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The traditional Chinese medicinal material Mugua is derived from the dried fruit of Chaenomeles speciosa (Sweet) Nakai (Rosaceae). The material produced in Xuancheng, Anhui Province, is regarded as a geo-authentic medicinal material and is commonly referred to as "Xuan Mugua". C. speciosa is a medicinal and edible plant with a long history of use in traditional Chinese medicine. In this study, we sequenced and assembled the complete chloroplast genome of C. speciosa using the Illumina platform and performed comprehensive genome annotation. Repetitive sequences were analyzed with REPuter and MISA, codon usage bias was evaluated via relative synonymous codon usage (RSCU), and comparative analyses of inverted repeat (IR) boundaries and phylogenetic relationships were conducted among closely related Chaenomeles species. The chloroplast genome is 159 991 bp in length, exhibiting a typical quadripartite structure with a GC content of 36.5%, and encodes 126 genes, including 83 protein-coding genes, 35 tRNAs, and 8 rRNAs. Seventy-six simple sequence repeats (SSRs) and 55 long repeat sequences were identified, with SSRs primarily consisting of A/T mononucleotides and predominantly located in the large single copy (LSC) and intergenic regions. Codon usage analysis showed that 30 codons have a preference (RSCU > 1), mostly ending with A/U. Comparative analysis of IR boundaries indicated high conservation within the genus. Genome variation analysis revealed four highly variable regions in the LSC (trnR-atpA, petN-psbM, trnT-GGU-psbD, trnV-M). Phylogenetic analysis confirmed that Chaenomeles is monophyletic, with C. speciosa closely related to C. japonica and C. tibetica. This work provides the first detailed characterization of the C. speciosa chloroplast genome and phylogeny, and the identified SSRs and highly variable regions represent valuable resources for germplasm identification and evolutionary studies in Chaenomeles.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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