International Journal of Molecular Sciences Article Comparative Analysis of two Sugarcane Ancestors Saccharum officinarum and S. spontaneum based on Complete Chloroplast Genome Sequences and Photosynthetic Ability in Cold Stress Fu Xu 1,2, Lilian He 1, Shiwu Gao 2, Yachun Su 2 , Fusheng Li 1,2,* and Liping Xu 2,* 1 College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China 2 Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Fuzhou 350002, China * Correspondence:
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[email protected] (L.X.); Tel.: +86-871-6522-0502 (F.L.); +86-591-8377-2604 (L.X.) Received: 7 July 2019; Accepted: 2 August 2019; Published: 5 August 2019 Abstract: Polyploid Saccharum with complex genomes hindered the progress of sugarcane improvement, while their chloroplast genomes are much smaller and simpler. Chloroplast (cp), the vital organelle, is the site of plant photosynthesis, which also evolves other functions, such as tolerance to environmental stresses. In this study, the cp genome of two sugarcane ancestors Saccharum officinarum and S. spontaneum were sequenced, and genome comparative analysis between these two species was carried out, together with the photosynthetic ability. The length is 141,187 bp for S. officinarum and that is 7 bp longer than S. spontaneum, with the same GC content (38.44%) and annotated gene number (134), 13 with introns among them. There is a typical tetrad structure, including LSC, SSC, IRb and IRa. Of them, LSC and IRa/IRb are 18 bp longer and 6 bp shorter than those in S. spontaneum (83,047 bp and 22,795 bp), respectively, while the size of SSC is same (12,544 bp).