ancient than the <i>S. offcinarum</i>/<i>S. robustum</i> linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing <i>Saccharum</i> from its relative species, 4 dCAPS markers for distinguishing <i>S. officinarum</i> from <i>S. robustum,</i> and 1 dCAPS marker for distinguishing <i>S. sinense</i> and <i>S. barberi</i> from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in <i>Saccharum</i> and relative species. |
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| ISSN: | 1661-6596 1422-0067 |